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Zamani H, Poorinmohammad N, Azimi A, Salavati R. From a bimodal to a multi-stage view on trypanosomes' differential RNA editing. Trends Parasitol 2024; 40:372-377. [PMID: 38494388 DOI: 10.1016/j.pt.2024.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 02/13/2024] [Accepted: 02/22/2024] [Indexed: 03/19/2024]
Abstract
Significant variations in the abundance of mitochondrial RNA processing proteins and their target RNAs across trypanosome life stages present an opportunity to explore the regulatory mechanisms that drive these changes. Utilizing omics approaches can uncover unconventional targets, aiding our understanding of the parasites' adaptation and enabling targeted interventions for differentiation.
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Affiliation(s)
- Homa Zamani
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec H9X 3V9, Canada
| | - Naghmeh Poorinmohammad
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec H9X 3V9, Canada
| | - Amin Azimi
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec H9X 3V9, Canada
| | - Reza Salavati
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec H9X 3V9, Canada; Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada.
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Cayla M, Spanos C, McWilliam K, Waskett E, Rappsilber J, Matthews KR. Differentiation granules, a dynamic regulator of T. brucei development. Nat Commun 2024; 15:2972. [PMID: 38582942 PMCID: PMC10998879 DOI: 10.1038/s41467-024-47309-1] [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: 10/13/2023] [Accepted: 03/26/2024] [Indexed: 04/08/2024] Open
Abstract
Adaptation to a change of environment is an essential process for survival, in particular for parasitic organisms exposed to a wide range of hosts. Such adaptations include rapid control of gene expression through the formation of membraneless organelles composed of poly-A RNA and proteins. The African trypanosome Trypanosoma brucei is exquisitely sensitive to well-defined environmental stimuli that trigger cellular adaptations through differentiation events that characterise its complex life cycle. The parasite has been shown to form stress granules in vitro, and it has been proposed that such a stress response could have been repurposed to enable differentiation and facilitate parasite transmission. Therefore, we explored the composition and positional dynamics of membraneless granules formed in response to starvation stress and during differentiation in the mammalian host between the replicative slender and transmission-adapted stumpy forms. We find that T. brucei differentiation does not reflect the default response to environmental stress. Instead, the developmental response of the parasites involves a specific and programmed hierarchy of membraneless granule assembly, with distinct components and regulation by protein kinases such as TbDYRK, that are required for the parasite to successfully progress through its life cycle development and prepare for transmission.
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Affiliation(s)
- Mathieu Cayla
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
- York Biomedical Research Institute, Department of Biology, University of York, York, UK.
| | - Christos Spanos
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Kirsty McWilliam
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Eliza Waskett
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Keith R Matthews
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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Nguyen A, Mustafa AHM, Leydecker AK, Halilovic M, Murr J, Butter F, Krämer OH. The protein phosphatase-2A subunit PR130 is involved in the formation of cytotoxic protein aggregates in pancreatic ductal adenocarcinoma cells. Cell Commun Signal 2024; 22:217. [PMID: 38570831 PMCID: PMC10993613 DOI: 10.1186/s12964-024-01597-8] [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: 11/11/2023] [Accepted: 03/26/2024] [Indexed: 04/05/2024] Open
Abstract
As a major source of cellular serine and threonine phosphatase activity, protein phosphatase-2A (PP2A) modulates signaling pathways in health and disease. PP2A complexes consist of catalytic, scaffolding, and B-type subunits. Seventeen PP2A B-type subunits direct PP2A complexes to selected substrates. It is ill-defined how PP2A B-type subunits determine the growth and drug responsiveness of tumor cells. Pancreatic ductal adenocarcinoma (PDAC) is a disease with poor prognosis. We analyzed the responses of murine and human mesenchymal and epithelial PDAC cells to the specific PP2A inhibitor phendione. We assessed protein levels by immunoblot and proteomics and cell fate by flow cytometry, confocal microscopy, and genetic manipulation. We show that murine mesenchymal PDAC cells express significantly higher levels of the PP2A B-type subunit PR130 than epithelial PDAC cells. This overexpression of PR130 is associated with a dependency of such metastasis-prone cells on the catalytic activity of PP2A. Phendione induces apoptosis and an accumulation of cytotoxic protein aggregates in murine mesenchymal and human PDAC cells. These processes occur independently of the frequently mutated tumor suppressor p53. Proteomic analyses reveal that phendione upregulates the chaperone HSP70 in mesenchymal PDAC cells. Inhibition of HSP70 promotes phendione-induced apoptosis and phendione promotes a proteasomal degradation of PR130. Genetic elimination of PR130 sensitizes murine and human PDAC cells to phendione-induced apoptosis and protein aggregate formation. These data suggest that the PP2A-PR130 complex dephosphorylates and thereby prevents the aggregation of proteins in tumor cells.
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Affiliation(s)
- Alexandra Nguyen
- Institute of Toxicology, University Medical Center of the Johannes Gutenberg University Mainz, Obere Zahlbacher St. 67, 55131, Mainz, Germany
| | - Al-Hassan M Mustafa
- Institute of Toxicology, University Medical Center of the Johannes Gutenberg University Mainz, Obere Zahlbacher St. 67, 55131, Mainz, Germany
- Department of Zoology, Faculty of Science, Aswan University, Aswan, Egypt
| | - Alessa K Leydecker
- Institute of Toxicology, University Medical Center of the Johannes Gutenberg University Mainz, Obere Zahlbacher St. 67, 55131, Mainz, Germany
| | - Melisa Halilovic
- Institute of Toxicology, University Medical Center of the Johannes Gutenberg University Mainz, Obere Zahlbacher St. 67, 55131, Mainz, Germany
| | - Janine Murr
- Medical Clinic and Polyclinic II, Klinikum Rechts Der Isar, Technical University Munich, 81675, Munich, Germany
| | - Falk Butter
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
- Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald, Insel Riems, Germany
| | - Oliver H Krämer
- Institute of Toxicology, University Medical Center of the Johannes Gutenberg University Mainz, Obere Zahlbacher St. 67, 55131, Mainz, Germany.
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Zahedifard F, Bansal M, Sharma N, Kumar S, Shen S, Singh P, Rathi B, Zoltner M. Phenotypic screening reveals a highly selective phthalimide-based compound with antileishmanial activity. PLoS Negl Trop Dis 2024; 18:e0012050. [PMID: 38527083 PMCID: PMC10994559 DOI: 10.1371/journal.pntd.0012050] [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: 12/01/2023] [Revised: 04/04/2024] [Accepted: 03/05/2024] [Indexed: 03/27/2024] Open
Abstract
Pharmacophores such as hydroxyethylamine (HEA) and phthalimide (PHT) have been identified as potential synthons for the development of compounds against various parasitic infections. In order to further advance our progress, we conducted an experiment utilising a collection of PHT and HEA derivatives through phenotypic screening against a diverse set of protist parasites. This approach led to the identification of a number of compounds that exhibited significant effects on the survival of Entamoeba histolytica, Trypanosoma brucei, and multiple life-cycle stages of Leishmania spp. The Leishmania hits were pursued due to the pressing necessity to expand our repertoire of reliable, cost-effective, and efficient medications for the treatment of leishmaniases. Antileishmanials must possess the essential capability to efficiently penetrate the host cells and their compartments in the disease context, to effectively eliminate the intracellular parasite. Hence, we performed a study to assess the effectiveness of eradicating L. infantum intracellular amastigotes in a model of macrophage infection. Among eleven L. infantum growth inhibitors with low-micromolar potency, PHT-39, which carries a trifluoromethyl substitution, demonstrated the highest efficacy in the intramacrophage assay, with an EC50 of 1.2 +/- 3.2 μM. Cytotoxicity testing of PHT-39 in HepG2 cells indicated a promising selectivity of over 90-fold. A chemogenomic profiling approach was conducted using an orthology-based method to elucidate the mode of action of PHT-39. This genome-wide RNA interference library of T. brucei identified sensitivity determinants for PHT-39, which included a P-type ATPase that is crucial for the uptake of miltefosine and amphotericin, strongly indicating a shared route for cellular entry. Notwithstanding the favourable properties and demonstrated efficacy in the Plasmodium berghei infection model, PHT-39 was unable to eradicate L. major infection in a murine infection model of cutaneous leishmaniasis. Currently, PHT-39 is undergoing derivatization to optimize its pharmacological characteristics.
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Affiliation(s)
- Farnaz Zahedifard
- Drug Discovery and Evaluation Unit, Department of Parasitology, Faculty of Science, Charles University in Prague, Biocev, Vestec, Czech Republic
| | - Meenakshi Bansal
- H. G. Khorana Centre for Chemical Biology, Department of Chemistry, Hansraj College, University of Delhi, Delhi, India
- Department of Chemistry, Deenbandhu Chhotu Ram, University of Science & Technology, Murthal, Sonepat Haryana, India
| | - Neha Sharma
- H. G. Khorana Centre for Chemical Biology, Department of Chemistry, Hansraj College, University of Delhi, Delhi, India
| | - Sumit Kumar
- Department of Chemistry, Deenbandhu Chhotu Ram, University of Science & Technology, Murthal, Sonepat Haryana, India
| | - Siqi Shen
- Drug Discovery and Evaluation Unit, Department of Parasitology, Faculty of Science, Charles University in Prague, Biocev, Vestec, Czech Republic
| | - Priyamvada Singh
- Department of Chemistry, Miranda House, University of Delhi, Delhi, India
- Delhi School of Public Health, Institution of Eminence, University of Delhi, Delhi, India
| | - Brijesh Rathi
- H. G. Khorana Centre for Chemical Biology, Department of Chemistry, Hansraj College, University of Delhi, Delhi, India
- Delhi School of Public Health, Institution of Eminence, University of Delhi, Delhi, India
| | - Martin Zoltner
- Drug Discovery and Evaluation Unit, Department of Parasitology, Faculty of Science, Charles University in Prague, Biocev, Vestec, Czech Republic
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Poorinmohammad N, Salavati R. Prioritization of Trypanosoma brucei editosome protein interactions interfaces at residue resolution through proteome-scale network analysis. BMC Mol Cell Biol 2024; 25:3. [PMID: 38279116 PMCID: PMC10811811 DOI: 10.1186/s12860-024-00499-4] [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: 09/26/2023] [Accepted: 01/19/2024] [Indexed: 01/28/2024] Open
Abstract
BACKGROUND Trypanosoma brucei is the causative agent for trypanosomiasis in humans and livestock, which presents a growing challenge due to drug resistance. While identifying novel drug targets is vital, the process is delayed due to a lack of functional information on many of the pathogen's proteins. Accordingly, this paper presents a computational framework for prioritizing drug targets within the editosome, a vital molecular machinery responsible for mitochondrial RNA processing in T. brucei. Importantly, this framework may eliminate the need for prior gene or protein characterization, potentially accelerating drug discovery efforts. RESULTS By integrating protein-protein interaction (PPI) network analysis, PPI structural modeling, and residue interaction network (RIN) analysis, we quantitatively ranked and identified top hub editosome proteins, their key interaction interfaces, and hotspot residues. Our findings were cross-validated and further prioritized by incorporating them into gene set analysis and differential expression analysis of existing quantitative proteomics data across various life stages of T. brucei. In doing so, we highlighted PPIs such as KREL2-KREPA1, RESC2-RESC1, RESC12A-RESC13, and RESC10-RESC6 as top candidates for further investigation. This includes examining their interfaces and hotspot residues, which could guide drug candidate selection and functional studies. CONCLUSION RNA editing offers promise for target-based drug discovery, particularly with proteins and interfaces that play central roles in the pathogen's life cycle. This study introduces an integrative drug target identification workflow combining information from the PPI network, PPI 3D structure, and reside-level information of their interface which can be applicable to diverse pathogens. In the case of T. brucei, via this pipeline, the present study suggested potential drug targets with residue-resolution from RNA editing machinery. However, experimental validation is needed to fully realize its potential in advancing urgently needed antiparasitic drug development.
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Affiliation(s)
- Naghmeh Poorinmohammad
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Montreal, Quebec, H9X 3V9, Canada
| | - Reza Salavati
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Montreal, Quebec, H9X 3V9, Canada.
- Department of Biochemistry, McGill University, Montreal, Quebec, H3G 1Y6, Canada.
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Poli ANR, Blyn RC, Buenconsejo GY, Hodanu M, Tang E, Danh C, Cassel J, Debler EW, Schulz D, Salvino JM. Synthesis and characterization of I-BET151 derivatives for use in identifying protein targets in the African trypanosome. CURRENT RESEARCH IN CHEMICAL BIOLOGY 2023; 3:100047. [PMID: 38152610 PMCID: PMC10751876 DOI: 10.1016/j.crchbi.2023.100047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Trypanosoma brucei, the causative agent of Human African Trypanosomiasis (HAT) and animal trypanosomiases, cycles between a bloodstream form in mammals and a procyclic form in the gut of its insect vector. We previously discovered that the human bromodomain inhibitor I-BET151 causes transcriptome changes that resemble the transition from the bloodstream to the procyclic form. In particular, I-BET151 induces replacement of variant surface glycoprotein (VSG) with procyclin protein. While modest binding of I-BET151 to TbBdf2 and TbBdf3 has been demonstrated, it is unknown whether I-BET151 binds to other identified T. brucei bromodomain proteins and/or other targets. To identify target(s) in T. brucei, we have synthesized I-BET151 derivatives maintaining the key pharmacophoric elements with functionality useful for chemoproteomic approaches. We identified compounds that are potent in inducing expression of procyclin, delineating a strategy towards the design of drugs against HAT and other trypanosomiases. Furthermore, these derivatives represent useful chemical probes to elucidate the molecular mechanism underlying I-BET151-induced differentiation.
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Affiliation(s)
| | - Rebecca C. Blyn
- Department of Biology, Harvey Mudd College, Claremont, CA, 91711, United States
| | | | - Melvin Hodanu
- Department of Biology, Harvey Mudd College, Claremont, CA, 91711, United States
| | - Eric Tang
- Department of Biology, Harvey Mudd College, Claremont, CA, 91711, United States
| | - Channy Danh
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, 19107, United States
| | - Joel Cassel
- The Wistar Cancer Center Molecular Screening, The Wistar Institute, Philadelphia, PA, 19104, United States
| | - Erik W. Debler
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, 19107, United States
| | - Danae Schulz
- Department of Biology, Harvey Mudd College, Claremont, CA, 91711, United States
| | - Joseph M. Salvino
- Medicinal Chemistry, Molecular and Cellular Oncogenesis (MCO) Program, United States
- The Wistar Cancer Center Molecular Screening, The Wistar Institute, Philadelphia, PA, 19104, United States
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Ehlert C, Poorinmohammad N, Mohammaei S, Zhang L, Salavati R. Structure-Function Analysis of RBP7910: An Editosome Z-Binding Protein in Trypanosomatids. Molecules 2023; 28:6963. [PMID: 37836806 PMCID: PMC10574248 DOI: 10.3390/molecules28196963] [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: 09/13/2023] [Revised: 10/01/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023] Open
Abstract
RNA editing, a unique post-transcriptional modification, is observed in trypanosomatid parasites as a crucial procedure for the maturation of mitochondrial mRNAs. The editosome protein complex, involving multiple protein components, plays a key role in this process. In Trypanosoma brucei, a putative Z-DNA binding protein known as RBP7910 is associated with the editosome. However, the specific Z-DNA/Z-RNA binding activity and the interacting interface of RBP7910 have yet to be determined. In this study, we conducted a comparative analysis of the binding behavior of RBP7910 with different potential ligands using microscale thermophoresis (MST). Additionally, we generated a 3D model of the protein, revealing potential Z-α and Z-β nucleic acid-binding domains of RBP7910. RBP7910 belongs to the winged-helix-turn-helix (HTH) superfamily of proteins with an α1α2α3β1β2 topology. Finally, using docking techniques, potential interacting surface regions of RBP7910 with notable oligonucleotide ligands were identified. Our findings indicate that RBP7910 exhibits a notable affinity for (CG)n Z-DNA, both in single-stranded and double-stranded forms. Moreover, we observed a broader interacting interface across its Z-α domain when bound to Z-DNA/Z-RNA compared to when bound to non-Z-form nucleic acid ligands.
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Affiliation(s)
- Curtis Ehlert
- Institute of Parasitology, McGill University, Montreal, QC H9X 3V9, Canada; (C.E.); (N.P.); (S.M.); (L.Z.)
| | - Naghmeh Poorinmohammad
- Institute of Parasitology, McGill University, Montreal, QC H9X 3V9, Canada; (C.E.); (N.P.); (S.M.); (L.Z.)
| | - Saba Mohammaei
- Institute of Parasitology, McGill University, Montreal, QC H9X 3V9, Canada; (C.E.); (N.P.); (S.M.); (L.Z.)
| | - Linhua Zhang
- Institute of Parasitology, McGill University, Montreal, QC H9X 3V9, Canada; (C.E.); (N.P.); (S.M.); (L.Z.)
| | - Reza Salavati
- Institute of Parasitology, McGill University, Montreal, QC H9X 3V9, Canada; (C.E.); (N.P.); (S.M.); (L.Z.)
- Department of Biochemistry, McGill University, Montreal, QC H3A 1A3, Canada
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Taleva G, Husová M, Panicucci B, Hierro-Yap C, Pineda E, Biran M, Moos M, Šimek P, Butter F, Bringaud F, Zíková A. Mitochondrion of the Trypanosoma brucei long slender bloodstream form is capable of ATP production by substrate-level phosphorylation. PLoS Pathog 2023; 19:e1011699. [PMID: 37819951 PMCID: PMC10593219 DOI: 10.1371/journal.ppat.1011699] [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: 07/12/2023] [Revised: 10/23/2023] [Accepted: 09/20/2023] [Indexed: 10/13/2023] Open
Abstract
The long slender bloodstream form Trypanosoma brucei maintains its essential mitochondrial membrane potential (ΔΨm) through the proton-pumping activity of the FoF1-ATP synthase operating in the reverse mode. The ATP that drives this hydrolytic reaction has long been thought to be generated by glycolysis and imported from the cytosol via an ATP/ADP carrier (AAC). Indeed, we demonstrate that AAC is the only carrier that can import ATP into the mitochondrial matrix to power the hydrolytic activity of the FoF1-ATP synthase. However, contrary to expectations, the deletion of AAC has no effect on parasite growth, virulence or levels of ΔΨm. This suggests that ATP is produced by substrate-level phosphorylation pathways in the mitochondrion. Therefore, we knocked out the succinyl-CoA synthetase (SCS) gene, a key mitochondrial enzyme that produces ATP through substrate-level phosphorylation in this parasite. Its absence resulted in changes to the metabolic landscape of the parasite, lowered virulence, and reduced mitochondrial ATP content. Strikingly, these SCS mutant parasites become more dependent on AAC as demonstrated by a 25-fold increase in their sensitivity to the AAC inhibitor, carboxyatractyloside. Since the parasites were able to adapt to the loss of SCS in culture, we also analyzed the more immediate phenotypes that manifest when SCS expression is rapidly suppressed by RNAi. Importantly, when performed under nutrient-limited conditions mimicking various host environments, SCS depletion strongly affected parasite growth and levels of ΔΨm. In totality, the data establish that the long slender bloodstream form mitochondrion is capable of generating ATP via substrate-level phosphorylation pathways.
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Affiliation(s)
- Gergana Taleva
- Institute of Parasitology, Biology Centre CAS, Ceske Budejovice, Czech republic
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech republic
| | - Michaela Husová
- Institute of Parasitology, Biology Centre CAS, Ceske Budejovice, Czech republic
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech republic
| | - Brian Panicucci
- Institute of Parasitology, Biology Centre CAS, Ceske Budejovice, Czech republic
| | - Carolina Hierro-Yap
- Institute of Parasitology, Biology Centre CAS, Ceske Budejovice, Czech republic
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech republic
| | - Erika Pineda
- Univ. Bordeaux, CNRS, Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP), Université de Bordeaux, Bordeaux, France
| | - Marc Biran
- Univ. Bordeaux, CNRS, Centre de Résonance Magnétique des Systèmes Biologiques (CRMSB), Bordeaux, France
| | - Martin Moos
- Institute of Entomology, Biology Centre CAS, Ceske Budejovice, Czech republic
| | - Petr Šimek
- Institute of Entomology, Biology Centre CAS, Ceske Budejovice, Czech republic
| | - Falk Butter
- Institute of Molecular Biology (IMB), Mainz, Germany
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institute, Greifswald, Germany
| | - Frédéric Bringaud
- Univ. Bordeaux, CNRS, Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP), Université de Bordeaux, Bordeaux, France
| | - Alena Zíková
- Institute of Parasitology, Biology Centre CAS, Ceske Budejovice, Czech republic
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech republic
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Briggs EM, Marques CA, Oldrieve GR, Hu J, Otto TD, Matthews KR. Profiling the bloodstream form and procyclic form Trypanosoma brucei cell cycle using single-cell transcriptomics. eLife 2023; 12:e86325. [PMID: 37166108 PMCID: PMC10212563 DOI: 10.7554/elife.86325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/10/2023] [Indexed: 05/12/2023] Open
Abstract
African trypanosomes proliferate as bloodstream forms (BSFs) and procyclic forms in the mammal and tsetse fly midgut, respectively. This allows them to colonise the host environment upon infection and ensure life cycle progression. Yet, understanding of the mechanisms that regulate and drive the cell replication cycle of these forms is limited. Using single-cell transcriptomics on unsynchronised cell populations, we have obtained high resolution cell cycle regulated (CCR) transcriptomes of both procyclic and slender BSF Trypanosoma brucei without prior cell sorting or synchronisation. Additionally, we describe an efficient freeze-thawing protocol that allows single-cell transcriptomic analysis of cryopreserved T. brucei. Computational reconstruction of the cell cycle using periodic pseudotime inference allowed the dynamic expression patterns of cycling genes to be profiled for both life cycle forms. Comparative analyses identify a core cycling transcriptome highly conserved between forms, as well as several genes where transcript levels dynamics are form specific. Comparing transcript expression patterns with protein abundance revealed that the majority of genes with periodic cycling transcript and protein levels exhibit a relative delay between peak transcript and protein expression. This work reveals novel detail of the CCR transcriptomes of both forms, which are available for further interrogation via an interactive webtool.
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Affiliation(s)
- Emma M Briggs
- Institute for Immunology and Infection Research, School of Biological Sciences, University of EdinburghEdinburghUnited Kingdom
- Wellcome Centre for Integrative Parasitology, School of Infection & Immunity, University of GlasgowGlasgowUnited Kingdom
| | - Catarina A Marques
- Wellcome Centre for Integrative Parasitology, School of Infection & Immunity, University of GlasgowGlasgowUnited Kingdom
| | - Guy R Oldrieve
- Institute for Immunology and Infection Research, School of Biological Sciences, University of EdinburghEdinburghUnited Kingdom
| | - Jihua Hu
- Institute for Immunology and Infection Research, School of Biological Sciences, University of EdinburghEdinburghUnited Kingdom
| | - Thomas D Otto
- Wellcome Centre for Integrative Parasitology, School of Infection & Immunity, University of GlasgowGlasgowUnited Kingdom
| | - Keith R Matthews
- Institute for Immunology and Infection Research, School of Biological Sciences, University of EdinburghEdinburghUnited Kingdom
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10
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Tinti M, Ferguson MAJ. Visualisation of proteome-wide ordered protein abundances in Trypanosoma brucei. Wellcome Open Res 2023; 7:34. [PMID: 35284642 PMCID: PMC8889043 DOI: 10.12688/wellcomeopenres.17607.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2023] [Indexed: 02/05/2023] Open
Abstract
Background: Trypanosoma brucei is a protozoan parasite and etiological agent of human and animal African trypanosomiasis. It has a complex life cycle, but the most studied cellular types are the in vitro cultivated bloodstream- and procyclic-forms. These correspond to the replicating, mammalian host bloodstream-dwelling, slender trypomastigotes and tsetse vector midgut-dwelling procyclic lifecycle stages, respectively. Several proteomics studies have reported the differential abundance of proteins between these in vitro cultivated cell types. However, there are no datasets providing protein abundance, from most to least abundant, within and between both cell types. Methods: We used MaxQuant software 1.6.10.4 to reprocess a recent large-scale proteomics experiment from our laboratory and extracted intensity-based quantifications of the bloodstream and procyclic form proteomes. Results: We created a web interface to visually explore protein abundances within and between the in vitro cultivated T. brucei bloodstream and procyclic form proteomes. Conclusions: The protein abundance visualization tool, searchable by protein name(s) and attribute(s), is likely to be useful to the trypanosome research community. It will allow users to contextualise their proteins of interest in terms of their abundances in the T. brucei bloodstream and procyclic form proteomes.
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Affiliation(s)
- Michele Tinti
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, DD1 5HN, UK
| | - Michael A. J. Ferguson
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, DD1 5HN, UK,
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11
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Tinti M, Ferguson MAJ. Visualisation of proteome-wide ordered protein abundances in Trypanosoma brucei. Wellcome Open Res 2023; 7:34. [PMID: 35284642 PMCID: PMC8889043 DOI: 10.12688/wellcomeopenres.17607.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2022] [Indexed: 02/06/2023] Open
Abstract
Background: Trypanosoma brucei is a protozoan parasite and etiological agent of human and animal African trypanosomiasis. It has a complex life cycle, but the most studied cellular types are the in vitro cultivated bloodstream- and procyclic-forms. These correspond to the replicating, mammalian host bloodstream-dwelling, slender trypomastigotes and tsetse vector midgut-dwelling procyclic lifecycle stages, respectively. Several proteomics studies have reported the differential abundance of proteins between these in vitro cultivated cell types. However, there are no datasets providing protein abundance, from most to least abundant, within and between both cell types. Methods: We used MaxQuant software 1.6.10.4 to reprocess a recent large-scale proteomics experiment from our laboratory and extracted intensity-based quantifications of the bloodstream and procyclic form proteomes. Results: We created a web interface to visually explore protein abundances within and between the in vitro cultivated T. brucei bloodstream and procyclic form proteomes. Conclusions: The protein abundance visualization tool, searchable by protein name(s) and attribute(s), is likely to be useful to the trypanosome research community. It will allow users to contextualise their proteins of interest in terms of their abundances in the T. brucei bloodstream and procyclic form proteomes.
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Affiliation(s)
- Michele Tinti
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, DD1 5HN, UK
| | - Michael A. J. Ferguson
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, DD1 5HN, UK,
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12
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Slow growing behavior in African trypanosomes during adipose tissue colonization. Nat Commun 2022; 13:7548. [PMID: 36481558 PMCID: PMC9732351 DOI: 10.1038/s41467-022-34622-w] [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: 08/17/2022] [Accepted: 11/01/2022] [Indexed: 12/13/2022] Open
Abstract
When Trypanosoma brucei parasites, the causative agent of sleeping sickness, colonize the adipose tissue, they rewire gene expression. Whether this adaptation affects population behavior and disease treatment remained unknown. By using a mathematical model, we estimate that the population of adipose tissue forms (ATFs) proliferates slower than blood parasites. Analysis of the ATFs proteome, measurement of protein synthesis and proliferation rates confirm that the ATFs divide on average every 12 h, instead of 6 h in the blood. Importantly, the population of ATFs is heterogeneous with parasites doubling times ranging between 5 h and 35 h. Slow-proliferating parasites remain capable of reverting to the fast proliferation profile in blood conditions. Intravital imaging shows that ATFs are refractory to drug treatment. We propose that in adipose tissue, a subpopulation of T. brucei parasites acquire a slow growing behavior, which contributes to disease chronicity and treatment failure.
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13
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Falk F, Melo Palhares R, Waithaka A, Clayton C. Roles and interactions of the specialized initiation factors EIF4E2, EIF4E5 and EIF4E6 in Trypanosoma brucei: EIF4E2 maintains the abundances of S-phase mRNAs. Mol Microbiol 2022; 118:457-476. [PMID: 36056730 DOI: 10.1111/mmi.14978] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 08/14/2022] [Accepted: 08/30/2022] [Indexed: 11/29/2022]
Abstract
Trypanosoma brucei has six versions of the cap-binding translation initiation factor EIF4E. We investigated the functions of EIF4E2, EIF4E3, EIF4E5 and EIF4E6 in bloodstream forms. We confirmed the protein associations previously found in procyclic forms, and detected specific co-purification of some RNA-binding proteins. Bloodstream forms lacking EIF4E5 grew normally and differentiated to replication-incompetent procyclic forms. Depletion of EIF4E6 inhibited bloodstream-form trypanosome growth and translation. EIF4E2 co-purified only the putative RNA binding protein SLBP2. Bloodstream forms lacking EIF4E2 multiplied slowly, had a low maximal cell density, and expressed the stumpy-form marker PAD1, but showed no evidence for enhanced stumpy-form signalling. EIF4E2 knock-out cells differentiated readily to replication-competent procyclic forms. EIF4E2 was strongly associated with a subset of mRNAs that are maximally abundant in S-phase, and these all had decreased abundances in EIF4E2 knock-out cells. Three EIF4E2 target mRNAs are also bound and stabilized by the Pumilio domain protein PUF9. Yeast 2-hybrid results suggested that PUF9 interacts directly with SLBP2, but PUF9 was not detected in EIF4E2 pull-downs. We speculate that the EIF4E2-SLBP2 complex might interact with its target mRNAs, perhaps via PUF9, only early during G1/S, stabilizing the mRNAs in preparation for translation later in S-phase or in early G2.
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Affiliation(s)
- Franziska Falk
- Heidelberg University Centre for Molecular Biology (ZMBH), Im Neuenheimer Feld, Heidelberg, Germany
| | - Rafael Melo Palhares
- Heidelberg University Centre for Molecular Biology (ZMBH), Im Neuenheimer Feld, Heidelberg, Germany.,Institut für Mikro- und Molekularbiologie, Justus-Liebig-Universität Giessen, IFZ, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Albina Waithaka
- Heidelberg University Centre for Molecular Biology (ZMBH), Im Neuenheimer Feld, Heidelberg, Germany
| | - Christine Clayton
- Heidelberg University Centre for Molecular Biology (ZMBH), Im Neuenheimer Feld, Heidelberg, Germany
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14
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Guegan F, Rajan KS, Bento F, Pinto-Neves D, Sequeira M, Gumińska N, Mroczek S, Dziembowski A, Cohen-Chalamish S, Doniger T, Galili B, Estévez AM, Notredame C, Michaeli S, Figueiredo LM. A long noncoding RNA promotes parasite differentiation in African trypanosomes. SCIENCE ADVANCES 2022; 8:eabn2706. [PMID: 35704590 PMCID: PMC9200285 DOI: 10.1126/sciadv.abn2706] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The parasite Trypanosoma brucei causes African sleeping sickness that is fatal to patients if untreated. Parasite differentiation from a replicative slender form into a quiescent stumpy form promotes host survival and parasite transmission. Long noncoding RNAs (lncRNAs) are known to regulate cell differentiation in other eukaryotes. To determine whether lncRNAs are also involved in parasite differentiation, we used RNA sequencing to survey the T. brucei genome, identifying 1428 previously uncharacterized lncRNA genes. We find that grumpy lncRNA is a key regulator that promotes parasite differentiation into the quiescent stumpy form. This function is promoted by a small nucleolar RNA encoded within the grumpy lncRNA. snoGRUMPY binds to messenger RNAs of at least two stumpy regulatory genes, promoting their expression. grumpy overexpression reduces parasitemia in infected mice. Our analyses suggest that T. brucei lncRNAs modulate parasite-host interactions and provide a mechanism by which grumpy regulates cell differentiation in trypanosomes.
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Affiliation(s)
- Fabien Guegan
- Instituto de Medicina Molecular–Joao Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Corresponding author. (F.G.); (L.M.F.)
| | - K. Shanmugha Rajan
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Fábio Bento
- Instituto de Medicina Molecular–Joao Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Daniel Pinto-Neves
- Instituto de Medicina Molecular–Joao Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Mariana Sequeira
- Instituto de Medicina Molecular–Joao Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Natalia Gumińska
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Seweryn Mroczek
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Smadar Cohen-Chalamish
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Tirza Doniger
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Beathrice Galili
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Antonio M. Estévez
- Instituto de Parasitologia y Biomedicina ‘Lopez-Neyra,’ IPBLN-CSIC, Parque Tecnológico de Ciencias de la Salud, Avda. del Conocimiento 17, 18016 Armilla, Granada, Spain
| | - Cedric Notredame
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Shulamit Michaeli
- The Mina and Everard Goodman Faculty of Life Sciences and Advanced Materials and Nanotechnology Institute, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Luisa M. Figueiredo
- Instituto de Medicina Molecular–Joao Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
- Corresponding author. (F.G.); (L.M.F.)
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15
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Kent RS, Briggs EM, Colon BL, Alvarez C, Silva Pereira S, De Niz M. Paving the Way: Contributions of Big Data to Apicomplexan and Kinetoplastid Research. Front Cell Infect Microbiol 2022; 12:900878. [PMID: 35734575 PMCID: PMC9207352 DOI: 10.3389/fcimb.2022.900878] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
In the age of big data an important question is how to ensure we make the most out of the resources we generate. In this review, we discuss the major methods used in Apicomplexan and Kinetoplastid research to produce big datasets and advance our understanding of Plasmodium, Toxoplasma, Cryptosporidium, Trypanosoma and Leishmania biology. We debate the benefits and limitations of the current technologies, and propose future advancements that may be key to improving our use of these techniques. Finally, we consider the difficulties the field faces when trying to make the most of the abundance of data that has already been, and will continue to be, generated.
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Affiliation(s)
- Robyn S. Kent
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, United States
| | - Emma M. Briggs
- Institute for Immunology and Infection Research, School of Biological Sciences, University Edinburgh, Edinburgh, United Kingdom
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Beatrice L. Colon
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Catalina Alvarez
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Sara Silva Pereira
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Mariana De Niz
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
- Institut Pasteur, Paris, France
- *Correspondence: Mariana De Niz,
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16
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Zíková A. Mitochondrial adaptations throughout the Trypanosoma brucei life cycle. J Eukaryot Microbiol 2022; 69:e12911. [PMID: 35325490 DOI: 10.1111/jeu.12911] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/18/2022] [Accepted: 03/18/2022] [Indexed: 12/01/2022]
Abstract
The unicellular parasite Trypanosoma brucei has a digenetic life cycle that alternates between a mammalian host and an insect vector. During programmed development, this extracellular parasite encounters strikingly different environments that determine its energy metabolism. Functioning as a bioenergetic, biosynthetic, and signaling center, the single mitochondrion of T. brucei is drastically remodeled to support the dynamic cellular demands of the parasite. This manuscript will provide an up-to-date overview of how the distinct T. brucei developmental stages differ in their mitochondrial metabolic and bioenergetic pathways, with a focus on the electron transport chain, proline oxidation, TCA cycle, acetate production, and ATP generation. Although mitochondrial metabolic rewiring has always been simply viewed as a consequence of the differentiation process, the possibility that certain mitochondrial activities reinforce parasite differentiation will be explored.
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Affiliation(s)
- Alena Zíková
- Biology Centre CAS, Institute of Parasitology, University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic
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17
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Bishola Tshitenge T, Reichert L, Liu B, Clayton C. Several different sequences are implicated in bloodstream-form-specific gene expression in Trypanosoma brucei. PLoS Negl Trop Dis 2022; 16:e0010030. [PMID: 35312693 PMCID: PMC8982893 DOI: 10.1371/journal.pntd.0010030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 04/05/2022] [Accepted: 03/03/2022] [Indexed: 12/30/2022] Open
Abstract
The parasite Trypanosoma brucei grows as bloodstream forms in mammalian hosts, and as procyclic forms in tsetse flies. In trypanosomes, gene expression regulation depends heavily on post-transcriptional mechanisms. Both the RNA-binding protein RBP10 and glycosomal phosphoglycerate kinase PGKC are expressed only in mammalian-infective forms. RBP10 targets procyclic-specific mRNAs for destruction, while PGKC is required for bloodstream-form glycolysis. Developmental regulation of both is essential: expression of either RBP10 or PGKC in procyclic forms inhibits their proliferation. We show that the 3’-untranslated region of the RBP10 mRNA is extraordinarily long—7.3kb—and were able to identify six different sequences, scattered across the untranslated region, which can independently cause bloodstream-form-specific expression. The 3’-untranslated region of the PGKC mRNA, although much shorter, still contains two different regions, of 125 and 153nt, that independently gave developmental regulation. No short consensus sequences were identified that were enriched either within these regulatory regions, or when compared with other mRNAs with similar regulation, suggesting that more than one regulatory RNA-binding protein is important for repression of mRNAs in procyclic forms. We also identified regions, including an AU repeat, that increased expression in bloodstream forms, or suppressed it in both forms. Trypanosome mRNAs that encode RNA-binding proteins often have extremely extended 3’-untranslated regions. We suggest that one function of this might be to act as a fail-safe mechanism to ensure correct regulation even if mRNA processing or expression of trans regulators is defective. The parasite Trypanosoma brucei causes sleeping sickness in humans, and nagana in cattle, and is transmitted by Tsetse flies. It grows in the bloodstream and tissue fluids of mammalian hosts, as "bloodstream forms", and as "procyclic forms" in the midgut of tsetse flies. Several hundred proteins are expressed in a stage-specific fashion, and this is essential for parasite survival in the different environments. RBP10 is an RNA-binding protein that is expressed only in bloodstream forms. It binds to procyclic-specific mRNAs, and causes their destruction. PGKC is an enzyme that is also specifically expressed in bloodstream forms. Developmental regulation of both is essential: expression of either RBP10 or PGKC in procyclic forms prevents their growth. The mRNAs encoding both proteins are very unstable in procyclic forms, and the sequences responsible are in an "untranslated region" of the mRNA—sequences that follow the part that codes for protein. We here show that the mRNA encoding PGKC has two regions that independently cause developmental regulation, and that the very long untranslated region of the RBP10 mRNA has no fewer than six regulatory regions, but there were no obvious similarities between them. We suggest that the presence of several different regulatory sequences in trypanosome mRNAs might be a fail-safe mechanism to ensure correct regulation.
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Affiliation(s)
| | - Lena Reichert
- Heidelberg University Center for Molecular Biology (ZMBH), Heidelberg, Germany
| | - Bin Liu
- Heidelberg University Center for Molecular Biology (ZMBH), Heidelberg, Germany
| | - Christine Clayton
- Heidelberg University Center for Molecular Biology (ZMBH), Heidelberg, Germany
- * E-mail:
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18
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Falk F, Kamanyi Marucha K, Clayton C. The EIF4E1-4EIP cap-binding complex of Trypanosoma brucei interacts with the terminal uridylyl transferase TUT3. PLoS One 2021; 16:e0258903. [PMID: 34807934 PMCID: PMC8608314 DOI: 10.1371/journal.pone.0258903] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/16/2021] [Indexed: 11/25/2022] Open
Abstract
Most transcription in Trypanosoma brucei is constitutive and polycistronic. Consequently, the parasite relies on post-transcriptional mechanisms, especially affecting translation initiation and mRNA decay, to control gene expression both at steady-state and for adaptation to different environments. The parasite has six isoforms of the cap-binding protein EIF4E as well as five EIF4Gs. EIF4E1 does not bind to any EIF4G, instead being associated with a 4E-binding protein, 4EIP. 4EIP represses translation and reduces the stability of a reporter mRNA when artificially tethered to the 3’-UTR, whether or not EIF4E1 is present. 4EIP is essential during the transition from the mammalian bloodstream form to the procyclic form that lives in the Tsetse vector. In contrast, EIF4E1 is dispensable during differentiation, but is required for establishment of growing procyclic forms. In Leishmania, there is some evidence that EIF4E1 might be active in translation initiation, via direct recruitment of EIF3. However in T. brucei, EIF4E1 showed no detectable association with other translation initiation factors, even in the complete absence of 4EIP. There was some evidence for interactions with NOT complex components, but if these occur they must be weak and transient. We found that EIF4E1is less abundant in the absence of 4EIP, and RNA pull-down results suggested this might occur through co-translational complex assembly. We also report that 4EIP directly recruits the cytosolic terminal uridylyl transferase TUT3 to EIF4E1/4EIP complexes. There was, however, no evidence that TUT3 is essential for 4EIP function.
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Affiliation(s)
- Franziska Falk
- DKFZ-ZMBH Alliance, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Kevin Kamanyi Marucha
- DKFZ-ZMBH Alliance, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Christine Clayton
- DKFZ-ZMBH Alliance, Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
- * E-mail:
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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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20
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Abstract
Abstract
In Trypanosoma brucei and related Kinetoplastids, regulation of gene expression occurs mostly post-transcriptionally, and RNA-binding proteins play a critical role in the regulation of mRNA and protein abundance. Trypanosoma brucei ZC3H28 is a 114 KDa cytoplasmic mRNA-binding protein with a single C(x)7C(x)5C(x)sH zinc finger at the C-terminus and numerous proline-, histidine- or glutamine-rich regions. ZC3H28 is essential for normal bloodstream-form trypanosome growth, and when tethered to a reporter mRNA, ZC3H28 increased reporter mRNA and protein levels. Purification of N-terminally tagged ZC3H28 followed by mass spectrometry showed enrichment of ribosomal proteins, various RNA-binding proteins including both poly(A) binding proteins, the translation initiation complex EIF4E4/EIF4G3, and the activator MKT1. Tagged ZC3H28 was preferentially associated with long RNAs that have low complexity sequences in their 3′-untranslated regions; their coding regions also have low ribosome densities. In agreement with the tethering results, after ZC3H28 depletion, the levels of a significant proportion of its bound mRNAs decreased. We suggest that ZC3H28 is implicated in the stabilization of long mRNAs that are poorly translated.
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Steketee PC, Giordani F, Vincent IM, Crouch K, Achcar F, Dickens NJ, Morrison LJ, MacLeod A, Barrett MP. Transcriptional differentiation of Trypanosoma brucei during in vitro acquisition of resistance to acoziborole. PLoS Negl Trop Dis 2021; 15:e0009939. [PMID: 34752454 PMCID: PMC8648117 DOI: 10.1371/journal.pntd.0009939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 12/06/2021] [Accepted: 10/21/2021] [Indexed: 11/19/2022] Open
Abstract
Subspecies of the protozoan parasite Trypanosoma brucei are the causative agents of Human African Trypanosomiasis (HAT), a debilitating neglected tropical disease prevalent across sub-Saharan Africa. HAT case numbers have steadily decreased since the start of the century, and sustainable elimination of one form of the disease is in sight. However, key to this is the development of novel drugs to combat the disease. Acoziborole is a recently developed benzoxaborole, currently in advanced clinical trials, for treatment of stage 1 and stage 2 HAT. Importantly, acoziborole is orally bioavailable, and curative with one dose. Recent studies have made significant progress in determining the molecular mode of action of acoziborole. However, less is known about the potential mechanisms leading to acoziborole resistance in trypanosomes. In this study, an in vitro-derived acoziborole-resistant cell line was generated and characterised. The AcoR line exhibited significant cross-resistance with the methyltransferase inhibitor sinefungin as well as hypersensitisation to known trypanocides. Interestingly, transcriptomics analysis of AcoR cells indicated the parasites had obtained a procyclic- or stumpy-like transcriptome profile, with upregulation of procyclin surface proteins as well as differential regulation of key metabolic genes known to be expressed in a life cycle-specific manner, even in the absence of major morphological changes. However, no changes were observed in transcripts encoding CPSF3, the recently identified protein target of acoziborole. The results suggest that generation of resistance to this novel compound in vitro can be accompanied by transcriptomic switches resembling a procyclic- or stumpy-type phenotype.
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Affiliation(s)
- Pieter C. Steketee
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Federica Giordani
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Isabel M. Vincent
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Kathryn Crouch
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Fiona Achcar
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Nicholas J. Dickens
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Liam J. Morrison
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Annette MacLeod
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
| | - Michael P. Barrett
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, United Kingdom
- Glasgow Polyomics, University of Glasgow, United Kingdom
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Trypanosoma brucei Tim50 Possesses PAP Activity and Plays a Critical Role in Cell Cycle Regulation and Parasite Infectivity. mBio 2021; 12:e0159221. [PMID: 34517757 PMCID: PMC8546626 DOI: 10.1128/mbio.01592-21] [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: 12/14/2022] Open
Abstract
Trypanosoma brucei, the infective agent for African trypanosomiasis, possesses a homologue of the translocase of the mitochondrial inner membrane 50 (TbTim50). It has a pair of characteristic phosphatase signature motifs, DXDX(T/V). Here, we demonstrated that, besides its protein phosphatase activity, the recombinant TbTim50 binds and hydrolyzes phosphatidic acid in a concentration-dependent manner. Mutations of D242 and D244, but not of D345and D347, to alanine abolished these activities. In silico structural homology models identified the putative binding interfaces that may accommodate different phosphosubstrates. Interestingly, TbTim50 depletion in the bloodstream form (BF) of T. brucei reduced cardiolipin (CL) levels and decreased mitochondrial membrane potential (ΔΨ). TbTim50 knockdown (KD) also reduced the population of G2/M phase and increased that of G1 phase cells; inhibited segregation and caused overreplication of kinetoplast DNA (kDNA), and reduced BF cell growth. Depletion of TbTim50 increased the levels of AMPK phosphorylation, and parasite morphology was changed with upregulation of expression of a few stumpy marker genes. Importantly, we observed that TbTim50-depleted parasites were unable to establish infection in mice. Proteomics analysis showed reductions in levels of the translation factors, flagellar transport proteins, and many proteasomal subunits, including those of the mitochondrial heat shock locus ATPase (HslVU), which is known to play a role in regulation of kinetoplast DNA (kDNA) replication. Reduction of the level of HslV in TbTim50 KD cells was further validated by immunoblot analysis. Together, our results showed that TbTim50 is essential for mitochondrial function, regulation of kDNA replication, and the cell cycle in the BF. Therefore, TbTim50 is an important target for structure-based drug design to combat African trypanosomiasis.
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23
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Single-cell transcriptomic analysis of bloodstream Trypanosoma brucei reconstructs cell cycle progression and developmental quorum sensing. Nat Commun 2021; 12:5268. [PMID: 34489460 PMCID: PMC8421343 DOI: 10.1038/s41467-021-25607-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 08/17/2021] [Indexed: 02/07/2023] Open
Abstract
Developmental steps in the trypanosome life-cycle involve transition between replicative and non-replicative forms specialised for survival in, and transmission between, mammalian and tsetse fly hosts. Here, using oligopeptide-induced differentiation in vitro, we model the progressive development of replicative 'slender' to transmissible 'stumpy' bloodstream form Trypanosoma brucei and capture the transcriptomes of 8,599 parasites using single cell transcriptomics (scRNA-seq). Using this framework, we detail the relative order of biological events during asynchronous development, profile dynamic gene expression patterns and identify putative regulators. We additionally map the cell cycle of proliferating parasites and position stumpy cell-cycle exit at early G1 before progression to a distinct G0 state. A null mutant for one transiently elevated developmental regulator, ZC3H20 is further analysed by scRNA-seq, identifying its point of failure in the developmental atlas. This approach provides a paradigm for the dissection of differentiation events in parasites, relevant to diverse transitions in pathogen biology.
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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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Melo do Nascimento L, Egler F, Arnold K, Papavasiliou N, Clayton C, Erben E. Functional insights from a surface antigen mRNA-bound proteome. eLife 2021; 10:e68136. [PMID: 33783358 PMCID: PMC8051951 DOI: 10.7554/elife.68136] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 03/18/2021] [Indexed: 01/13/2023] Open
Abstract
Trypanosoma brucei is the causative agent of human sleeping sickness. The parasites' variant surface glycoprotein (VSG) enables them to evade adaptive immunity via antigenic variation. VSG comprises 10% of total cell protein and the high stability of VSG mRNA is essential for trypanosome survival. To determine how VSG mRNA stability is maintained, we used mRNA affinity purification to identify all its associated proteins. CFB2 (cyclin F-box protein 2), an unconventional RNA-binding protein with an F-box domain, was specifically enriched with VSG mRNA. We demonstrate that CFB2 is essential for VSG mRNA stability, describe cis acting elements within the VSG 3'-untranslated region that regulate the interaction, identify trans-acting factors that are present in the VSG messenger ribonucleoprotein particle, and mechanistically explain how CFB2 stabilizes the mRNA of this key pathogenicity factor. Beyond T. brucei, the mRNP purification approach has the potential to supply detailed biological insight into metabolism of relatively abundant mRNAs in any eukaryote.
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Affiliation(s)
| | - Franziska Egler
- Centre for Molecular Biology of Heidelberg University (ZMBH)HeidelbergGermany
| | - Katharina Arnold
- Centre for Molecular Biology of Heidelberg University (ZMBH)HeidelbergGermany
| | - Nina Papavasiliou
- Division of Immune Diversity, Deutsche Krebsforschungszentrum (DKFZ)HeidelbergGermany
| | - Christine Clayton
- Centre for Molecular Biology of Heidelberg University (ZMBH)HeidelbergGermany
| | - Esteban Erben
- Centre for Molecular Biology of Heidelberg University (ZMBH)HeidelbergGermany
- Division of Immune Diversity, Deutsche Krebsforschungszentrum (DKFZ)HeidelbergGermany
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26
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Bevkal S, Naguleswaran A, Rehmann R, Kaiser M, Heller M, Roditi I. An Alba-domain protein required for proteome remodelling during trypanosome differentiation and host transition. PLoS Pathog 2021; 17:e1009239. [PMID: 33493187 PMCID: PMC7861527 DOI: 10.1371/journal.ppat.1009239] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 02/04/2021] [Accepted: 12/10/2020] [Indexed: 11/19/2022] Open
Abstract
The transition between hosts is a challenge for digenetic parasites as it is unpredictable. For Trypanosoma brucei subspecies, which are disseminated by tsetse flies, adaptation to the new host requires differentiation of stumpy forms picked up from mammals to procyclic forms in the fly midgut. Here we show that the Alba-domain protein Alba3 is not essential for mammalian slender forms, nor is it required for differentiation of slender to stumpy forms in culture or in mice. It is crucial, however, for the development of T. brucei procyclic forms during the host transition. While steady state levels of mRNAs in differentiating cells are barely affected by the loss of Alba3, there are major repercussions for the proteome. Mechanistically, Alba3 aids differentiation by rapidly releasing stumpy forms from translational repression and stimulating polysome formation. In its absence, parasites fail to remodel their proteome appropriately, lack components of the mitochondrial respiratory chain and show reduced infection of tsetse. Interestingly, Alba3 and the closely related Alba4 are functionally redundant in slender forms, but Alba4 cannot compensate for the lack of Alba3 during differentiation from the stumpy to the procyclic form. We postulate that Alba-domain proteins play similar roles in regulating translation in other protozoan parasites, in particular during life-cycle and host transitions. Trypanosoma brucei is a unicellular eukaryotic parasite that is responsible for African trypanosomiasis. The parasite needs two hosts, mammals and tsetse flies, in order to complete its life cycle. Throughout its developmental cycle, T. brucei encounters diverse environments to which it has to adapt in order to maintain its transmission and infectivity. Successful adaptation to the new environment and transition to different life-cycle stages are the general challenges faced by many digenetic parasites. In this study we show that the Alba-domain protein Alba3 is essential for differentiation of the mammalian stumpy form (transition form) to the procyclic form in the tsetse host. An Alba3 deletion mutant infects mice and shows characteristic waves of parasitaemia, but is severely compromised in its ability to infect tsetse flies. Stumpy forms are translationally repressed, but are poised to resume protein synthesis during differentiation. We show that Alba3 is key to efficient escape from translation repression; in its absence, there is a delay in the formation of polysomes and resumption of protein synthesis. This impacts the formation of procyclic-specific mitochondrial respiratory complex proteins as well as the repression of some bloodstream-specific proteins. This is the first time that a single protein has been shown to have a major influence on translation as an adaptive response to changing hosts. It is also the first time that a mechanism has been established for Alba-domain proteins in parasites.
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Affiliation(s)
- Shubha Bevkal
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- Graduate School of Cellular and Biomedical Science, University of Bern, Bern, Switzerland
| | | | - Ruth Rehmann
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Marcel Kaiser
- Department of Medical and Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Manfred Heller
- Proteomics and Mass Spectrometry Core Facility, Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Isabel Roditi
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- * E-mail:
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27
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Haindrich AC, Ernst V, Naguleswaran A, Oliveres QF, Roditi I, Rentsch D. Nutrient availability regulates proline/alanine transporters in Trypanosoma brucei. J Biol Chem 2021; 296:100566. [PMID: 33745971 PMCID: PMC8094907 DOI: 10.1016/j.jbc.2021.100566] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 03/09/2021] [Accepted: 03/17/2021] [Indexed: 11/23/2022] Open
Abstract
Trypanosoma brucei is a species of unicellular parasite that can cause severe diseases in livestock and humans, including African trypanosomiasis and Chagas disease. Adaptation to diverse environments and changes in nutritional conditions is essential for T. brucei to establish an infection when changing hosts or during invasion of different host tissues. One such adaptation is the ability of T. brucei to rapidly switch its energy metabolism from glucose metabolism in the mammalian blood to proline catabolism in the insect stages and vice versa. However, the mechanisms that support the parasite's response to nutrient availability remain unclear. Using RNAseq and qRT-PCR, we investigated the response of T. brucei to amino acid or glucose starvation and found increased mRNA levels of several amino acid transporters, including all genes of the amino acid transporter AAT7-B subgroup. Functional characterization revealed that AAT7-B members are plasma membrane-localized in T. brucei and when expressed in Saccharomyces cerevisiae supported the uptake of proline, alanine, and cysteine, while other amino acids were poorly recognized. All AAT7-B members showed a preference for proline, which is transported with high or low affinity. RNAi-mediated AAT7-B downregulation resulted in a reduction of intracellular proline concentrations and growth arrest under low proline availability in cultured procyclic form parasites. Taken together, these results suggest a role of AAT7-B transporters in the response of T. brucei to proline starvation and proline catabolism.
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Affiliation(s)
| | - Viona Ernst
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | | | | | - Isabel Roditi
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Doris Rentsch
- Institute of Plant Sciences, University of Bern, Bern, Switzerland.
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Maldonado E, Rojas DA, Morales S, Miralles V, Solari A. Dual and Opposite Roles of Reactive Oxygen Species (ROS) in Chagas Disease: Beneficial on the Pathogen and Harmful on the Host. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:8867701. [PMID: 33376582 PMCID: PMC7746463 DOI: 10.1155/2020/8867701] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/22/2020] [Accepted: 11/25/2020] [Indexed: 11/18/2022]
Abstract
Chagas disease is a neglected tropical disease, which affects an estimate of 6-7 million people worldwide. Chagas disease is caused by Trypanosoma cruzi, which is a eukaryotic flagellate unicellular organism. At the primary infection sites, these parasites are phagocytized by macrophages, which produce reactive oxygen species (ROS) in response to the infection with T. cruzi. The ROS produce damage to the host tissues; however, macrophage-produced ROS is also used as a signal for T. cruzi proliferation. At the later stages of infection, mitochondrial ROS is produced by the infected cardiomyocytes that contribute to the oxidative damage, which persists at the chronic stage of the disease. The oxidative damage leads to a functional impairment of the heart. In this review article, we will discuss the mechanisms by which T. cruzi is able to deal with the oxidative stress and how this helps the parasite growth at the acute phase of infection and how the oxidative stress affects the cardiomyopathy at the chronic stage of the Chagas disease. We will describe the mechanisms used by the parasite to deal with ROS and reactive nitrogen species (RNS) through the trypanothione and the mechanisms used to repair the damaged DNA. Also, a description of the events produced by ROS at the acute and chronic stages of the disease is presented. Lastly, we discuss the benefits of ROS for T. cruzi growth and proliferation and the possible mechanisms involved in this phenomenon. Hypothesis is put forward to explain the molecular mechanisms by which ROS triggers parasite growth and proliferation and how ROS is able to produce a long persisting damage on cardiomyocytes even in the absence of the parasite.
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Affiliation(s)
- Edio Maldonado
- Programa Biología Celular y Molecular, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Diego A. Rojas
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago, Chile
| | - Sebastian Morales
- Programa Biología Celular y Molecular, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Vicente Miralles
- Departamento de Bioquímica y Biología Molecular, Universidad de Valencia, Valencia, Spain
| | - Aldo Solari
- Programa Biología Celular y Molecular, Facultad de Medicina, Universidad de Chile, Santiago, Chile
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Mochizuki K, Inaoka DK, Mazet M, Shiba T, Fukuda K, Kurasawa H, Millerioux Y, Boshart M, Balogun EO, Harada S, Hirayama K, Bringaud F, Kita K. The ASCT/SCS cycle fuels mitochondrial ATP and acetate production in Trypanosoma brucei. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1861:148283. [PMID: 32763239 PMCID: PMC7402102 DOI: 10.1016/j.bbabio.2020.148283] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/22/2020] [Accepted: 07/29/2020] [Indexed: 11/03/2022]
Abstract
Acetate:succinate CoA transferase (ASCT) is a mitochondrial enzyme that catalyzes the production of acetate and succinyl-CoA, which is coupled to ATP production with succinyl-CoA synthetase (SCS) in a process called the ASCT/SCS cycle. This cycle has been studied in Trypanosoma brucei (T. brucei), a pathogen of African sleeping sickness, and is involved in (i) ATP and (ii) acetate production and proceeds independent of oxygen and an electrochemical gradient. Interestingly, knockout of ASCT in procyclic form (PCF) of T. brucei cause oligomycin A-hypersensitivity phenotype indicating that ASCT/SCS cycle complements the deficiency of ATP synthase activity. In bloodstream form (BSF) of T. brucei, ATP synthase works in reverse to maintain the electrochemical gradient by hydrolyzing ATP. However, no information has been available on the source of ATP, although ASCT/SCS cycle could be a potential candidate. Regarding mitochondrial acetate production, which is essential for fatty acid biosynthesis and growth of T. brucei, ASCT or acetyl-CoA hydrolase (ACH) are known to be its source. Despite the importance of this cycle, direct evidence of its function is lacking, and there are no comprehensive biochemical or structural biology studies reported so far. Here, we show that in vitro–reconstituted ASCT/SCS cycle is highly specific towards acetyl-CoA and has a higher kcat than that of yeast and bacterial ATP synthases. Our results provide the first biochemical basis for (i) rescue of ATP synthase-deficient phenotype by ASCT/SCS cycle in PCF and (ii) a potential source of ATP for the reverse reaction of ATP synthase in BSF. First biochemical and structural characterization of mitochondrial ASCT/SCS cycle It is essential for mitochondrial acetate/ATP production and T. brucei BSF growth. TbASCT/SCS cycle shows higher kcat than that of yeast and bacterial ATP synthases. Detailed comparative biochemical analysis between ASCT and human SCOT Active site residue and X-CoA binding site determined by site-directed mutagenesis
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Affiliation(s)
- Kota Mochizuki
- Department of Immunogenetics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Japan; Graduate School of Biomedical Sciences, Nagasaki University, Japan
| | - Daniel Ken Inaoka
- Department of Molecular Infection Dynamics, Shionogi Global Infectious Diseases Division, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Japan; School of Tropical Medicine and Global Health, Nagasaki University, Japan; Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Japan.
| | - Muriel Mazet
- Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP), Université de Bordeaux, CNRS UMR-5234, France
| | - Tomoo Shiba
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Japan.
| | - Keisuke Fukuda
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Japan
| | - Hana Kurasawa
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Japan
| | - Yoann Millerioux
- Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP), Université de Bordeaux, CNRS UMR-5234, France
| | - Michael Boshart
- Fakultät für Biologie, Genetik, Ludwig-Maximilians-Universität München, Germany
| | - Emmanuel O Balogun
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Japan; Department of Biochemistry, Ahmadu Bello University, Nigeria
| | - Shigeharu Harada
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Japan
| | - Kenji Hirayama
- Department of Immunogenetics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Japan
| | - Frédéric Bringaud
- Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP), Université de Bordeaux, CNRS UMR-5234, France
| | - Kiyoshi Kita
- School of Tropical Medicine and Global Health, Nagasaki University, Japan; Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Japan; Department of Host - Defense Biochemistry, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Japan
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30
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Melo do Nascimento L, Terrao M, Marucha KK, Liu B, Egler F, Clayton C. The RNA-associated proteins MKT1 and MKT1L form alternative PBP1-containing complexes in Trypanosoma brucei. J Biol Chem 2020; 295:10940-10955. [PMID: 32532821 DOI: 10.1074/jbc.ra120.013306] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 06/03/2020] [Indexed: 01/20/2023] Open
Abstract
Control of gene expression in kinetoplastids such as trypanosomes depends heavily on RNA-binding proteins that influence mRNA decay and translation. We previously showed that the trypanosome protein MKT1 forms a multicomponent protein complex: MKT1 interacts with PBP1, which in turn recruits LSM12 and poly(A)-binding protein. MKT1 is recruited to mRNAs by sequence-specific RNA-binding proteins, resulting in stabilization of the bound mRNA. We here show that PBP1, LSM12, and a 117-residue protein, XAC1 (Tb927.7.2780), are present in complexes that contain either MKT1 or an MKT1-like protein, MKT1L (Tb927.10.1490). All five proteins are present predominantly in the complexes, and we found evidence for a minor subset of complexes containing both MKT1 and MKT1L. XAC1-containing complexes reproducibly contained RNA-binding proteins that were previously found associated with MKT1. Moreover, XAC1- or MKT1-containing complexes specifically recruited one of the two poly(A)-binding proteins, PABP2, and one of the six cap-binding translation initiation complexes, EIF4E6-EIF4G5. Yeast two-hybrid assay results indicated that MKT1 directly interacts with EIF4G5. MKT1-PBP1 complexes can therefore interact with mRNAs via their poly(A) tails and caps, as well as through sequence-specific RNA-binding proteins. Correspondingly, MKT1 is associated with many mRNAs, although not with those encoding ribosomal proteins. Meanwhile, MKT1L resembles MKT1 at the C terminus but additionally features an N-terminal extension with low-complexity regions. Although MKT1L depletion inhibited cell proliferation, we found no evidence that it specifically interacts with RNA-binding proteins or mRNA. We speculate that MKT1L may compete with MKT1 for PBP1 binding and thereby modulate the function of MKT1-containing complexes.
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Affiliation(s)
| | - Monica Terrao
- Heidelberg University Centre for Molecular Biology (ZMBH), Heidelberg, Germany
| | | | - Bin Liu
- Heidelberg University Centre for Molecular Biology (ZMBH), Heidelberg, Germany
| | - Franziska Egler
- Heidelberg University Centre for Molecular Biology (ZMBH), Heidelberg, Germany
| | - Christine Clayton
- Heidelberg University Centre for Molecular Biology (ZMBH), Heidelberg, Germany
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31
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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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Zoltner M, Campagnaro GD, Taleva G, Burrell A, Cerone M, Leung KF, Achcar F, Horn D, Vaughan S, Gadelha C, Zíková A, Barrett MP, de Koning HP, Field MC. Suramin exposure alters cellular metabolism and mitochondrial energy production in African trypanosomes. J Biol Chem 2020; 295:8331-8347. [PMID: 32354742 PMCID: PMC7294092 DOI: 10.1074/jbc.ra120.012355] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/21/2020] [Indexed: 12/27/2022] Open
Abstract
Introduced about a century ago, suramin remains a frontline drug for the management of early-stage East African trypanosomiasis (sleeping sickness). Cellular entry into the causative agent, the protozoan parasite Trypanosoma brucei, occurs through receptor-mediated endocytosis involving the parasite's invariant surface glycoprotein 75 (ISG75), followed by transport into the cytosol via a lysosomal transporter. The molecular basis of the trypanocidal activity of suramin remains unclear, but some evidence suggests broad, but specific, impacts on trypanosome metabolism (i.e. polypharmacology). Here we observed that suramin is rapidly accumulated in trypanosome cells proportionally to ISG75 abundance. Although we found little evidence that suramin disrupts glycolytic or glycosomal pathways, we noted increased mitochondrial ATP production, but a net decrease in cellular ATP levels. Metabolomics highlighted additional impacts on mitochondrial metabolism, including partial Krebs' cycle activation and significant accumulation of pyruvate, corroborated by increased expression of mitochondrial enzymes and transporters. Significantly, the vast majority of suramin-induced proteins were normally more abundant in the insect forms compared with the blood stage of the parasite, including several proteins associated with differentiation. We conclude that suramin has multiple and complex effects on trypanosomes, but unexpectedly partially activates mitochondrial ATP-generating activity. We propose that despite apparent compensatory mechanisms in drug-challenged cells, the suramin-induced collapse of cellular ATP ultimately leads to trypanosome cell death.
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Affiliation(s)
- Martin Zoltner
- School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Gustavo D Campagnaro
- Institute for Infection, Immunity, and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Gergana Taleva
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Institute of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Alana Burrell
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Michela Cerone
- Institute for Infection, Immunity, and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Ka-Fai Leung
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Fiona Achcar
- Wellcome Centre for Integrative Parasitology and Glasgow Polyomics, University of Glasgow, Glasgow, United Kingdom
| | - David Horn
- School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom
| | - Sue Vaughan
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Catarina Gadelha
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Alena Zíková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Institute of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Michael P Barrett
- Wellcome Centre for Integrative Parasitology and Glasgow Polyomics, University of Glasgow, Glasgow, United Kingdom
| | - Harry P de Koning
- Institute for Infection, Immunity, and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Mark C Field
- School of Life Sciences, University of Dundee, Dundee, Scotland, United Kingdom .,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Institute of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
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33
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Zhang N, Jiang N, Zhang K, Zheng L, Zhang D, Sang X, Feng Y, Chen R, Yang N, Wang X, Cheng Z, Suo X, Lun Z, Chen Q. Landscapes of Protein Posttranslational Modifications of African Trypanosoma Parasites. iScience 2020; 23:101074. [PMID: 32403088 PMCID: PMC7218301 DOI: 10.1016/j.isci.2020.101074] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/22/2020] [Accepted: 04/14/2020] [Indexed: 12/13/2022] Open
Abstract
Proteins of all living cells undergo a myriad of post-translational modifications (PTMs) that are critical to multifarious life processes. In this study, we describe the first comprehensive multiple PTM-omics atlas in parallel with quantitative proteome analyses of two representative species of African trypanosomes, Trypanosoma brucei and Trypanosoma evansi. Ten PTM types with approximately 40,000 modified sites and 150 histone marks with a fine map on each protein of the two African trypanosomes were accomplished. The two biologically different trypanosomal species displayed distinct PTM-omic features, regulation pathways, and networks. Modifications in the proteins involved in the redox system were mainly upregulated in T. brucei, whereas proteins associated with motility were predominantly modified in T. evansi. The establishment of a database of multiple PTMs in the two parasites provides us with a deep insight into the biological mechanisms that underpin life processes in trypanosomes with different life cycles. The first multi-proteomic profiles of T. brucei and T. evansi were generated Histones are modified heavily and are highly conserved in trypanosomes The two biologically different trypanosomes displayed distinct PTM-omic features Crosstalk between different PTMs involved in critical biological processes
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Affiliation(s)
- Naiwen Zhang
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Key Laboratory of Zoonosis, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China; The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, 120 Dongling Road, Shenyang 110866, China
| | - Ning Jiang
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Key Laboratory of Zoonosis, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China; The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, 120 Dongling Road, Shenyang 110866, China
| | - Kai Zhang
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Key Laboratory of Zoonosis, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China; The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, 120 Dongling Road, Shenyang 110866, China
| | - Lili Zheng
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Key Laboratory of Zoonosis, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China; The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, 120 Dongling Road, Shenyang 110866, China
| | - Di Zhang
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Key Laboratory of Zoonosis, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Xiaoyu Sang
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Key Laboratory of Zoonosis, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China; The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, 120 Dongling Road, Shenyang 110866, China
| | - Ying Feng
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Key Laboratory of Zoonosis, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China; The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, 120 Dongling Road, Shenyang 110866, China
| | - Ran Chen
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Key Laboratory of Zoonosis, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China; The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, 120 Dongling Road, Shenyang 110866, China
| | - Na Yang
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Key Laboratory of Zoonosis, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Xinyi Wang
- College of Basic Sciences, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China
| | - Zhongyi Cheng
- Jingjie PTM Biolab (Hangzhou) Co. Ltd, Hangzhou 310018, China
| | - Xun Suo
- National Animal Protozoa Laboratory & College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Zhaorong Lun
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Qijun Chen
- Key Laboratory of Livestock Infectious Diseases in Northeast China, Ministry of Education, Key Laboratory of Zoonosis, College of Animal Science and Veterinary Medicine, Shenyang Agricultural University, 120 Dongling Road, Shenyang 110866, China; The Research Unit for Pathogenic Mechanisms of Zoonotic Parasites, Chinese Academy of Medical Sciences, 120 Dongling Road, Shenyang 110866, China.
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Nunes VS, Moretti NS, da Silva MS, Elias MC, Janzen CJ, Schenkman S. Trimethylation of histone H3K76 by Dot1B enhances cell cycle progression after mitosis in Trypanosoma cruzi. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118694. [PMID: 32151656 DOI: 10.1016/j.bbamcr.2020.118694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 03/03/2020] [Accepted: 03/05/2020] [Indexed: 12/11/2022]
Abstract
Dot1 enzymes are histone methyltransferases that mono-, di- and trimethylate lysine 79 of histone H3 to affect several nuclear processes. The functions of these different methylation states are still largely unknown. Trypanosomes, which are flagellated protozoa that cause several parasitic diseases, have two Dot1 homologues. Dot1A catalyzes the mono- and dimethylation of lysine 76 during late G2 and mitosis, and Dot1B catalyzes trimethylation, which is a modification found in all stages of the cell cycle. Here, we generated Trypanosoma cruzi lines lacking Dot1B. Deletion of one allele resulted in parasites with increased levels of mono- and dimethylation and a reduction in H3K76me3. In the full knockout (DKO), no trimethylation was observed. Both the DKO and the single knockout (SKO) showed aberrant morphology and decreased growth due to cell cycle arrest after G2. This phenotype could be rescued by caffeine in the DKO, as caffeine is a checkpoint inhibitor of the cell cycle. The knockouts also phosphorylated γH2A without producing extensive DNA breaks, and Dot1B-depleted cells were more susceptible to general checkpoint kinase inhibitors, suggesting that a lack of H3K76 trimethylation prevents the initiation and/or completion of cytokinesis.
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Affiliation(s)
- Vinicius Santana Nunes
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, 04032-039 São Paulo, SP, Brazil; Centro de Ensino, Pesquisa e Inovação, Hospital Evangélico de Vila Velha, 29118-060 Vila Velha, ES, Brazil
| | - Nilmar Silvio Moretti
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, 04032-039 São Paulo, SP, Brazil
| | | | - Maria Carolina Elias
- Laboratório Especial de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil
| | - Christian J Janzen
- Department of Cell & Developmental Biology, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Sergio Schenkman
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, 04032-039 São Paulo, SP, Brazil.
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Szöőr B, Silvester E, Matthews KR. A Leap Into the Unknown - Early Events in African Trypanosome Transmission. Trends Parasitol 2020; 36:266-278. [PMID: 32014419 DOI: 10.1016/j.pt.2019.12.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/19/2019] [Accepted: 12/25/2019] [Indexed: 01/09/2023]
Abstract
African trypanosomes are mainly transmitted by tsetse flies. In recent years there has been good progress in understanding how the parasites prepare for transmission, detect their changed environment through the perception of different environmental cues, and respond by changing their developmental gene expression. In this review, we discuss the different signals and signaling mechanisms used by the parasites to carry out the early events necessary for their establishment in the fly. We also compare Trypanosoma brucei and Trypanosoma congolense, parasites that share a common pathway in the early stages of fly colonization but apparently use different mechanisms to achieve this.
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Affiliation(s)
- Balázs Szöőr
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK.
| | - Eleanor Silvester
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Keith R Matthews
- Institute for Immunology and Infection Research, School of Biological Sciences, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK.
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36
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Histone deacetylase inhibitors dysregulate DNA repair proteins and antagonize metastasis-associated processes. J Cancer Res Clin Oncol 2020; 146:343-356. [PMID: 31932908 PMCID: PMC6985217 DOI: 10.1007/s00432-019-03118-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 12/19/2019] [Indexed: 02/07/2023]
Abstract
Purpose We set out to determine whether clinically tested epigenetic drugs against class I histone deacetylases (HDACs) affect hallmarks of the metastatic process. Methods We treated permanent and primary renal, lung, and breast cancer cells with the class I histone deacetylase inhibitors (HDACi) entinostat (MS-275) and valproic acid (VPA), the replicative stress inducer hydroxyurea (HU), the DNA-damaging agent cis-platinum (L-OHP), and the cytokine transforming growth factor-β (TGFβ). We used proteomics, quantitative PCR, immunoblot, single cell DNA damage assays, and flow cytometry to analyze cell fate after drug exposure. Results We show that HDACi interfere with DNA repair protein expression and trigger DNA damage and apoptosis alone and in combination with established chemotherapeutics. Furthermore, HDACi disrupt the balance of cell adhesion protein expression and abrogate TGFβ-induced cellular plasticity of transformed cells. Conclusion HDACi suppress the epithelial–mesenchymal transition (EMT) and compromise the DNA integrity of cancer cells. These data encourage further testing of HDACi against tumor cells. Electronic supplementary material The online version of this article (10.1007/s00432-019-03118-4) contains supplementary material, which is available to authorized users.
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37
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Liu B, Kamanyi Marucha K, Clayton C. The zinc finger proteins ZC3H20 and ZC3H21 stabilise mRNAs encoding membrane proteins and mitochondrial proteins in insect-form Trypanosoma brucei. Mol Microbiol 2019; 113:430-451. [PMID: 31743541 DOI: 10.1111/mmi.14429] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 10/24/2019] [Accepted: 11/17/2019] [Indexed: 12/26/2022]
Abstract
ZC3H20 and ZC3H21 are related trypanosome proteins with two C(x)8 C(x)5 C(x)3 H zinc finger motifs. ZC3H20 is present at a low level in replicating mammalian-infective bloodstream forms, but becomes more abundant when they undergo growth arrest at high density; ZC3H21 appears only in the procyclic form of the parasite, which infects Tsetse flies. Each protein binds to several hundred mRNAs, with overlapping but not identical specificities. Both increase expression of bound mRNAs, probably through recruitment of the MKT1-PBP1 complex. At least 28 of the bound mRNAs decrease after depletion of ZC3H20, or of ZC3H20 and ZC3H21 together; their products include procyclic-specific proteins of the plasma membrane and energy metabolism. Simultaneous depletion of ZC3H20 and ZC3H21 causes procyclic forms to shrink and stop growing; in addition to decreases in target mRNAs, there are other changes suggestive of loss of developmental regulation. The bloodstream-form-specific protein RBP10 controls ZC3H20 and ZC3H21 expression. Interestingly, some ZC3H20/21 target mRNAs also bind to and are repressed by RBP10, allowing for dynamic regulation as RBP10 decreases and ZC3H20 and ZC3H21 increase during differentiation.
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Affiliation(s)
- Bin Liu
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Kevin Kamanyi Marucha
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Christine Clayton
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
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38
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Tinti M, Güther MLS, Crozier TWM, Lamond AI, Ferguson MAJ. Proteome turnover in the bloodstream and procyclic forms of Trypanosoma brucei measured by quantitative proteomics. Wellcome Open Res 2019; 4:152. [PMID: 31681858 PMCID: PMC6816455 DOI: 10.12688/wellcomeopenres.15421.1] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2019] [Indexed: 12/20/2022] Open
Abstract
Background: Cellular proteins vary significantly in both abundance and turnover rates. These parameters depend upon their rates of synthesis and degradation and it is useful to have access to data on protein turnover rates when, for example, designing genetic knock-down experiments or assessing the potential usefulness of covalent enzyme inhibitors. Little is known about the nature and regulation of protein turnover in Trypanosoma brucei, the etiological agent of human and animal African trypanosomiasis. Methods: To establish baseline data on T. brucei proteome turnover, a Stable Isotope Labelling with Amino acids in Cell culture (SILAC)-based mass spectrometry analysis was performed to reveal the synthesis and degradation profiles for thousands of proteins in the bloodstream and procyclic forms of this parasite. Results: This analysis revealed a slower average turnover rate of the procyclic form proteome relative to the bloodstream proteome. As expected, many of the proteins with the fastest turnover rates have functions in the cell cycle and in the regulation of cytokinesis in both bloodstream and procyclic forms. Moreover, the cellular localization of T. brucei proteins correlates with their turnover, with mitochondrial and glycosomal proteins exhibiting slower than average turnover rates. Conclusions: The intention of this study is to provide the trypanosome research community with a resource for protein turnover data for any protein or group of proteins. To this end, bioinformatic analyses of these data are made available via an open-access web resource with data visualization functions.
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Affiliation(s)
- Michele Tinti
- The Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, UK
| | - Maria Lucia S Güther
- The Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, UK
| | - Thomas W M Crozier
- The Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, UK.,Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK.,Department of Medicine, Cambridge Institute for Medical Research, Cambridge, UK
| | - Angus I Lamond
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Michael A J Ferguson
- The Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, UK
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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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40
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Terrao M, Marucha KK, Mugo E, Droll D, Minia I, Egler F, Braun J, Clayton C. The suppressive cap-binding complex factor 4EIP is required for normal differentiation. Nucleic Acids Res 2019; 46:8993-9010. [PMID: 30124912 PMCID: PMC6158607 DOI: 10.1093/nar/gky733] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 08/01/2018] [Indexed: 12/27/2022] Open
Abstract
Trypanosoma brucei live in mammals as bloodstream forms and in the Tsetse midgut as procyclic forms. Differentiation from one form to the other proceeds via a growth-arrested stumpy form with low messenger RNA (mRNA) content and translation. The parasites have six eIF4Es and five eIF4Gs. EIF4E1 pairs with the mRNA-binding protein 4EIP but not with any EIF4G. EIF4E1 and 4EIP each inhibit expression when tethered to a reporter mRNA, but while tethered EIF4E1 suppresses only when 4EIP is present, suppression by tethered 4EIP does not require the interaction with EIF4E1. In growing bloodstream forms, 4EIP is preferentially associated with unstable mRNAs. Bloodstream- or procyclic-form trypanosomes lacking 4EIP have only a marginal growth disadvantage. Bloodstream forms without 4EIP are, however, defective in translation suppression during stumpy-form differentiation and cannot subsequently convert to growing procyclic forms. Intriguingly, the differentiation defect can be complemented by a truncated 4EIP that does not interact with EIF4E1. In contrast, bloodstream forms lacking EIF4E1 have a growth defect, stumpy formation seems normal, but they appear unable to grow as procyclic forms. We suggest that 4EIP and EIF4E1 fine-tune mRNA levels in growing cells, and that 4EIP contributes to translation suppression during differentiation to the stumpy form.
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Affiliation(s)
- Monica Terrao
- Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Kevin K Marucha
- Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Elisha Mugo
- Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Dorothea Droll
- Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Igor Minia
- Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Franziska Egler
- Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Johanna Braun
- Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Christine Clayton
- Centre for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
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41
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Abstract
In trypanosomes, RNA polymerase II transcription is polycistronic and individual mRNAs are excised by trans-splicing and polyadenylation. The lack of individual gene transcription control is compensated by control of mRNA processing, translation and degradation. Although the basic mechanisms of mRNA decay and translation are evolutionarily conserved, there are also unique aspects, such as the existence of six cap-binding translation initiation factor homologues, a novel decapping enzyme and an mRNA stabilizing complex that is recruited by RNA-binding proteins. High-throughput analyses have identified nearly a hundred regulatory mRNA-binding proteins, making trypanosomes valuable as a model system to investigate post-transcriptional regulation.
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Affiliation(s)
- Christine Clayton
- University of Heidelberg Center for Molecular Biology (ZMBH), Im Neuenheimer Feld 282, D69120 Heidelberg, Germany
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42
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Chakraborty C, Clayton C. Stress susceptibility in Trypanosoma brucei lacking the RNA-binding protein ZC3H30. PLoS Negl Trop Dis 2018; 12:e0006835. [PMID: 30273340 PMCID: PMC6181440 DOI: 10.1371/journal.pntd.0006835] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 10/11/2018] [Accepted: 09/11/2018] [Indexed: 01/17/2023] Open
Abstract
Trypanosomes rely on post-transcriptional mechanisms and mRNA-binding proteins for control of gene expression. Trypanosoma brucei ZC3H30 is an mRNA-binding protein that is expressed in both the bloodstream form (which grows in mammals) and the procyclic form (which grows in the tsetse fly midgut). Attachment of ZC3H30 to an mRNA causes degradation of that mRNA. Cells lacking ZC3H30 showed no growth defect under normal culture conditions; but they were more susceptible than wild-type cells to heat shock, starvation, and treatment with DTT, arsenite or ethanol. Transcriptomes of procyclic-form trypanosomes lacking ZC3H30 were indistinguishable from those of cells in which ZC3H30 had been re-expressed, but un-stressed bloodstream forms lacking ZC3H30 had about 2-fold more HSP70 mRNA. Results from pull-downs suggested that ZC3H30 mRNA binding may not be very specific. ZC3H30 was found in stress-induced granules and co-purified with another stress granule protein, Tb927.8.3820; but RNAi targeting Tb927.8.3820 did not affect either ZC3H30 granule association or stress resistance. The conservation of the ZC3H30 gene in both monogenetic and digenetic kinetoplastids, combined with the increased stress susceptibility of cells lacking it, suggests that ZC3H30 confers a selective advantage in the wild, where the parasites are subject to temperature fluctuations and immune attack in both the insect and mammalian hosts.
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Affiliation(s)
| | - Christine Clayton
- Zentrum für Molekular Biologie, Universität Heidelberg, Heidelberg, Germany
- * E-mail:
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43
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Jojic B, Amodeo S, Ochsenreiter T. The translationally controlled tumor protein TCTP is involved in cell cycle progression and heat stress response in the bloodstream form of Trypanosoma brucei. MICROBIAL CELL 2018; 5:460-468. [PMID: 30386790 PMCID: PMC6206406 DOI: 10.15698/mic2018.10.652] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The translationally controlled tumor protein TCTP, is a universally conserved protein that seems to be of essential function in all systems tested so far. TCTP is involved in a multitude of cellular functions including cell cycle control, cell division, apoptosis and many more. The mechanism of how TCTP is involved in most of these functions remains elusive. Here we describe that TCTP is a cytoplasmic protein involved in cell cycle regulation and heat stress response in the bloodstream form of Trypanosoma brucei.
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Affiliation(s)
- Borka Jojic
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Simona Amodeo
- Institute of Cell Biology, University of Bern, Bern, Switzerland.,Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
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44
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Mitochondrial DNA is critical for longevity and metabolism of transmission stage Trypanosoma brucei. PLoS Pathog 2018; 14:e1007195. [PMID: 30020996 PMCID: PMC6066258 DOI: 10.1371/journal.ppat.1007195] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 07/30/2018] [Accepted: 07/02/2018] [Indexed: 01/19/2023] Open
Abstract
The sleeping sickness parasite Trypanosoma brucei has a complex life cycle, alternating between a mammalian host and the tsetse fly vector. A tightly controlled developmental programme ensures parasite transmission between hosts as well as survival within them and involves strict regulation of mitochondrial activities. In the glucose-rich bloodstream, the replicative 'slender' stage is thought to produce ATP exclusively via glycolysis and uses the mitochondrial F1FO-ATP synthase as an ATP hydrolysis-driven proton pump to generate the mitochondrial membrane potential (ΔΨm). The 'procyclic' stage in the glucose-poor tsetse midgut depends on mitochondrial catabolism of amino acids for energy production, which involves oxidative phosphorylation with ATP production via the F1FO-ATP synthase. Both modes of the F1FO enzyme critically depend on FO subunit a, which is encoded in the parasite's mitochondrial DNA (kinetoplast or kDNA). Comparatively little is known about mitochondrial function and the role of kDNA in non-replicative 'stumpy' bloodstream forms, a developmental stage essential for disease transmission. Here we show that the L262P mutation in the nuclear-encoded F1 subunit γ that permits survival of 'slender' bloodstream forms lacking kDNA ('akinetoplastic' forms), via FO-independent generation of ΔΨm, also permits their differentiation into stumpy forms. However, these akinetoplastic stumpy cells lack a ΔΨm and have a reduced lifespan in vitro and in mice, which significantly alters the within-host dynamics of the parasite. We further show that generation of ΔΨm in stumpy parasites and their ability to use α-ketoglutarate to sustain viability depend on F1-ATPase activity. Surprisingly, however, loss of ΔΨm does not reduce stumpy life span. We conclude that the L262P γ subunit mutation does not enable FO-independent generation of ΔΨm in stumpy cells, most likely as a consequence of mitochondrial ATP production in these cells. In addition, kDNA-encoded genes other than FO subunit a are important for stumpy form viability.
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45
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Kiweler N, Brill B, Wirth M, Breuksch I, Laguna T, Dietrich C, Strand S, Schneider G, Groner B, Butter F, Heinzel T, Brenner W, Krämer OH. The histone deacetylases HDAC1 and HDAC2 are required for the growth and survival of renal carcinoma cells. Arch Toxicol 2018; 92:2227-2243. [DOI: 10.1007/s00204-018-2229-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 05/23/2018] [Indexed: 12/11/2022]
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46
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Abstract
Sleeping sickness is a neglected tropical disease caused by Trypanosoma brucei parasites, affecting the poorest communities in sub-Saharan Africa. The great efforts done by the scientific community, local governments, and non-governmental organizations (NGOs) via active patients' screening, vector control, and introduction of improved treatment regimens have significantly contributed to the reduction of human African trypanosomiasis (HAT) incidence during the last 15 years. Consequently, the WHO has announced the objective of HAT elimination as a public health problem by 2020. Studies at both parasite and host levels have improved our understanding of the parasite biology and the mechanisms of parasite interaction with its mammalian host. In this review, the impact that 'omics studies have had on sleeping sickness by revealing novel properties of parasite's subcellular organelles are summarized, by highlighting changes induced in the host during the infection and by proposing potential disease markers and therapeutic targets.
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Affiliation(s)
- Natalia Tiberti
- Translational Biomarker Group, University of Geneva, Geneva, Switzerland
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47
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Naguleswaran A, Doiron N, Roditi I. RNA-Seq analysis validates the use of culture-derived Trypanosoma brucei and provides new markers for mammalian and insect life-cycle stages. BMC Genomics 2018; 19:227. [PMID: 29606092 PMCID: PMC5879877 DOI: 10.1186/s12864-018-4600-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 03/13/2018] [Indexed: 01/03/2023] Open
Abstract
Background Trypanosoma brucei brucei, the parasite causing Nagana in domestic animals, is closely related to the parasites causing sleeping sickness, but does not infect humans. In addition to its importance as a pathogen, the relative ease of genetic manipulation and an innate capacity for RNAi extend its use as a model organism in cell and infection biology. During its development in its mammalian and insect (tsetse fly) hosts, T. b. brucei passes through several different life-cycle stages. There are currently four life-cycle stages that can be cultured: slender forms and stumpy forms, which are equivalent to forms found in the mammal, and early and late procyclic forms, which are equivalent to forms in the tsetse midgut. Early procyclic forms show coordinated group movement (social motility) on semi-solid surfaces, whereas late procyclic forms do not. Results RNA-Seq was performed on biological replicates of each life-cycle stage. These constitute the first datasets for culture-derived slender and stumpy bloodstream forms and early and late procyclic forms. Expression profiles confirmed that genes known to be stage-regulated in the animal and insect hosts were also regulated in culture. Sequence reads of 100–125 bases provided sufficient precision to uncover differential expression of closely related genes. More than 100 transcripts showed peak expression in stumpy forms, including adenylate cyclases and several components of inositol metabolism. Early and late procyclic forms showed differential expression of 73 transcripts, a number of which encoded proteins that were previously shown to be stage-regulated. Moreover, two adenylate cyclases previously shown to reduce social motility are up-regulated in late procyclic forms. Conclusions This study validates the use of cultured bloodstream forms as alternatives to animal-derived parasites and yields new markers for all four stages. In addition to underpinning recent findings that early and late procyclic forms are distinct life-cycle stages, it could provide insights into the reasons for their different biological properties. Electronic supplementary material The online version of this article (10.1186/s12864-018-4600-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Nicholas Doiron
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, CH-3012, Bern, Switzerland
| | - Isabel Roditi
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, CH-3012, Bern, Switzerland.
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48
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Colasante C, Zheng F, Kemp C, Voncken F. A plant-like mitochondrial carrier family protein facilitates mitochondrial transport of di- and tricarboxylates in Trypanosoma brucei. Mol Biochem Parasitol 2018; 221:36-51. [PMID: 29581011 DOI: 10.1016/j.molbiopara.2018.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 02/22/2018] [Accepted: 03/21/2018] [Indexed: 12/31/2022]
Abstract
The procyclic form of the human parasite Trypanosoma brucei harbors one single, large mitochondrion containing all tricarboxylic acid (TCA) cycle enzymes and respiratory chain complexes present also in higher eukaryotes. Metabolite exchange among subcellular compartments such as the cytoplasm, the mitochondrion, and the peroxisomes is crucial for redox homeostasis and for metabolic pathways whose enzymes are dispersed among different organelles. In higher eukaryotes, mitochondrial carrier family (MCF) proteins transport TCA-cycle intermediates across the inner mitochondrial membrane. Previously, we identified several MCF members that are essential for T. brucei survival. Among these, only one MCF protein, TbMCP12, potentially could transport dicarboxylates and tricarboxylates. Here, we conducted phylogenetic and sequence analyses and functionally characterised TbMCP12 in vivo. Our results suggested that similarly to its homologues in plants, TbMCP12 transports both dicarboxylates and tricarboxylates across the mitochondrial inner membrane. Deleting this carrier in T. brucei was not lethal, while its overexpression was deleterious. Our results suggest that the intracellular abundance of TbMCP12 is an important regulatory element for the NADPH balance and mitochondrial ATP-production.
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Affiliation(s)
- Claudia Colasante
- Institute for Anatomy and Cell Biology, Division of Medical Cell Biology, Aulweg 123, University of Giessen, 35392, Giessen, Germany.
| | - Fuli Zheng
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, 1 Xue Yuan Road, Fu Zhou, Fujian, PR China
| | - Cordula Kemp
- Department of Biomedical Sciences, School of Life Sciences, University of Hull, Cottingham Road, Hull, HU6 7RX, United Kingdom
| | - Frank Voncken
- Department of Biomedical Sciences, School of Life Sciences, University of Hull, Cottingham Road, Hull, HU6 7RX, United Kingdom
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Cestari I, Anupama A, Stuart K. Inositol polyphosphate multikinase regulation of Trypanosoma brucei life stage development. Mol Biol Cell 2018. [PMID: 29514930 PMCID: PMC5921579 DOI: 10.1091/mbc.e17-08-0515] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The regulation of Trypanosoma brucei life stage development remains unclear. Inositol polyphosphate multikinase regulates the development of mammalian bloodforms to insect stages that normally develop in flies. Specific inositol phosphates, perhaps as second messengers, interact with proteins of the regulatory network that controls development. Many cellular processes change during the Trypanosoma brucei life cycle as this parasite alternates between the mammalian host and tsetse fly vector. We show that the inositol phosphate pathway helps regulate these developmental changes. Knockdown of inositol polyphosphate multikinase (IPMK), which phosphorylates Ins(1,4,5)P3 and Ins(1,3,4,5)P4, resulted in changes in bloodstream forms that are characteristic of insect stage procyclic forms. These changes include expression of the procyclic surface coat, up-regulation of RNA-binding proteins that we show to regulate stage-specific transcripts, and activation of oxidative phosphorylation with increased ATP production in bloodstream forms. These changes were accompanied by development of procyclic morphology, which also occurred by the expression of a catalytically inactive IPMK, implying that regulation of these processes entails IPMK activity. Proteins involved in signaling, protein synthesis and turnover, and metabolism were affinity-enriched with the IPMK substrate or product. Developmental changes associated with IPMK knockdown or catalytic inactivation reflected processes that are enriched with inositol phosphates, and chemical and genetic perturbation of these processes affected T. brucei development. Hence, IPMK helps regulate T. brucei development, perhaps by affecting inositol phosphate interactions with proteins of the regulatory network that controls energy metabolism and development.
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Affiliation(s)
- Igor Cestari
- Center for Infectious Disease Research, Seattle, WA 98109
| | - Atashi Anupama
- Center for Infectious Disease Research, Seattle, WA 98109
| | - Kenneth Stuart
- Center for Infectious Disease Research, Seattle, WA 98109.,Department of Global Health, University of Washington, Seattle, WA 98195
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50
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Crozier TWM, Tinti M, Wheeler RJ, Ly T, Ferguson MAJ, Lamond AI. Proteomic Analysis of the Cell Cycle of Procylic Form Trypanosoma brucei. Mol Cell Proteomics 2018; 17:1184-1195. [PMID: 29555687 PMCID: PMC5986242 DOI: 10.1074/mcp.ra118.000650] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 03/01/2018] [Indexed: 12/24/2022] Open
Abstract
We describe a single-step centrifugal elutriation method to produce synchronous Gap1 (G1)-phase procyclic trypanosomes at a scale amenable for proteomic analysis of the cell cycle. Using ten-plex tandem mass tag (TMT) labeling and mass spectrometry (MS)-based proteomics technology, the expression levels of 5325 proteins were quantified across the cell cycle in this parasite. Of these, 384 proteins were classified as cell-cycle regulated and subdivided into nine clusters with distinct temporal regulation. These groups included many known cell cycle regulators in trypanosomes, which validates the approach. In addition, we identify 40 novel cell cycle regulated proteins that are essential for trypanosome survival and thus represent potential future drug targets for the prevention of trypanosomiasis. Through cross-comparison to the TrypTag endogenous tagging microscopy database, we were able to validate the cell-cycle regulated patterns of expression for many of the proteins of unknown function detected in our proteomic analysis. A convenient interface to access and interrogate these data is also presented, providing a useful resource for the scientific community. Data are available via ProteomeXchange with identifier PXD008741 (https://www.ebi.ac.uk/pride/archive/).
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Affiliation(s)
- Thomas W M Crozier
- From the ‡Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.,§Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Michele Tinti
- From the ‡Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Richard J Wheeler
- ‖Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Tony Ly
- §Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Michael A J Ferguson
- From the ‡Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK;
| | - Angus I Lamond
- §Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK;
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