1
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Butterfield ER, Obado SO, Scutts SR, Zhang W, Chait BT, Rout MP, Field MC. A lineage-specific protein network at the trypanosome nuclear envelope. Nucleus 2024; 15:2310452. [PMID: 38605598 PMCID: PMC11018031 DOI: 10.1080/19491034.2024.2310452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/18/2024] [Indexed: 04/13/2024] Open
Abstract
The nuclear envelope (NE) separates translation and transcription and is the location of multiple functions, including chromatin organization and nucleocytoplasmic transport. The molecular basis for many of these functions have diverged between eukaryotic lineages. Trypanosoma brucei, a member of the early branching eukaryotic lineage Discoba, highlights many of these, including a distinct lamina and kinetochore composition. Here, we describe a cohort of proteins interacting with both the lamina and NPC, which we term lamina-associated proteins (LAPs). LAPs represent a diverse group of proteins, including two candidate NPC-anchoring pore membrane proteins (POMs) with architecture conserved with S. cerevisiae and H. sapiens, and additional peripheral components of the NPC. While many of the LAPs are Kinetoplastid specific, we also identified broadly conserved proteins, indicating an amalgam of divergence and conservation within the trypanosome NE proteome, highlighting the diversity of nuclear biology across the eukaryotes, increasing our understanding of eukaryotic and NPC evolution.
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Affiliation(s)
| | - Samson O. Obado
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
| | - Simon R. Scutts
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Wenzhu Zhang
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Brian T. Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Michael P. Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, USA
| | - Mark C. Field
- School of Life Sciences, University of Dundee, Dundee, UK
- Biology Centre, Czech Academy of Sciences, Institute of Parasitology, České Budějovice, Czech Republic
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2
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Canela-Pérez I, Azuara-Liceaga E, Cuéllar P, Saucedo-Cárdenas O, Valdés J. Multiple types of nuclear localization signals in Entamoeba histolytica. Biochem Biophys Rep 2024; 39:101770. [PMID: 39055170 PMCID: PMC11269297 DOI: 10.1016/j.bbrep.2024.101770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 06/20/2024] [Accepted: 06/27/2024] [Indexed: 07/27/2024] Open
Abstract
Entamoeba histolytica is a protozoan parasite that belongs to the Amoebozoa supergroup whose study related to the nucleocytoplasmic transport of proteins through the nucleus is poorly studied. In this work, we have performed in silico predictions of the potential nuclear localization signals (NLS) corresponding to the proteome of 8201 proteins from Entamoeba histolytica annotated in the AmoebaDB database. We have found the presence of monopartite nuclear localization signals (MNLSs), bipartite nuclear localization signals (BNLSs), and non-canonical monopartite NLSs with lengths exceeding 20 amino acid residues. Additionally, we detected a new type of NLS consisting of multiple juxtaposed bipartite NLSs (JNLSs) that have not been described in any eukaryotic organism. Also, we have generated consensus sequences for the nuclear import of proteins with the NLSs obtained. Docking experiments between EhImportin α and an MNLS, BNLS, and JNLS outlined the interacting residues between the Importin and cargo proteins, emphasizing their putative roles in nuclear import. By transfecting HA-tagged protein constructs, we assessed the nuclear localization of MNLS (U1A and U2AF1), JMNLS (U2AF2), and non-canonical NLS (N-terminus of Pol ll) in vivo. Our data provide the basis for understanding the nuclear transport process in E. histolytica.
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Affiliation(s)
- Israel Canela-Pérez
- Departamento de Bioquímica, CINVESTAV-México, Av. IPN 2508 colonia San Pedro Zacatenco, GAM, CDMX, 07360, Mexico
| | - Elisa Azuara-Liceaga
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City, 03100, Mexico
| | - Patricia Cuéllar
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City, 03100, Mexico
| | - Odila Saucedo-Cárdenas
- Departamento de Histología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, 67700, Mexico
| | - Jesús Valdés
- Departamento de Bioquímica, CINVESTAV-México, Av. IPN 2508 colonia San Pedro Zacatenco, GAM, CDMX, 07360, Mexico
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3
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Quan JJ, Nikolov LA, Sha J, Wohlschlegel JA, Coppens I, Bradley PJ. Systematic characterization of all Toxoplasma gondii TBC domain-containing proteins identifies an essential regulator of Rab2 in the secretory pathway. PLoS Biol 2024; 22:e3002634. [PMID: 38713739 PMCID: PMC11101121 DOI: 10.1371/journal.pbio.3002634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 05/17/2024] [Accepted: 04/22/2024] [Indexed: 05/09/2024] Open
Abstract
Toxoplasma gondii resides in its intracellular niche by employing a series of specialized secretory organelles that play roles in invasion, host cell manipulation, and parasite replication. Rab GTPases are major regulators of the parasite's secretory traffic that function as nucleotide-dependent molecular switches to control vesicle trafficking. While many of the Rab proteins have been characterized in T. gondii, precisely how these Rabs are regulated remains poorly understood. To better understand the parasite's secretory traffic, we investigated the entire family of Tre2-Bub2-Cdc16 (TBC) domain-containing proteins, which are known to be involved in vesicle fusion and secretory protein trafficking. We first determined the localization of all 18 TBC domain-containing proteins to discrete regions of the secretory pathway or other vesicles in the parasite. Second, we use an auxin-inducible degron approach to demonstrate that the protozoan-specific TgTBC9 protein, which localizes to the endoplasmic reticulum (ER), is essential for parasite survival. Knockdown of TgTBC9 results in parasite growth arrest and affects the organization of the ER and mitochondrial morphology. TgTBC9 knockdown also results in the formation of large lipid droplets (LDs) and multi-membranous structures surrounded by ER membranes, further indicating a disruption of ER functions. We show that the conserved dual-finger active site in the TBC domain of the protein is critical for its GTPase-activating protein (GAP) function and that the Plasmodium falciparum orthologue of TgTBC9 can rescue the lethal knockdown. We additionally show by immunoprecipitation and yeast 2 hybrid analyses that TgTBC9 preferentially binds Rab2, indicating that the TBC9-Rab2 pair controls ER morphology and vesicular trafficking in the parasite. Together, these studies identify the first essential TBC protein described in any protozoan and provide new insight into intracellular vesicle trafficking in T. gondii.
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Affiliation(s)
- Justin J. Quan
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Lachezar A. Nikolov
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Jihui Sha
- Department of Biological Chemistry and Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - James A. Wohlschlegel
- Department of Biological Chemistry and Institute of Genomics and Proteomics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Isabelle Coppens
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Peter J. Bradley
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, California, United States of America
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4
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Moloney NM, Barylyuk K, Tromer E, Crook OM, Breckels LM, Lilley KS, Waller RF, MacGregor P. Mapping diversity in African trypanosomes using high resolution spatial proteomics. Nat Commun 2023; 14:4401. [PMID: 37479728 PMCID: PMC10361982 DOI: 10.1038/s41467-023-40125-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 07/06/2023] [Indexed: 07/23/2023] Open
Abstract
African trypanosomes are dixenous eukaryotic parasites that impose a significant human and veterinary disease burden on sub-Saharan Africa. Diversity between species and life-cycle stages is concomitant with distinct host and tissue tropisms within this group. Here, the spatial proteomes of two African trypanosome species, Trypanosoma brucei and Trypanosoma congolense, are mapped across two life-stages. The four resulting datasets provide evidence of expression of approximately 5500 proteins per cell-type. Over 2500 proteins per cell-type are classified to specific subcellular compartments, providing four comprehensive spatial proteomes. Comparative analysis reveals key routes of parasitic adaptation to different biological niches and provides insight into the molecular basis for diversity within and between these pathogen species.
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Affiliation(s)
- Nicola M Moloney
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | | | - Eelco Tromer
- Cell Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, Netherlands
| | - Oliver M Crook
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
- Department of Statistics, University of Oxford, Oxford, OX1 3LB, UK
| | - Lisa M Breckels
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Kathryn S Lilley
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Ross F Waller
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Paula MacGregor
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK.
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK.
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5
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Quan JJ, Nikolov LA, Sha J, Wohlschlegel JA, Bradley PJ. Toxoplasma gondii encodes an array of TBC-domain containing proteins including an essential regulator that targets Rab2 in the secretory pathway. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.28.542599. [PMID: 37398139 PMCID: PMC10312441 DOI: 10.1101/2023.05.28.542599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Toxoplasma gondii resides in its intracellular niche by employing a series of specialized secretory organelles that play roles in invasion, host-cell manipulation and parasite replication. Rab GTPases are major regulators of the parasite's secretory traffic that function as nucleotide dependent molecular switches to control vesicle trafficking. While many of the Rab proteins have been characterized in T. gondii , precisely how these Rabs are regulated remains poorly understood. To better understand the parasite's secretory traffic, we investigated the entire family of Tre2-Bub2-Cdc16 (TBC)-domain containing proteins, which are known to be involved in vesicle fusion and secretory protein trafficking. We first determined the localization of all 18 TBC-domain containing proteins to discrete regions of the secretory pathway or other vesicles in the parasite. We then use an auxin-inducible degron approach to demonstrate that the protozoan-specific TgTBC9 protein that localizes to the ER is essential for parasite survival. Knockdown of TgTBC9 results in parasite growth arrest and affects the organization of the ER and Golgi apparatus. We show that the conserved dual-finger active site in the TBC-domain of the protein is critical for its GTPase-activating protein (GAP) function and that the P. falciparum orthologue of TgTBC9 can rescue the lethal knockdown. We additionally show by immunoprecipitation and yeast two hybrid analyses that TgTBC9 directly binds Rab2, indicating that this TBC-Rab pair controls ER to Golgi traffic in the parasite. Together, these studies identify the first essential TBC protein described in any protozoan, provide new insight into intracellular vesicle trafficking in T. gondii , and reveal promising targets for the design of novel therapeutics that can specifically target apicomplexan parasites.
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6
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Comparative genomics and interactomics of polyadenylation factors for the prediction of new parasite targets: Entamoeba histolytica as a working model. Biosci Rep 2023; 43:232462. [PMID: 36651565 PMCID: PMC9912109 DOI: 10.1042/bsr20221911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 01/05/2023] [Accepted: 01/13/2023] [Indexed: 01/19/2023] Open
Abstract
Protein-protein interactions (PPI) play a key role in predicting the function of a target protein and drug ability to affect an entire biological system. Prediction of PPI networks greatly contributes to determine a target protein and signal pathways related to its function. Polyadenylation of mRNA 3'-end is essential for gene expression regulation and several polyadenylation factors have been shown as valuable targets for controlling protozoan parasites that affect human health. Here, by using a computational strategy based on sequence-based prediction approaches, phylogenetic analyses, and computational prediction of PPI networks, we compared interactomes of polyadenylation factors in relevant protozoan parasites and the human host, to identify key proteins and define potential targets for pathogen control. Then, we used Entamoeba histolytica as a working model to validate our computational results. RT-qPCR assays confirmed the coordinated modulation of connected proteins in the PPI network and evidenced that silencing of the bottleneck protein EhCFIm25 affects the expression of interacting proteins. In addition, molecular dynamics simulations and docking approaches allowed to characterize the relationships between EhCFIm25 and Ehnopp34, two connected bottleneck proteins. Interestingly, the experimental identification of EhCFIm25 interactome confirmed the close relationships among proteins involved in gene expression regulation and evidenced new links with moonlight proteins in E. histolytica, suggesting a connection between RNA biology and metabolism as described in other organisms. Altogether, our results strengthened the relevance of comparative genomics and interactomics of polyadenylation factors for the prediction of new targets for the control of these human pathogens.
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7
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Genome-wide subcellular protein map for the flagellate parasite Trypanosoma brucei. Nat Microbiol 2023; 8:533-547. [PMID: 36804636 PMCID: PMC9981465 DOI: 10.1038/s41564-022-01295-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 11/21/2022] [Indexed: 02/22/2023]
Abstract
Trypanosoma brucei is a model trypanosomatid, an important group of human, animal and plant unicellular parasites. Understanding their complex cell architecture and life cycle is challenging because, as with most eukaryotic microbes, ~50% of genome-encoded proteins have completely unknown functions. Here, using fluorescence microscopy and cell lines expressing endogenously tagged proteins, we mapped the subcellular localization of 89% of the T. brucei proteome, a resource we call TrypTag. We provide clues to function and define lineage-specific organelle adaptations for parasitism, mapping the ultraconserved cellular architecture of eukaryotes, including the first comprehensive 'cartographic' analysis of the eukaryotic flagellum, which is vital for morphogenesis and pathology. To demonstrate the power of this resource, we identify novel organelle subdomains and changes in molecular composition through the cell cycle. TrypTag is a transformative resource, important for hypothesis generation for both eukaryotic evolutionary molecular cell biology and fundamental parasite cell biology.
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8
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Gómez-Liñán C, Gómez-Díaz E, Ceballos-Pérez G, Fernández-Moya S, Estévez AM. The RNA-binding protein RBP33 dampens non-productive transcription in trypanosomes. Nucleic Acids Res 2022; 50:12251-12265. [PMID: 36454008 PMCID: PMC9757043 DOI: 10.1093/nar/gkac1123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 11/01/2022] [Accepted: 11/09/2022] [Indexed: 12/02/2022] Open
Abstract
In-depth analysis of the transcriptomes of several model organisms has revealed that genomes are pervasively transcribed, giving rise to an abundance of non-canonical and mainly antisense RNA polymerase II-derived transcripts that are produced from almost any genomic context. Pervasive RNAs are degraded by surveillance mechanisms, but the repertoire of proteins that control the fate of these non-productive transcripts is still incomplete. Trypanosomes are single-celled eukaryotes that show constitutive RNA polymerase II transcription and in which initiation and termination of transcription occur at a limited number of sites per chromosome. It is not known whether pervasive transcription exists in organisms with unregulated RNA polymerase II activity, and which factors could be involved in the process. We show here that depletion of RBP33 results in overexpression of ∼40% of all annotated genes in the genome, with a marked accumulation of sense and antisense transcripts derived from silenced regions. RBP33 loss does not result in a significant increase in chromatin accessibility. Finally, we have found that transcripts that increase in abundance upon RBP33 knockdown are significantly more stable in RBP33-depleted trypanosomes, and that the exosome complex is responsible for their degradation. Our results provide strong evidence that RBP33 dampens non-productive transcription in trypanosomes.
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Affiliation(s)
- Claudia Gómez-Liñán
- Instituto de Parasitología y Biomedicina ‘López-Neyra’ (IPBLN), CSIC, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 17, 18016, Armilla, Granada, Spain
| | - Elena Gómez-Díaz
- Instituto de Parasitología y Biomedicina ‘López-Neyra’ (IPBLN), CSIC, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 17, 18016, Armilla, Granada, Spain
| | - Gloria Ceballos-Pérez
- Instituto de Parasitología y Biomedicina ‘López-Neyra’ (IPBLN), CSIC, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 17, 18016, Armilla, Granada, Spain
| | - Sandra M Fernández-Moya
- Instituto de Parasitología y Biomedicina ‘López-Neyra’ (IPBLN), CSIC, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 17, 18016, Armilla, Granada, Spain
| | - Antonio M Estévez
- To whom correspondence should be addressed. Tel: +34 958 181652; Fax: +34 958 181632;
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9
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Impact of inherent biases built into proteomic techniques: Proximity labeling and affinity capture compared. J Biol Chem 2022; 299:102726. [PMID: 36410438 PMCID: PMC9791439 DOI: 10.1016/j.jbc.2022.102726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/26/2022] [Accepted: 11/14/2022] [Indexed: 11/20/2022] Open
Abstract
The characterization of protein-protein interactions (PPIs) is of high value for understanding protein function. Two strategies are popular for identification of PPIs direct from the cellular environment: affinity capture (pulldown) isolates the protein of interest with an immobilized matrix that specifically captures the target and potential partners, whereas in BioID, genetic fusion of biotin ligase facilitates proximity biotinylation, and labeled proteins are isolated with streptavidin. Whilst both methods provide valuable insights, they can reveal distinct PPIs, but the basis for these differences is less obvious. Here, we compare both methods using four different trypanosome proteins as baits: poly(A)-binding proteins PABP1 and PABP2, mRNA export receptor MEX67, and the nucleoporin NUP158. With BioID, we found that the population of candidate interacting proteins decreases with more confined bait protein localization, but the candidate population is less variable with affinity capture. BioID returned more likely false positives, in particular for proteins with less confined localization, and identified low molecular weight proteins less efficiently. Surprisingly, BioID for MEX67 identified exclusively proteins lining the inner channel of the nuclear pore complex (NPC), consistent with the function of MEX67, whereas the entire NPC was isolated by pulldown. Similarly, for NUP158, BioID returned surprisingly few PPIs within NPC outer rings that were by contrast detected with pulldown but instead returned a larger cohort of nuclear proteins. These rather significant differences highlight a clear issue with reliance on a single method to identify PPIs and suggest that BioID and affinity capture are complementary rather than alternative approaches.
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10
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Bezerra MJR, Moura DMN, Freire ER, Holetz FB, Reis CRS, Monteiro TTS, Pinto ARS, Zhang N, Rezende AM, Pereira-Neves A, Figueiredo RCBQ, Clayton C, Field MC, Carrington M, de Melo Neto OP. Distinct mRNA and protein interactomes highlight functional differentiation of major eIF4F-like complexes from Trypanosoma brucei. Front Mol Biosci 2022; 9:971811. [PMID: 36275617 PMCID: PMC9585242 DOI: 10.3389/fmolb.2022.971811] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Gene expression in pathogenic protozoans of the family Trypanosomatidae has several novel features, including multiple eIF4F-like complexes involved in protein synthesis. The eukaryotic eIF4F complex, formed mainly by eIF4E and eIF4G subunits, is responsible for the canonical selection of mRNAs required for the initiation of mRNA translation. The best-known complexes implicated in translation in trypanosomatids are based on two related pairs of eIF4E and eIF4G subunits (EIF4E3/EIF4G4 and EIF4E4/EIF4G3), whose functional distinctions remain to be fully described. Here, to define interactomes associated with both complexes in Trypanosoma brucei procyclic forms, we performed parallel immunoprecipitation experiments followed by identification of proteins co-precipitated with the four tagged eIF4E and eIF4G subunits. A number of different protein partners, including RNA binding proteins and helicases, specifically co-precipitate with each complex. Highlights with the EIF4E4/EIF4G3 pair include RBP23, PABP1, EIF4AI and the CRK1 kinase. Co-precipitated partners with the EIF4E3/EIF4G4 pair are more diverse and include DRBD2, PABP2 and different zinc-finger proteins and RNA helicases. EIF4E3/EIF4G4 are essential for viability and to better define their role, we further investigated their phenotypes after knockdown. Depletion of either EIF4E3/EIF4G4 mRNAs lead to aberrant morphology with a more direct impact on events associated with cytokinesis. We also sought to identify those mRNAs differentially associated with each complex through CLIP-seq with the two eIF4E subunits. Predominant among EIF4E4-bound transcripts are those encoding ribosomal proteins, absent from those found with EIF4E3, which are generally more diverse. RNAi mediated depletion of EIF4E4, which does not affect proliferation, does not lead to changes in mRNAs or proteins associated with EIF4E3, confirming a lack of redundancy and distinct roles for the two complexes.
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Affiliation(s)
- Maria J. R. Bezerra
- Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Pernambuco, Brazil
- Department of Genetics, Federal University of Pernambuco, Recife, Pernambuco, Brazil
| | | | - Eden R. Freire
- Carlos Chagas Institute, Oswaldo Cruz Foundation, Curitiba, Pernambuco, Brazil
| | - Fabiola B. Holetz
- Carlos Chagas Institute, Oswaldo Cruz Foundation, Curitiba, Pernambuco, Brazil
| | | | | | - Adriana R. S. Pinto
- Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Pernambuco, Brazil
| | - Ning Zhang
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Antonio M. Rezende
- Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Pernambuco, Brazil
| | | | | | - Christine Clayton
- Heidelberg University Center for Molecular Biology, Heidelberg, Germany
| | - Mark C. Field
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Osvaldo P. de Melo Neto
- Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, Pernambuco, Brazil
- *Correspondence: Osvaldo P. de Melo Neto,
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11
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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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12
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Jamabo M, Bentley SJ, Macucule-Tinga P, Tembo P, Edkins AL, Boshoff A. In silico analysis of the HSP90 chaperone system from the African trypanosome, Trypanosoma brucei. Front Mol Biosci 2022; 9:947078. [PMID: 36213128 PMCID: PMC9538636 DOI: 10.3389/fmolb.2022.947078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
African trypanosomiasis is a neglected tropical disease caused by Trypanosoma brucei (T. brucei) and spread by the tsetse fly in sub-Saharan Africa. The trypanosome relies on heat shock proteins for survival in the insect vector and mammalian host. Heat shock protein 90 (HSP90) plays a crucial role in the stress response at the cellular level. Inhibition of its interactions with chaperones and co-chaperones is being explored as a potential therapeutic target for numerous diseases. This study provides an in silico overview of HSP90 and its co-chaperones in both T. brucei brucei and T. brucei gambiense in relation to human and other trypanosomal species, including non-parasitic Bodo saltans and the insect infecting Crithidia fasciculata. A structural analysis of T. brucei HSP90 revealed differences in the orientation of the linker and C-terminal domain in comparison to human HSP90. Phylogenetic analysis displayed the T. brucei HSP90 proteins clustering into three distinct groups based on subcellular localizations, namely, cytosol, mitochondria, and endoplasmic reticulum. Syntenic analysis of cytosolic HSP90 genes revealed that T. b. brucei encoded for 10 tandem copies, while T. b. gambiense encoded for three tandem copies; Leishmania major (L. major) had the highest gene copy number with 17 tandem copies. The updated information on HSP90 from recently published proteomics on T. brucei was examined for different life cycle stages and subcellular localizations. The results show a difference between T. b. brucei and T. b. gambiense with T. b. brucei encoding a total of twelve putative HSP90 genes, while T. b. gambiense encodes five HSP90 genes. Eighteen putative co-chaperones were identified with one notable absence being cell division cycle 37 (Cdc37). These results provide an updated framework on approaching HSP90 and its interactions as drug targets in the African trypanosome.
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Affiliation(s)
- Miebaka Jamabo
- Biotechnology Innovation Centre, Rhodes University, Grahamstown, South Africa
| | | | | | - Praise Tembo
- Biotechnology Innovation Centre, Rhodes University, Grahamstown, South Africa
| | - Adrienne Lesley Edkins
- Department of Biochemistry and Microbiology, Biomedical Biotechnology Research Unit (BioBRU), Rhodes University, Grahamstown, South Africa
| | - Aileen Boshoff
- Biotechnology Innovation Centre, Rhodes University, Grahamstown, South Africa
- *Correspondence: Aileen Boshoff,
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13
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Bromodomain factor 5 is an essential regulator of transcription in Leishmania. Nat Commun 2022; 13:4071. [PMID: 35831302 PMCID: PMC9279504 DOI: 10.1038/s41467-022-31742-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 06/30/2022] [Indexed: 11/23/2022] Open
Abstract
Leishmania are unicellular parasites that cause human and animal diseases. Like other kinetoplastids, they possess large transcriptional start regions (TSRs) which are defined by histone variants and histone lysine acetylation. Cellular interpretation of these chromatin marks is not well understood. Eight bromodomain factors, the reader modules for acetyl-lysine, are found across Leishmania genomes. Using L. mexicana, Cas9-driven gene deletions indicate that BDF1–5 are essential for promastigotes. Dimerisable, split Cre recombinase (DiCre)-inducible gene deletion of BDF5 show it is essential for both promastigotes and murine infection. ChIP-seq identifies BDF5 as enriched at TSRs. XL-BioID proximity proteomics shows the BDF5 landscape is enriched for BDFs, HAT2, proteins involved in transcriptional activity, and RNA processing; revealing a Conserved Regulators of Kinetoplastid Transcription (CRKT) Complex. Inducible deletion of BDF5 causes global reduction in RNA polymerase II transcription. Our results indicate the requirement of Leishmania to interpret histone acetylation marks through the bromodomain-enriched CRKT complex for normal gene expression and cellular viability. Leishmania use large (5–10 kb) transcriptional start regions, where the chromatin is highly enriched for acetylated histones, to drive the expression of polycistronic gene arrays. Here the authors show bromodomain-containing protein BDF5 is enriched at transcriptional start sites and its depletion leads to cell death in vitro and in murine infections, and they identify its interactors.
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14
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A novel SNF2 ATPase complex in Trypanosoma brucei with a role in H2A.Z-mediated chromatin remodelling. PLoS Pathog 2022; 18:e1010514. [PMID: 35675371 PMCID: PMC9236257 DOI: 10.1371/journal.ppat.1010514] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/27/2022] [Accepted: 04/08/2022] [Indexed: 11/25/2022] Open
Abstract
A cascade of histone acetylation events with subsequent incorporation of a histone H2A variant plays an essential part in transcription regulation in various model organisms. A key player in this cascade is the chromatin remodelling complex SWR1, which replaces the canonical histone H2A with its variant H2A.Z. Transcriptional regulation of polycistronic transcription units in the unicellular parasite Trypanosoma brucei has been shown to be highly dependent on acetylation of H2A.Z, which is mediated by the histone-acetyltransferase HAT2. The chromatin remodelling complex which mediates H2A.Z incorporation is not known and an SWR1 orthologue in trypanosomes has not yet been reported. In this study, we identified and characterised an SWR1-like remodeller complex in T. brucei that is responsible for Pol II-dependent transcriptional regulation. Bioinformatic analysis of potential SNF2 DEAD/Box helicases, the key component of SWR1 complexes, identified a 1211 amino acids-long protein that exhibits key structural characteristics of the SWR1 subfamily. Systematic protein-protein interaction analysis revealed the existence of a novel complex exhibiting key features of an SWR1-like chromatin remodeller. RNAi-mediated depletion of the ATPase subunit of this complex resulted in a significant reduction of H2A.Z incorporation at transcription start sites and a subsequent decrease of steady-state mRNA levels. Furthermore, depletion of SWR1 and RNA-polymerase II (Pol II) caused massive chromatin condensation. The potential function of several proteins associated with the SWR1-like complex and with HAT2, the key factor of H2A.Z incorporation, is discussed. Trypanosoma brucei is the causative agent of African trypanosomiasis (sleeping sickness) in humans and nagana in cattle. Its unusual genomic organisation featuring large polycistronic units requires a general mechanism of transcription initiation, because individual gene promoters are mostly absent. Despite the fact that the histone variant H2A.Z has previously been identified as a key player of transcription regulation, the complex responsible for correct H2A.Z incorporation at transcription start sites (TSS) remains elusive. In other eukaryotes, SWR1, a SNF2 ATPase-associated chromatin remodelling complex, is responsible for correct incorporation of this histone variant. This study identified a SWR1-like complex in T. brucei. Depletion of the SNF2 ATPase resulted in a reduction of H2A.Z incorporation at the TSS and decreased steady-state mRNA levels accompanied by chromatin condensation. In addition to the SWR1-like complex, we also identified a trypanosome-specific HAT2 complex that includes the histone acetyltransferases HAT2, a key player in the H2A.Z incorporation process. This complex has a trypanosome-specific composition that is different from the NuA4/TIP60 complex in Saccharomyces cerevisiae.
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15
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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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16
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Pezza A, Tavernelli LE, Alonso VL, Perdomo V, Gabarro R, Prinjha R, Rodríguez Araya E, Rioja I, Docampo R, Calderón F, Martin J, Serra E. Essential Bromodomain TcBDF2 as a Drug Target against Chagas Disease. ACS Infect Dis 2022; 8:1062-1074. [PMID: 35482332 DOI: 10.1021/acsinfecdis.2c00057] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Trypanosoma cruzi is a unicellular parasite that causes Chagas disease, which is endemic in the American continent but also worldwide, distributed by migratory movements. A striking feature of trypanosomatids is the polycistronic transcription associated with post-transcriptional mechanisms that regulate the levels of translatable mRNA. In this context, epigenetic regulatory mechanisms have been revealed to be of great importance, since they are the only ones that would control the access of RNA polymerases to chromatin. Bromodomains are epigenetic protein readers that recognize and specifically bind to acetylated lysine residues, mostly at histone proteins. There are seven coding sequences for BD-containing proteins in trypanosomatids, named TcBDF1 to TcBDF7, and a putative new protein containing a bromodomain was recently described. Using the Tet-regulated overexpression plasmid pTcINDEX-GW and CRISPR/Cas9 genome editing, we were able to demonstrate the essentiality of TcBDF2 in T. cruzi. This bromodomain is located in the nucleus, through a bipartite nuclear localization signal. TcBDF2 was shown to be important for host cell invasion, amastigote replication, and differentiation from amastigotes to trypomastigotes. Overexpression of TcBDF2 diminished epimastigote replication. Also, some processes involved in pathogenesis were altered in these parasites, such as infection of mammalian cells, replication of amastigotes, and the number of trypomastigotes released from host cells. In in vitro studies, TcBDF2 was also able to bind inhibitors showing a specificity profile different from that of the previously characterized TcBDF3. These results point to TcBDF2 as a druggable target against T. cruzi.
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Affiliation(s)
- Alejandro Pezza
- Instituto de Biología Molecular y Celular de Rosario, CONICET, 2000 Rosario, Santa Fe, Argentina
| | - Luis E. Tavernelli
- Instituto de Biología Molecular y Celular de Rosario, CONICET, 2000 Rosario, Santa Fe, Argentina
| | - Victoria L. Alonso
- Instituto de Biología Molecular y Celular de Rosario, CONICET, 2000 Rosario, Santa Fe, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000 Rosario, Santa Fe, Argentina
| | - Virginia Perdomo
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000 Rosario, Santa Fe, Argentina
| | - Raquel Gabarro
- GlaxoSmithKline Global Health, Tres Cantos, 28760 Madrid, Spain
| | - Rab Prinjha
- Immunology Research Unit, Research, R&D GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts SG1 2NY, U.K
| | - Elvio Rodríguez Araya
- Instituto de Biología Molecular y Celular de Rosario, CONICET, 2000 Rosario, Santa Fe, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000 Rosario, Santa Fe, Argentina
| | - Inmaculada Rioja
- Immunology Research Unit, Research, R&D GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts SG1 2NY, U.K
| | - Roberto Docampo
- Department of Cellular Biology and Center for Tropical and Global Emerging Diseases, University of Georgia, Athens, Georgia30602, United States
| | - Felix Calderón
- GlaxoSmithKline Global Health, Tres Cantos, 28760 Madrid, Spain
| | - Julio Martin
- GlaxoSmithKline Global Health, Tres Cantos, 28760 Madrid, Spain
| | - Esteban Serra
- Instituto de Biología Molecular y Celular de Rosario, CONICET, 2000 Rosario, Santa Fe, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, 2000 Rosario, Santa Fe, Argentina
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17
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Smith A, Wall RJ, Patterson S, Rowan T, Rico Vidal E, Stojanovski L, Huggett M, Hampton SE, Thomas MG, Corpas Lopez V, Gillingwater K, Duke J, Napier G, Peter R, Vitouley HS, Harrison JR, Milne R, Jeacock L, Baker N, Davis SH, Simeons F, Riley J, Horn D, Brun R, Zuccotto F, Witty MJ, Wyllie S, Read KD, Gilbert IH. Repositioning of a Diaminothiazole Series Confirmed to Target the Cyclin-Dependent Kinase CRK12 for Use in the Treatment of African Animal Trypanosomiasis. J Med Chem 2022; 65:5606-5624. [PMID: 35303411 PMCID: PMC9014415 DOI: 10.1021/acs.jmedchem.1c02104] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Indexed: 11/29/2022]
Abstract
African animal trypanosomiasis or nagana, caused principally by infection of the protozoan parasites Trypanosoma congolense and Trypanosoma vivax, is a major problem in cattle and other livestocks in sub-Saharan Africa. Current treatments are threatened by the emergence of drug resistance and there is an urgent need for new, effective drugs. Here, we report the repositioning of a compound series initially developed for the treatment of human African trypanosomiasis. A medicinal chemistry program, focused on deriving more soluble analogues, led to development of a lead compound capable of curing cattle infected with both T. congolense and T. vivax via intravenous dosing. Further optimization has the potential to yield a single-dose intramuscular treatment for this disease. Comprehensive mode of action studies revealed that the molecular target of this promising compound and related analogues is the cyclin-dependent kinase CRK12.
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Affiliation(s)
- Alasdair Smith
- Drug
Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division
of Biological Chemistry and Drug Discovery, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Richard J. Wall
- Wellcome
Centre for Anti-Infectives Research, Division of Biological Chemistry
and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Stephen Patterson
- Wellcome
Centre for Anti-Infectives Research, Division of Biological Chemistry
and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Tim Rowan
- GALVmed, Doherty Building, Pentlands Science
Park, Bush Loan, Penicuik, Edinburgh EH26 0PZ, United Kingdom
| | - Eva Rico Vidal
- Wellcome
Centre for Anti-Infectives Research, Division of Biological Chemistry
and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Laste Stojanovski
- Drug
Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division
of Biological Chemistry and Drug Discovery, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Margaret Huggett
- Drug
Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division
of Biological Chemistry and Drug Discovery, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Shahienaz E. Hampton
- Drug
Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division
of Biological Chemistry and Drug Discovery, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Michael G. Thomas
- Drug
Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division
of Biological Chemistry and Drug Discovery, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Victoriano Corpas Lopez
- Wellcome
Centre for Anti-Infectives Research, Division of Biological Chemistry
and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Kirsten Gillingwater
- Swiss
Tropical and Public Health Institute, Socinstrasse 57, CH-4002 Basel, Switzerland
- University
of Basel, Petersplatz 1, CH-4001 Basel, Switzerland
| | - Jeff Duke
- University
of Greenwich, Medway Campus, Central Avenue, Chatham Maritime, Chatham, Kent ME4 4TB United Kingdom
| | - Grant Napier
- GALVmed, Doherty Building, Pentlands Science
Park, Bush Loan, Penicuik, Edinburgh EH26 0PZ, United Kingdom
| | - Rose Peter
- GALVmed, Doherty Building, Pentlands Science
Park, Bush Loan, Penicuik, Edinburgh EH26 0PZ, United Kingdom
| | - Hervé S. Vitouley
- Centre
International de Recherche-Développement sur l’Elevage
en zone Subhumide (CIRDES), No 559 ru
5-31 angle Av. du Gouverneur Louveau, 01 BP: 454 Bobo-Dioulasso 01, Burkina Faso
| | - Justin R. Harrison
- Drug
Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division
of Biological Chemistry and Drug Discovery, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Rachel Milne
- Wellcome
Centre for Anti-Infectives Research, Division of Biological Chemistry
and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Laura Jeacock
- Wellcome
Centre for Anti-Infectives Research, Division of Biological Chemistry
and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Nicola Baker
- Wellcome
Centre for Anti-Infectives Research, Division of Biological Chemistry
and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Susan H. Davis
- Drug
Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division
of Biological Chemistry and Drug Discovery, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Frederick Simeons
- Drug
Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division
of Biological Chemistry and Drug Discovery, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Jennifer Riley
- Drug
Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division
of Biological Chemistry and Drug Discovery, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - David Horn
- Wellcome
Centre for Anti-Infectives Research, Division of Biological Chemistry
and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Reto Brun
- Swiss
Tropical and Public Health Institute, Socinstrasse 57, CH-4002 Basel, Switzerland
- University
of Basel, Petersplatz 1, CH-4001 Basel, Switzerland
| | - Fabio Zuccotto
- Drug
Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division
of Biological Chemistry and Drug Discovery, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Michael J Witty
- GALVmed, Doherty Building, Pentlands Science
Park, Bush Loan, Penicuik, Edinburgh EH26 0PZ, United Kingdom
| | - Susan Wyllie
- Wellcome
Centre for Anti-Infectives Research, Division of Biological Chemistry
and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Kevin D. Read
- Drug
Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division
of Biological Chemistry and Drug Discovery, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
| | - Ian H. Gilbert
- Drug
Discovery Unit, Wellcome Centre for Anti-Infectives Research, Division
of Biological Chemistry and Drug Discovery, University of Dundee, Dow Street, Dundee DD1
5EH, United Kingdom
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18
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Rosón JN, Vitarelli MDO, Costa-Silva HM, Pereira KS, Pires DDS, Lopes LDS, Cordeiro B, Kraus AJ, Cruz KNT, Calderano SG, Fragoso SP, Siegel TN, Elias MC, da Cunha JPC. H2B.V demarcates divergent strand-switch regions, some tDNA loci, and genome compartments in Trypanosoma cruzi and affects parasite differentiation and host cell invasion. PLoS Pathog 2022; 18:e1009694. [PMID: 35180281 PMCID: PMC8893665 DOI: 10.1371/journal.ppat.1009694] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 03/03/2022] [Accepted: 01/31/2022] [Indexed: 11/19/2022] Open
Abstract
Histone variants play a crucial role in chromatin structure organization and gene expression. Trypanosomatids have an unusual H2B variant (H2B.V) that is known to dimerize with the variant H2A.Z generating unstable nucleosomes. Previously, we found that H2B.V protein is enriched in tissue-derived trypomastigote (TCT) life forms, a nonreplicative stage of Trypanosoma cruzi, suggesting that this variant may contribute to the differences in chromatin structure and global transcription rates observed among parasite life forms. Here, we performed the first genome-wide profiling of histone localization in T. cruzi using epimastigotes and TCT life forms, and we found that H2B.V was preferentially located at the edges of divergent transcriptional strand switch regions, which encompass putative transcriptional start regions; at some tDNA loci; and between the conserved and disrupted genome compartments, mainly at trans-sialidase, mucin and MASP genes. Remarkably, the chromatin of TCT forms was depleted of H2B.V-enriched peaks in comparison to epimastigote forms. Interactome assays indicated that H2B.V associated specifically with H2A.Z, bromodomain factor 2, nucleolar proteins and a histone chaperone, among others. Parasites expressing reduced H2B.V levels were associated with higher rates of parasite differentiation and mammalian cell infectivity. Taken together, H2B.V demarcates critical genomic regions and associates with regulatory chromatin proteins, suggesting a scenario wherein local chromatin structures associated with parasite differentiation and invasion are regulated during the parasite life cycle.
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Affiliation(s)
- Juliana Nunes Rosón
- Laboratory of Cell Cycle, Butantan Institute, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, São Paulo, Brazil
- Department of Microbiology, Immunology and Parasitology, Escola Paulista de Medicina–UNIFESP, São Paulo, Brazil
| | - Marcela de Oliveira Vitarelli
- Laboratory of Cell Cycle, Butantan Institute, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, São Paulo, Brazil
| | - Héllida Marina Costa-Silva
- Laboratory of Cell Cycle, Butantan Institute, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, São Paulo, Brazil
| | - Kamille Schmitt Pereira
- Department of Bioprocesses and Biotechnology, Universidade Federal do Paraná, Curitiba, Brazil
- Laboratory of Molecular and Systems Biology of Trypanosomatids, Carlos Chagas Institute, FIOCRUZ, Curitiba, Brazil
| | - David da Silva Pires
- Laboratory of Cell Cycle, Butantan Institute, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, São Paulo, Brazil
| | - Leticia de Sousa Lopes
- Laboratory of Cell Cycle, Butantan Institute, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, São Paulo, Brazil
| | - Barbara Cordeiro
- Laboratory of Cell Cycle, Butantan Institute, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, São Paulo, Brazil
| | - Amelie J. Kraus
- Division of Experimental Parasitology, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität in Munich, Munich, Germany
- Biomedical Center, Division of Physiological Chemistry, Faculty of Medicine, Ludwig-Maximilians-Universitäat in Munch, Munich, Germany
| | - Karin Navarro Tozzi Cruz
- Laboratory of Cell Cycle, Butantan Institute, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, São Paulo, Brazil
| | - Simone Guedes Calderano
- Laboratory of Cell Cycle, Butantan Institute, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, São Paulo, Brazil
| | - Stenio Perdigão Fragoso
- Department of Bioprocesses and Biotechnology, Universidade Federal do Paraná, Curitiba, Brazil
- Laboratory of Molecular and Systems Biology of Trypanosomatids, Carlos Chagas Institute, FIOCRUZ, Curitiba, Brazil
| | - T. Nicolai Siegel
- Division of Experimental Parasitology, Faculty of Veterinary Medicine, Ludwig-Maximilians-Universität in Munich, Munich, Germany
- Biomedical Center, Division of Physiological Chemistry, Faculty of Medicine, Ludwig-Maximilians-Universitäat in Munch, Munich, Germany
| | - Maria Carolina Elias
- Laboratory of Cell Cycle, Butantan Institute, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, São Paulo, Brazil
| | - Julia Pinheiro Chagas da Cunha
- Laboratory of Cell Cycle, Butantan Institute, São Paulo, Brazil
- Center of Toxins, Immune Response and Cell Signaling (CeTICS), Butantan Institute, São Paulo, Brazil
- * E-mail:
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19
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Padilla-Mejia NE, Makarov AA, Barlow LD, Butterfield ER, Field MC. Evolution and diversification of the nuclear envelope. Nucleus 2021; 12:21-41. [PMID: 33435791 PMCID: PMC7889174 DOI: 10.1080/19491034.2021.1874135] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/08/2020] [Accepted: 12/11/2020] [Indexed: 02/06/2023] Open
Abstract
Eukaryotic cells arose ~1.5 billion years ago, with the endomembrane system a central feature, facilitating evolution of intracellular compartments. Endomembranes include the nuclear envelope (NE) dividing the cytoplasm and nucleoplasm. The NE possesses universal features: a double lipid bilayer membrane, nuclear pore complexes (NPCs), and continuity with the endoplasmic reticulum, indicating common evolutionary origin. However, levels of specialization between lineages remains unclear, despite distinct mechanisms underpinning various nuclear activities. Several distinct modes of molecular evolution facilitate organellar diversification and to understand which apply to the NE, we exploited proteomic datasets of purified nuclear envelopes from model systems for comparative analysis. We find enrichment of core nuclear functions amongst the widely conserved proteins to be less numerous than lineage-specific cohorts, but enriched in core nuclear functions. This, together with consideration of additional evidence, suggests that, despite a common origin, the NE has evolved as a highly diverse organelle with significant lineage-specific functionality.
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Affiliation(s)
- Norma E. Padilla-Mejia
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Alexandr A. Makarov
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Lael D. Barlow
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Erin R. Butterfield
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Mark C. Field
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České, Czech Republic
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A DOT1B/Ribonuclease H2 Protein Complex Is Involved in R-Loop Processing, Genomic Integrity, and Antigenic Variation in Trypanosoma brucei. mBio 2021; 12:e0135221. [PMID: 34749530 PMCID: PMC8576533 DOI: 10.1128/mbio.01352-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The parasite Trypanosoma brucei periodically changes the expression of protective variant surface glycoproteins (VSGs) to evade its host’s immune system in a process known as antigenic variation. One route to change VSG expression is the transcriptional activation of a previously silent VSG expression site (ES), a subtelomeric region containing the VSG genes. Homologous recombination of a different VSG from a large reservoir into the active ES represents another route. The conserved histone methyltransferase DOT1B is involved in transcriptional silencing of inactive ES and influences ES switching kinetics. The molecular machinery that enables DOT1B to execute these regulatory functions remains elusive, however. To better understand DOT1B-mediated regulatory processes, we purified DOT1B-associated proteins using complementary biochemical approaches. We identified several novel DOT1B interactors. One of these was the RNase H2 complex, previously shown to resolve RNA-DNA hybrids, maintain genome integrity, and play a role in antigenic variation. Our study revealed that DOT1B depletion results in an increase in RNA-DNA hybrids, accumulation of DNA damage, and ES switching events. Surprisingly, a similar pattern of VSG deregulation was observed in RNase H2 mutants. We propose that both proteins act together in resolving R-loops to ensure genome integrity and contribute to the tightly regulated process of antigenic variation.
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The nucleolar DExD/H protein Hel66 is involved in ribosome biogenesis in Trypanosoma brucei. Sci Rep 2021; 11:18325. [PMID: 34526538 PMCID: PMC8443567 DOI: 10.1038/s41598-021-97020-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/30/2021] [Indexed: 01/23/2023] Open
Abstract
The biosynthesis of ribosomes is a complex cellular process involving ribosomal RNA, ribosomal proteins and several further trans-acting factors. DExD/H box proteins constitute the largest family of trans-acting protein factors involved in this process. Several members of this protein family have been directly implicated in ribosome biogenesis in yeast. In trypanosomes, ribosome biogenesis differs in several features from the process described in yeast. Here, we have identified the DExD/H box helicase Hel66 as being involved in ribosome biogenesis. The protein is unique to Kinetoplastida, localises to the nucleolus and its depletion via RNAi caused a severe growth defect. Loss of the protein resulted in a decrease of global translation and accumulation of rRNA processing intermediates for both the small and large ribosomal subunits. Only a few factors involved in trypanosome rRNA biogenesis have been described so far and our findings contribute to gaining a more comprehensive picture of this essential process.
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Dean S. Basic Biology of Trypanosoma brucei with Reference to the Development of Chemotherapies. Curr Pharm Des 2021; 27:1650-1670. [PMID: 33463458 DOI: 10.2174/1381612827666210119105008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 12/01/2020] [Accepted: 12/08/2020] [Indexed: 11/22/2022]
Abstract
Trypanosoma brucei are protozoan parasites that cause the lethal human disease African sleeping sickness and the economically devastating disease of cattle, Nagana. African sleeping sickness, also known as Human African Trypanosomiasis (HAT), threatens 65 million people and animal trypanosomiasis makes large areas of farmland unusable. There is no vaccine and licensed therapies against the most severe, late-stage disease are toxic, impractical and ineffective. Trypanosomes are transmitted by tsetse flies, and HAT is therefore predominantly confined to the tsetse fly belt in sub-Saharan Africa. They are exclusively extracellular and they differentiate between at least seven developmental forms that are highly adapted to host and vector niches. In the mammalian (human) host they inhabit the blood, cerebrospinal fluid (late-stage disease), skin, and adipose fat. In the tsetse fly vector they travel from the tsetse midgut to the salivary glands via the ectoperitrophic space and proventriculus. Trypanosomes are evolutionarily divergent compared with most branches of eukaryotic life. Perhaps most famous for their extraordinary mechanisms of monoallelic gene expression and antigenic variation, they have also been investigated because much of their biology is either highly unconventional or extreme. Moreover, in addition to their importance as pathogens, many researchers have been attracted to the field because trypanosomes have some of the most advanced molecular genetic tools and database resources of any model system. The following will cover just some aspects of trypanosome biology and how its divergent biochemistry has been leveraged to develop drugs to treat African sleeping sickness. This is by no means intended to be a comprehensive survey of trypanosome features. Rather, I hope to present trypanosomes as one of the most fascinating and tractable systems to do discovery biology.
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Affiliation(s)
- Samuel Dean
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, United Kingdom
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23
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Padilla-Mejia NE, Koreny L, Holden J, Vancová M, Lukeš J, Zoltner M, Field MC. A hub-and-spoke nuclear lamina architecture in trypanosomes. J Cell Sci 2021; 134:jcs251264. [PMID: 34151975 PMCID: PMC8255026 DOI: 10.1242/jcs.251264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 05/10/2021] [Indexed: 01/11/2023] Open
Abstract
The nuclear lamina supports many functions, including maintaining nuclear structure and gene expression control, and correct spatio-temporal assembly is vital to meet these activities. Recently, multiple lamina systems have been described that, despite independent evolutionary origins, share analogous functions. In trypanosomatids the two known lamina proteins, NUP-1 and NUP-2, have molecular masses of 450 and 170 kDa, respectively, which demands a distinct architecture from the ∼60 kDa lamin-based system of metazoa and other lineages. To uncover organizational principles for the trypanosome lamina we generated NUP-1 deletion mutants to identify domains and their arrangements responsible for oligomerization. We found that both the N- and C-termini act as interaction hubs, and that perturbation of these interactions impacts additional components of the lamina and nuclear envelope. Furthermore, the assembly of NUP-1 terminal domains suggests intrinsic organizational capacity. Remarkably, there is little impact on silencing of telomeric variant surface glycoprotein genes. We suggest that both terminal domains of NUP-1 have roles in assembling the trypanosome lamina and propose a novel architecture based on a hub-and-spoke configuration.
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Affiliation(s)
| | - Ludek Koreny
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Jennifer Holden
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Marie Vancová
- Institute of Parasitology, Biology Centre and Faculty of Sciences, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre and Faculty of Sciences, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Martin Zoltner
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Department of Parasitology, Faculty of Science, Charles University in Prague, BIOCEV 252 50, Vestec, Czech Republic
| | - Mark C. Field
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Institute of Parasitology, Biology Centre and Faculty of Sciences, University of South Bohemia, 37005 České Budějovice, Czech Republic
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Casein kinase TbCK1.2 regulates division of kinetoplast DNA, and movement of basal bodies in the African trypanosome. PLoS One 2021; 16:e0249908. [PMID: 33861760 PMCID: PMC8051774 DOI: 10.1371/journal.pone.0249908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/26/2021] [Indexed: 01/15/2023] Open
Abstract
The single mitochondrial nucleoid (kinetoplast) of Trypanosoma brucei is found proximal to a basal body (mature (mBB)/probasal body (pBB) pair). Kinetoplast inheritance requires synthesis of, and scission of kinetoplast DNA (kDNA) generating two kinetoplasts that segregate with basal bodies into daughter cells. Molecular details of kinetoplast scission and the extent to which basal body separation influences the process are unavailable. To address this topic, we followed basal body movements in bloodstream trypanosomes following depletion of protein kinase TbCK1.2 which promotes kinetoplast division. In control cells we found that pBBs are positioned 0.4 um from mBBs in G1, and they mature after separating from mBBs by at least 0.8 um: mBB separation reaches ~2.2 um. These data indicate that current models of basal body biogenesis in which pBBs mature in close proximity to mBBs may need to be revisited. Knockdown of TbCK1.2 produced trypanosomes containing one kinetoplast and two nuclei (1K2N), increased the percentage of cells with uncleaved kDNA 400%, decreased mBB spacing by 15%, and inhibited cytokinesis 300%. We conclude that (a) separation of mBBs beyond a threshold of 1.8 um correlates with division of kDNA, and (b) TbCK1.2 regulates kDNA scission. We propose a Kinetoplast Division Factor hypothesis that integrates these data into a pathway for biogenesis of two daughter mitochondrial nucleoids.
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25
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Kramer S, Meyer-Natus E, Stigloher C, Thoma H, Schnaufer A, Engstler M. Parallel monitoring of RNA abundance, localization and compactness with correlative single molecule FISH on LR White embedded samples. Nucleic Acids Res 2021; 49:e14. [PMID: 33275141 PMCID: PMC7897490 DOI: 10.1093/nar/gkaa1142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 10/16/2020] [Accepted: 11/17/2020] [Indexed: 01/19/2023] Open
Abstract
Single mRNA molecules are frequently detected by single molecule fluorescence in situ hybridization (smFISH) using branched DNA technology. While providing strong and background-reduced signals, the method is inefficient in detecting mRNAs within dense structures, in monitoring mRNA compactness and in quantifying abundant mRNAs. To overcome these limitations, we have hybridized slices of high pressure frozen, freeze-substituted and LR White embedded cells (LR White smFISH). mRNA detection is physically restricted to the surface of the resin. This enables single molecule detection of RNAs with accuracy comparable to RNA sequencing, irrespective of their abundance, while at the same time providing spatial information on RNA localization that can be complemented with immunofluorescence and electron microscopy, as well as array tomography. Moreover, LR White embedding restricts the number of available probe pair recognition sites for each mRNA to a small subset. As a consequence, differences in signal intensities between RNA populations reflect differences in RNA structures, and we show that the method can be employed to determine mRNA compactness. We apply the method to answer some outstanding questions related to trans-splicing, RNA granules and mitochondrial RNA editing in single-cellular trypanosomes and we show an example of differential gene expression in the metazoan Caenorhabditis elegans.
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Affiliation(s)
- Susanne Kramer
- Zell- und Entwicklungsbiologie, Biozentrum, Universität Würzburg, Würzburg, Germany
| | | | - Christian Stigloher
- Zell- und Entwicklungsbiologie, Biozentrum, Universität Würzburg, Würzburg, Germany.,Imaging Core Facility, Biozentrum, Universität Würzburg, Würzburg, Germany
| | - Hanna Thoma
- Zell- und Entwicklungsbiologie, Biozentrum, Universität Würzburg, Würzburg, Germany
| | - Achim Schnaufer
- Institute for Immunology & Infection Research, University of Edinburgh, Edinburgh, UK
| | - Markus Engstler
- Zell- und Entwicklungsbiologie, Biozentrum, Universität Würzburg, Würzburg, Germany
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26
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Mokdadi M, Abdelkrim YZ, Banroques J, Huvelle E, Oualha R, Yeter-Alat H, Guizani I, Barhoumi M, Tanner NK. The In Silico Identification of Potential Members of the Ded1/DDX3 Subfamily of DEAD-Box RNA Helicases from the Protozoan Parasite Leishmania infantum and Their Analyses in Yeast. Genes (Basel) 2021; 12:212. [PMID: 33535521 PMCID: PMC7912733 DOI: 10.3390/genes12020212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/27/2021] [Accepted: 01/29/2021] [Indexed: 12/14/2022] Open
Abstract
DEAD-box RNA helicases are ubiquitous proteins found in all kingdoms of life and that are associated with all processes involving RNA. Their central roles in biology make these proteins potential targets for therapeutic or prophylactic drugs. The Ded1/DDX3 subfamily of DEAD-box proteins is of particular interest because of their important role(s) in translation. In this paper, we identified and aligned the protein sequences of 28 different DEAD-box proteins from the kinetoplast-protozoan parasite Leishmania infantum, which is the cause of the visceral form of leishmaniasis that is often lethal if left untreated, and compared them with the consensus sequence derived from DEAD-box proteins in general, and from the Ded1/DDX3 subfamily in particular, from a wide variety of other organisms. We identified three potential homologs of the Ded1/DDX3 subfamily and the equivalent proteins from the related protozoan parasite Trypanosoma brucei, which is the causative agent of sleeping sickness. We subsequently tested these proteins for their ability to complement a yeast strain deleted for the essential DED1 gene. We found that the DEAD-box proteins from Trypanosomatids are highly divergent from other eukaryotes, and consequently they are suitable targets for protein-specific drugs.
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Affiliation(s)
- Molka Mokdadi
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France; (M.M.); (Y.Z.A.); (J.B.); (E.H.); (H.Y.-A.)
- PSL Research University, 75005 Paris, France
- Laboratory of Molecular Epidemiology and Experimental Pathology (LR16IPT04), Institut Pasteur de Tunis, Université de Tunis El Manar, 13 Place Pasteur, BP74 Tunis-Belvédère 1002, Tunisia; (R.O.); (I.G.)
- Institut National des Sciences Appliquées et Technologies, Université de Carthage, CEDEX, Tunis 1080, Tunisia
| | - Yosser Zina Abdelkrim
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France; (M.M.); (Y.Z.A.); (J.B.); (E.H.); (H.Y.-A.)
- Laboratory of Molecular Epidemiology and Experimental Pathology (LR16IPT04), Institut Pasteur de Tunis, Université de Tunis El Manar, 13 Place Pasteur, BP74 Tunis-Belvédère 1002, Tunisia; (R.O.); (I.G.)
| | - Josette Banroques
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France; (M.M.); (Y.Z.A.); (J.B.); (E.H.); (H.Y.-A.)
- PSL Research University, 75005 Paris, France
| | - Emmeline Huvelle
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France; (M.M.); (Y.Z.A.); (J.B.); (E.H.); (H.Y.-A.)
- PSL Research University, 75005 Paris, France
| | - Rafeh Oualha
- Laboratory of Molecular Epidemiology and Experimental Pathology (LR16IPT04), Institut Pasteur de Tunis, Université de Tunis El Manar, 13 Place Pasteur, BP74 Tunis-Belvédère 1002, Tunisia; (R.O.); (I.G.)
| | - Hilal Yeter-Alat
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France; (M.M.); (Y.Z.A.); (J.B.); (E.H.); (H.Y.-A.)
- PSL Research University, 75005 Paris, France
| | - Ikram Guizani
- Laboratory of Molecular Epidemiology and Experimental Pathology (LR16IPT04), Institut Pasteur de Tunis, Université de Tunis El Manar, 13 Place Pasteur, BP74 Tunis-Belvédère 1002, Tunisia; (R.O.); (I.G.)
| | - Mourad Barhoumi
- Laboratory of Molecular Epidemiology and Experimental Pathology (LR16IPT04), Institut Pasteur de Tunis, Université de Tunis El Manar, 13 Place Pasteur, BP74 Tunis-Belvédère 1002, Tunisia; (R.O.); (I.G.)
| | - N. Kyle Tanner
- Expression Génétique Microbienne, UMR8261 CNRS, Université de Paris, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France; (M.M.); (Y.Z.A.); (J.B.); (E.H.); (H.Y.-A.)
- PSL Research University, 75005 Paris, France
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27
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Abstract
The passage of mRNAs through the nuclear pores into the cytoplasm is essential in all eukaryotes. For regulation, mRNA export is tightly connected to the full machinery of nuclear mRNA processing, starting at transcription. Export competence of pre-mRNAs gradually increases by both transient and permanent interactions with multiple RNA processing and export factors. mRNA export is best understood in opisthokonts, with limited knowledge in plants and protozoa. Here, I review and compare nuclear mRNA processing and export between opisthokonts and Trypanosoma brucei. The parasite has many unusual features in nuclear mRNA processing, such as polycistronic transcription and trans-splicing. It lacks several nuclear complexes and nuclear-pore-associated proteins that in opisthokonts play major roles in mRNA export. As a consequence, trypanosome mRNA export control is not tight and export can even start co-transcriptionally. Whether trypanosomes regulate mRNA export at all, or whether leakage of immature mRNA to the cytoplasm is kept to a low level by a fast kinetics of mRNA processing remains to be investigated. mRNA export had to be present in the last common ancestor of eukaryotes. Trypanosomes are evolutionary very distant from opisthokonts and a comparison helps understanding the evolution of mRNA export.
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28
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Leal AZ, Schwebs M, Briggs E, Weisert N, Reis H, Lemgruber L, Luko K, Wilkes J, Butter F, McCulloch R, Janzen CJ. Genome maintenance functions of a putative Trypanosoma brucei translesion DNA polymerase include telomere association and a role in antigenic variation. Nucleic Acids Res 2020; 48:9660-9680. [PMID: 32890403 PMCID: PMC7515707 DOI: 10.1093/nar/gkaa686] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 08/03/2020] [Accepted: 09/03/2020] [Indexed: 12/17/2022] Open
Abstract
Maintenance of genome integrity is critical to guarantee transfer of an intact genome from parent to offspring during cell division. DNA polymerases (Pols) provide roles in both replication of the genome and the repair of a wide range of lesions. Amongst replicative DNA Pols, translesion DNA Pols play a particular role: replication to bypass DNA damage. All cells express a range of translesion Pols, but little work has examined their function in parasites, including whether the enzymes might contribute to host-parasite interactions. Here, we describe a dual function of one putative translesion Pol in African trypanosomes, which we now name TbPolIE. Previously, we demonstrated that TbPolIE is associated with telomeric sequences and here we show that RNAi-mediated depletion of TbPolIE transcripts results in slowed growth, altered DNA content, changes in cell morphology, and increased sensitivity to DNA damaging agents. We also show that TbPolIE displays pronounced localization at the nuclear periphery, and that its depletion leads to chromosome segregation defects and increased levels of endogenous DNA damage. Finally, we demonstrate that TbPolIE depletion leads to deregulation of telomeric variant surface glycoprotein genes, linking the function of this putative translesion DNA polymerase to host immune evasion by antigenic variation.
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Affiliation(s)
- Andrea Zurita Leal
- The Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Marie Schwebs
- Department of Cell & Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Emma Briggs
- The Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Nadine Weisert
- Department of Cell & Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Helena Reis
- Department of Cell & Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
| | - Leandro Lemgruber
- The Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Katarina Luko
- Quantitative Proteomics, Institute of Molecular Biology (IMB), Mainz, Germany
| | - Jonathan Wilkes
- The Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Falk Butter
- Quantitative Proteomics, Institute of Molecular Biology (IMB), Mainz, Germany
| | - Richard McCulloch
- The Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Christian J Janzen
- Department of Cell & Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany
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29
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Trypanosoma cruzi Importin α: ability to bind to a functional classical nuclear localization signal of the bipartite type. Parasitol Res 2020; 119:3899-3907. [PMID: 32951146 DOI: 10.1007/s00436-020-06885-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 09/13/2020] [Indexed: 02/07/2023]
Abstract
Importin α, a transport factor in the classical pathway of nuclear transport of proteins in eukaryotes, has not been experimentally studied in trypanosomatids. A chimeric fluorescent version of this protein (TcImportin α-EGFP) expressed in transfected epimastigotes of Trypanosoma cruzi is characterized here. Initially, the cellular localization of the tagged protein was analysed in exponentially growing and non-growing quiescent cells in a stationary phase. In growing epimastigotes, the fluorescence signal appeared to be mostly localized in the nucleolus, with additional minor fluorescent dots observed close to the nuclear periphery. In the stationary phase, both aged epimastigotes and metacyclic trypomastigotes presented with dispersed fluorescence of a granular form within the nucleoplasm of the cells that predominantly localized in poorly DAPI-stained regions. On the other hand, the ability of a tagged (6×His) version of TcImportin α to bind the nuclear protein cargo TcRPA31 (TcRPA31-EGFP) was determined by pull-down assays of co-transfected cultures. In addition, the results from the in vitro analyses with these tagged recombinant proteins showed that the functional nuclear localization signal (NLS) previously mapped to TcRPA31 was sufficient to sustain binding to TcImportin α. Moreover, the second cluster of basic amino acids within this bipartite NLS (formerly termed element B) was found to be essential for complex formation, as previously described for the nuclear translocation of these fluorescent chimeras. To our knowledge, this approach is the first in which Importin α was experimentally researched in kinetoplastids. The ability of TcImportin α to bind the NLS motif analysed here, is an essential feature expected for its potential functional role as a soluble transport factor.
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30
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Baudouin HCM, Pfeiffer L, Ochsenreiter T. A comparison of three approaches for the discovery of novel tripartite attachment complex proteins in Trypanosoma brucei. PLoS Negl Trop Dis 2020; 14:e0008568. [PMID: 32936798 PMCID: PMC7521757 DOI: 10.1371/journal.pntd.0008568] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 09/28/2020] [Accepted: 07/07/2020] [Indexed: 11/19/2022] Open
Abstract
Trypanosoma brucei is a single celled eukaryotic parasite and the causative agent of human African trypanosomiasis and nagana in cattle. Aside from its medical relevance, T. brucei has also been key to the discovery of several general biological principles including GPI-anchoring, RNA-editing and trans-splicing. The parasite contains a single mitochondrion with a singular genome. Recent studies have identified several molecular components of the mitochondrial genome segregation machinery (tripartite attachment complex, TAC), which connects the basal body of the flagellum to the mitochondrial DNA of T. brucei. The TAC component in closest proximity to the mitochondrial DNA is TAC102. Here we apply and compare three different approaches (proximity labelling, immunoprecipitation and yeast two-hybrid) to identify novel interactors of TAC102 and subsequently verify their localisation. Furthermore, we establish the direct interaction of TAC102 and p166 in the unilateral filaments of the TAC. Trypanosoma brucei belongs to a group of organisms that exist as human, animal and plant parasites. T. brucei (a human and animal parasite) has been developed as a model system to study basic biological as well as disease related questions in this group of organisms. We study how the parasite duplicates and divides its mitochondrial genome, an essential component of its energy generating machinery. The structure involved in dividing the mitochondrial genome into the daughter cells during cell division is called the tripartite attachment complex (TAC). The TAC is likely a unique structure not present in the host and thus might provide a new avenue for drug development. In this manuscript, we compare different techniques that allow the identification of novel components of this structure and verify the localisation of some of them. Furthermore, we also establish the interaction of two previously identified protein components.
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Affiliation(s)
- Hélène Clémentine Margareta Baudouin
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Laura Pfeiffer
- Institute of Cell Biology, University of Bern, Bern, Switzerland
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31
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Faktorová D, Kaur B, Valach M, Graf L, Benz C, Burger G, Lukeš J. Targeted integration by homologous recombination enables in situ tagging and replacement of genes in the marine microeukaryote Diplonema papillatum. Environ Microbiol 2020; 22:3660-3670. [PMID: 32548939 DOI: 10.1111/1462-2920.15130] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/07/2020] [Accepted: 06/13/2020] [Indexed: 12/17/2022]
Abstract
Diplonemids are a group of highly diverse and abundant marine microeukaryotes that belong to the phylum Euglenozoa and form a sister clade to the well-studied, mostly parasitic kinetoplastids. Very little is known about the biology of diplonemids, as few species have been formally described and just one, Diplonema papillatum, has been studied to a decent extent at the molecular level. Following up on our previous results showing stable but random integration of delivered extraneous DNA, we demonstrate here homologous recombination in D. papillatum. Targeting various constructs to the intended position in the nuclear genome was successful when 5' and 3' homologous regions longer than 1 kbp were used, achieving N-terminal tagging with mCherry and gene replacement of α- and β-tubulins. For more convenient genetic manipulation, we designed a modular plasmid, pDP002, which bears a protein-A tag and used it to generate and express a C-terminally tagged mitoribosomal protein. Lastly, we developed an improved transformation protocol for broader applicability across laboratories. Our robust methodology allows the replacement, integration as well as endogenous tagging of D. papillatum genes, thus opening the door to functional studies in this species and establishing a basic toolkit for reverse genetics of diplonemids in general.
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Affiliation(s)
- Drahomíra Faktorová
- Czech Academy of Sciences, Institute of Parasitology, Biology Centre, Czech Republic.,Faculty of Sciences, University of South Bohemia, Cˇeské Budějovice (Budweis), Czech Republic
| | - Binnypreet Kaur
- Czech Academy of Sciences, Institute of Parasitology, Biology Centre, Czech Republic.,Faculty of Sciences, University of South Bohemia, Cˇeské Budějovice (Budweis), Czech Republic
| | - Matus Valach
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Canada
| | - Lena Graf
- Faculty of Sciences, University of South Bohemia, Cˇeské Budějovice (Budweis), Czech Republic.,Present address: Johannes Kepler University, Linz, Austria
| | - Corinna Benz
- Czech Academy of Sciences, Institute of Parasitology, Biology Centre, Czech Republic
| | - Gertraud Burger
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Canada
| | - Julius Lukeš
- Czech Academy of Sciences, Institute of Parasitology, Biology Centre, Czech Republic.,Faculty of Sciences, University of South Bohemia, Cˇeské Budějovice (Budweis), Czech Republic
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Parthasarathy A, Kalesh K. Defeating the trypanosomatid trio: proteomics of the protozoan parasites causing neglected tropical diseases. RSC Med Chem 2020; 11:625-645. [PMID: 33479664 PMCID: PMC7549140 DOI: 10.1039/d0md00122h] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/12/2020] [Indexed: 12/20/2022] Open
Abstract
Mass spectrometry-based proteomics enables accurate measurement of the modulations of proteins on a large scale upon perturbation and facilitates the understanding of the functional roles of proteins in biological systems. It is a particularly relevant methodology for studying Leishmania spp., Trypanosoma cruzi and Trypanosoma brucei, as the gene expression in these parasites is primarily regulated by posttranscriptional mechanisms. Large-scale proteomics studies have revealed a plethora of information regarding modulated proteins and their molecular interactions during various life processes of the protozoans, including stress adaptation, life cycle changes and interactions with the host. Important molecular processes within the parasite that regulate the activity and subcellular localisation of its proteins, including several co- and post-translational modifications, are also accurately captured by modern proteomics mass spectrometry techniques. Finally, in combination with synthetic chemistry, proteomic techniques facilitate unbiased profiling of targets and off-targets of pharmacologically active compounds in the parasites. This provides important data sets for their mechanism of action studies, thereby aiding drug development programmes.
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Affiliation(s)
- Anutthaman Parthasarathy
- Rochester Institute of Technology , Thomas H. Gosnell School of Life Sciences , 85 Lomb Memorial Dr , Rochester , NY 14623 , USA
| | - Karunakaran Kalesh
- Department of Chemistry , Durham University , Lower Mount Joy, South Road , Durham DH1 3LE , UK .
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Kieft R, Zhang Y, Marand AP, Moran JD, Bridger R, Wells L, Schmitz RJ, Sabatini R. Identification of a novel base J binding protein complex involved in RNA polymerase II transcription termination in trypanosomes. PLoS Genet 2020; 16:e1008390. [PMID: 32084124 PMCID: PMC7055916 DOI: 10.1371/journal.pgen.1008390] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 03/04/2020] [Accepted: 01/08/2020] [Indexed: 11/18/2022] Open
Abstract
Base J, β-D-glucosyl-hydroxymethyluracil, is a modification of thymine DNA base involved in RNA Polymerase (Pol) II transcription termination in kinetoplastid protozoa. Little is understood regarding how specific thymine residues are targeted for J-modification or the mechanism of J regulated transcription termination. To identify proteins involved in J-synthesis, we expressed a tagged version of the J-glucosyltransferase (JGT) in Leishmania tarentolae, and identified four co-purified proteins by mass spectrometry: protein phosphatase (PP1), a homolog of Wdr82, a potential PP1 regulatory protein (PNUTS) and a protein containing a J-DNA binding domain (named JBP3). Gel shift studies indicate JBP3 is a J-DNA binding protein. Reciprocal tagging, co-IP and sucrose gradient analyses indicate PP1, JGT, JBP3, Wdr82 and PNUTS form a multimeric complex in kinetoplastids, similar to the mammalian PTW/PP1 complex involved in transcription termination via PP1 mediated dephosphorylation of Pol II. Using RNAi and analysis of Pol II termination by RNA-seq and RT-PCR, we demonstrate that ablation of PNUTS, JBP3 and Wdr82 lead to defects in Pol II termination at the 3'-end of polycistronic gene arrays in Trypanosoma brucei. Mutants also contain increased antisense RNA levels upstream of transcription start sites, suggesting an additional role of the complex in regulating termination of bi-directional transcription. In addition, PNUTS loss causes derepression of silent Variant Surface Glycoprotein genes involved in host immune evasion. Our results suggest a novel mechanistic link between base J and Pol II polycistronic transcription termination in kinetoplastids.
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Affiliation(s)
- Rudo Kieft
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Yang Zhang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Alexandre P. Marand
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Jose Dagoberto Moran
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Robert Bridger
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Lance Wells
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Robert J. Schmitz
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
| | - Robert Sabatini
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
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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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Reis H, Schwebs M, Dietz S, Janzen CJ, Butter F. TelAP1 links telomere complexes with developmental expression site silencing in African trypanosomes. Nucleic Acids Res 2019; 46:2820-2833. [PMID: 29385523 PMCID: PMC5888660 DOI: 10.1093/nar/gky028] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 01/25/2018] [Indexed: 11/14/2022] Open
Abstract
During its life cycle, Trypanosoma brucei shuttles between a mammalian host and the tsetse fly vector. In the mammalian host, immune evasion of T. brucei bloodstream form (BSF) cells relies on antigenic variation, which includes monoallelic expression and periodic switching of variant surface glycoprotein (VSG) genes. The active VSG is transcribed from only 1 of the 15 subtelomeric expression sites (ESs). During differentiation from BSF to the insect-resident procyclic form (PCF), the active ES is transcriptionally silenced. We used mass spectrometry-based interactomics to determine the composition of telomere protein complexes in T. brucei BSF and PCF stages to learn more about the structure and functions of telomeres in trypanosomes. Our data suggest a different telomere complex composition in the two forms of the parasite. One of the novel telomere-associated proteins, TelAP1, forms a complex with telomeric proteins TbTRF, TbRAP1 and TbTIF2 and influences ES silencing kinetics during developmental differentiation.
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Affiliation(s)
- Helena Reis
- Department of Cell & Developmental Biology, Biocenter University of Würzburg, Würzburg 97074, Germany
| | - Marie Schwebs
- Department of Cell & Developmental Biology, Biocenter University of Würzburg, Würzburg 97074, Germany
| | - Sabrina Dietz
- Quantitative Proteomics, Institute of Molecular Biology (IMB), Mainz 55128, Germany
| | - Christian J Janzen
- Department of Cell & Developmental Biology, Biocenter University of Würzburg, Würzburg 97074, Germany
| | - Falk Butter
- Quantitative Proteomics, Institute of Molecular Biology (IMB), Mainz 55128, Germany
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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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Bentley SJ, Jamabo M, Boshoff A. The Hsp70/J-protein machinery of the African trypanosome, Trypanosoma brucei. Cell Stress Chaperones 2019; 24:125-148. [PMID: 30506377 PMCID: PMC6363631 DOI: 10.1007/s12192-018-0950-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 11/06/2018] [Accepted: 11/12/2018] [Indexed: 12/28/2022] Open
Abstract
The etiological agent of the neglected tropical disease African trypanosomiasis, Trypanosoma brucei, possesses an expanded and diverse repertoire of heat shock proteins, which have been implicated in cytoprotection, differentiation, as well as progression and transmission of the disease. Hsp70 plays a crucial role in proteostasis, and inhibition of its interactions with co-chaperones is emerging as a potential therapeutic target for numerous diseases. In light of genome annotations and the release of the genome sequence of the human infective subspecies, an updated and current in silico overview of the Hsp70/J-protein machinery in both T. brucei brucei and T. brucei gambiense was conducted. Functional, structural, and evolutionary analyses of the T. brucei Hsp70 and J-protein families were performed. The Hsp70 and J-proteins from humans and selected kinetoplastid parasites were used to assist in identifying proteins from T. brucei, as well as the prediction of potential Hsp70-J-protein partnerships. The Hsp70 and J-proteins were mined from numerous genome-wide proteomics studies, which included different lifecycle stages and subcellular localisations. In this study, 12 putative Hsp70 proteins and 67 putative J-proteins were identified to be encoded on the genomes of both T. brucei subspecies. Interestingly there are 6 type III J-proteins that possess tetratricopeptide repeat-containing (TPR) motifs. Overall, it is envisioned that the results of this study will provide a future context for studying the biology of the African trypanosome and evaluating Hsp70 and J-protein interactions as potential drug targets.
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Affiliation(s)
| | - Miebaka Jamabo
- Biotechnology Innovation Centre, Rhodes University, Grahamstown, South Africa
| | - Aileen Boshoff
- Biotechnology Innovation Centre, Rhodes University, Grahamstown, South Africa.
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Iribarren PA, Di Marzio LA, Berazategui MA, De Gaudenzi JG, Alvarez VE. SUMO polymeric chains are involved in nuclear foci formation and chromatin organization in Trypanosoma brucei procyclic forms. PLoS One 2018; 13:e0193528. [PMID: 29474435 PMCID: PMC5825156 DOI: 10.1371/journal.pone.0193528] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 02/13/2018] [Indexed: 01/10/2023] Open
Abstract
SUMOylation is a post-translational modification conserved in eukaryotic organisms that involves the covalent attachment of the small ubiquitin-like protein SUMO to internal lysine residues in target proteins. This tag usually alters the interaction surface of the modified protein and can be translated into changes in its biological activity, stability or subcellular localization, among other possible outputs. SUMO can be attached as a single moiety or as SUMO polymers in case there are internal acceptor sites in SUMO itself. These chains have been shown to be important for proteasomal degradation as well as for the formation of subnuclear structures such as the synaptonemal complex in Saccharomyces cerevisiae or promyelocytic leukemia nuclear bodies in mammals. In this work, we have examined SUMO chain formation in the protozoan parasite Trypanosoma brucei. Using a recently developed bacterial strain engineered to produce SUMOylated proteins we confirmed the ability of TbSUMO to form polymers and determined the type of linkage using site-directed mutational analysis. By generating transgenic procyclic parasites unable to form chains we demonstrated that although not essential for normal growth, SUMO polymerization determines the localization of the modified proteins in the nucleus. In addition, FISH analysis of telomeres showed a differential positioning depending on the polySUMOylation abilities of the cells. Thus, our observations suggest that TbSUMO chains might play a role in establishing interaction platforms contributing to chromatin organization.
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Affiliation(s)
- Paula Ana Iribarren
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde—Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Campus Miguelete, Av. 25 de Mayo y Francia, San Martín, Buenos Aires, Argentina
| | - Lucía Ayelén Di Marzio
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde—Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Campus Miguelete, Av. 25 de Mayo y Francia, San Martín, Buenos Aires, Argentina
| | - María Agustina Berazategui
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde—Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Campus Miguelete, Av. 25 de Mayo y Francia, San Martín, Buenos Aires, Argentina
| | - Javier Gerardo De Gaudenzi
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde—Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Campus Miguelete, Av. 25 de Mayo y Francia, San Martín, Buenos Aires, Argentina
- * E-mail: (VEA); (JGDG)
| | - Vanina Eder Alvarez
- Instituto de Investigaciones Biotecnológicas Dr. Rodolfo A. Ugalde—Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martín (UNSAM)—Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Campus Miguelete, Av. 25 de Mayo y Francia, San Martín, Buenos Aires, Argentina
- * E-mail: (VEA); (JGDG)
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