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Acquah FA, Mooers BHM. Targeting RNA Structure to Inhibit Editing in Trypanosomes. Int J Mol Sci 2023; 24:10110. [PMID: 37373258 PMCID: PMC10298474 DOI: 10.3390/ijms241210110] [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: 05/01/2023] [Revised: 06/01/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Mitochondrial RNA editing in trypanosomes represents an attractive target for developing safer and more efficient drugs for treating infections with trypanosomes because this RNA editing pathway is not found in humans. Other workers have targeted several enzymes in this editing system, but not the RNA. Here, we target a universal domain of the RNA editing substrate, which is the U-helix formed between the oligo-U tail of the guide RNA and the target mRNA. We selected a part of the U-helix that is rich in G-U wobble base pairs as the target site for the virtual screening of 262,000 compounds. After chemoinformatic filtering of the top 5000 leads, we subjected 50 representative complexes to 50 nanoseconds of molecular dynamics simulations. We identified 15 compounds that retained stable interactions in the deep groove of the U-helix. The microscale thermophoresis binding experiments on these five compounds show low-micromolar to nanomolar binding affinities. The UV melting studies show an increase in the melting temperatures of the U-helix upon binding by each compound. These five compounds can serve as leads for drug development and as research tools to probe the role of the RNA structure in trypanosomal RNA editing.
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Affiliation(s)
- Francis A. Acquah
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
| | - Blaine H. M. Mooers
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Laboratory of Biomolecular Structure and Function, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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Del Campo C, Leeder WM, Reißig P, Göringer HU. Analyzing editosome function in high-throughput. Nucleic Acids Res 2020; 48:e99. [PMID: 32756897 PMCID: PMC7515698 DOI: 10.1093/nar/gkaa658] [Citation(s) in RCA: 4] [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: 05/19/2020] [Revised: 07/08/2020] [Accepted: 07/30/2020] [Indexed: 12/16/2022] Open
Abstract
Mitochondrial gene expression in African trypanosomes and other trypanosomatid pathogens requires a U-nucleotide specific insertion/deletion-type RNA-editing reaction. The process is catalyzed by a macromolecular protein complex known as the editosome. Editosomes are restricted to the trypanosomatid clade and since editing is essential for the parasites, the protein complex represents a near perfect target for drug intervention strategies. Here, we report the development of an improved in vitro assay to monitor editosome function. The test system utilizes fluorophore-labeled substrate RNAs to analyze the processing reaction by automated, high-throughput capillary electrophoresis (CE) in combination with a laser-induced fluorescence (LIF) readout. We optimized the assay for high-throughput screening (HTS)-experiments and devised a multiplex fluorophore-labeling regime to scrutinize the U-insertion/U-deletion reaction simultaneously. The assay is robust, it requires only nanogram amounts of materials and it meets all performance criteria for HTS-methods. As such the test system should be helpful in the search for trypanosome-specific pharmaceuticals.
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Affiliation(s)
- Cristian Del Campo
- Molecular Genetics, Technical University Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Wolf-Matthias Leeder
- Molecular Genetics, Technical University Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Paul Reißig
- Molecular Genetics, Technical University Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - H Ulrich Göringer
- Molecular Genetics, Technical University Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
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Voigt C, Dobrychlop M, Kruse E, Czerwoniec A, Kasprzak JM, Bytner P, Campo CD, Leeder WM, Bujnicki JM, Göringer HU. The OB-fold proteins of the Trypanosoma brucei editosome execute RNA-chaperone activity. Nucleic Acids Res 2019; 46:10353-10367. [PMID: 30060205 PMCID: PMC6212840 DOI: 10.1093/nar/gky668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 07/13/2018] [Indexed: 02/01/2023] Open
Abstract
Sequence-deficient mitochondrial pre-mRNAs in African trypanosomes are substrates of a U-nucleotide-specific RNA editing reaction to generate translation-competent mRNAs. The reaction is catalyzed by a macromolecular protein complex termed the editosome. Editosomes execute RNA-chaperone activity to overcome the highly folded nature of pre-edited substrate mRNAs. The molecular basis for this activity is unknown. Here we test five of the OB-fold proteins of the Trypanosoma brucei editosome as candidates. We demonstrate that all proteins execute RNA-chaperone activity albeit to different degrees. We further show that the activities correlate to the surface areas of the proteins and we map the protein-induced RNA-structure changes using SHAPE-chemical probing. To provide a structural context for our findings we calculate a coarse-grained model of the editosome. The model has a shell-like structure: Structurally well-defined protein domains are separated from an outer shell of intrinsically disordered protein domains, which suggests a surface-driven mechanism for the chaperone activity.
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Affiliation(s)
- Christin Voigt
- Molecular Genetics, Darmstadt University of Technology, Darmstadt, Germany
| | - Mateusz Dobrychlop
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Elisabeth Kruse
- Molecular Genetics, Darmstadt University of Technology, Darmstadt, Germany
| | - Anna Czerwoniec
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Joanna M Kasprzak
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Patrycja Bytner
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Cristian Del Campo
- Molecular Genetics, Darmstadt University of Technology, Darmstadt, Germany
| | - W-Matthias Leeder
- Molecular Genetics, Darmstadt University of Technology, Darmstadt, Germany
| | - Janusz M Bujnicki
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland.,Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - H Ulrich Göringer
- Molecular Genetics, Darmstadt University of Technology, Darmstadt, Germany
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Zimmermann S, Hall L, Riley S, Sørensen J, Amaro RE, Schnaufer A. A novel high-throughput activity assay for the Trypanosoma brucei editosome enzyme REL1 and other RNA ligases. Nucleic Acids Res 2015; 44:e24. [PMID: 26400159 PMCID: PMC4756849 DOI: 10.1093/nar/gkv938] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 09/08/2015] [Indexed: 01/12/2023] Open
Abstract
The protist parasite Trypanosoma brucei causes Human African trypanosomiasis (HAT), which threatens millions of people in sub-Saharan Africa. Without treatment the infection is almost always lethal. Current drugs for HAT are difficult to administer and have severe side effects. Together with increasing drug resistance this results in urgent need for new treatments. T. brucei and other trypanosomatid pathogens require a distinct form of post-transcriptional mRNA modification for mitochondrial gene expression. A multi-protein complex called the editosome cleaves mitochondrial mRNA, inserts or deletes uridine nucleotides at specific positions and re-ligates the mRNA. RNA editing ligase 1 (REL1) is essential for the re-ligation step and has no close homolog in the mammalian host, making it a promising target for drug discovery. However, traditional assays for RELs use radioactive substrates coupled with gel analysis and are not suitable for high-throughput screening of compound libraries. Here we describe a fluorescence-based REL activity assay. This assay is compatible with a 384-well microplate format and sensitive, satisfies statistical criteria for high-throughput methods and is readily adaptable for other polynucleotide ligases. We validated the assay by determining kinetic properties of REL1 and by identifying REL1 inhibitors in a library of small, pharmacologically active compounds.
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Affiliation(s)
- Stephan Zimmermann
- Institute of Immunology & Infection Research and Centre for Immunity, Infection & Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Laurence Hall
- Institute of Immunology & Infection Research and Centre for Immunity, Infection & Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Sean Riley
- The Scripps Research Institute, 4122 Sorrento Valley Boulevard, San Diego, CA 92121, USA
| | - Jesper Sørensen
- Department of Chemistry & Biochemistry and the National Biomedical Computation Resource, University of California, San Diego, CA 92093, USA
| | - Rommie E Amaro
- Department of Chemistry & Biochemistry and the National Biomedical Computation Resource, University of California, San Diego, CA 92093, USA
| | - Achim Schnaufer
- Institute of Immunology & Infection Research and Centre for Immunity, Infection & Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK
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Czerwoniec A, Kasprzak JM, Bytner P, Dobrychłop M, Bujnicki JM. Structure and intrinsic disorder of the proteins of the Trypanosoma brucei editosome. FEBS Lett 2015; 589:2603-10. [PMID: 26226426 DOI: 10.1016/j.febslet.2015.07.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/21/2015] [Accepted: 07/22/2015] [Indexed: 01/02/2023]
Abstract
Mitochondrial pre-mRNAs in trypanosomatids undergo RNA editing to be converted into translatable mRNAs. The reaction is characterized by the insertion and deletion of uridine residues and is catalyzed by a macromolecular protein complex called the editosome. Despite intensive research, structural information for the majority of editosome proteins is still missing and no high resolution structure for the editosome exists. Here we present a comprehensive structural bioinformatics analysis of all proteins of the Trypanosoma brucei editosome. We specifically focus on the interplay between intrinsic order and disorder. According to computational predictions, editosome proteins involved in the basal reaction steps of the processing cycle are mostly ordered. By contrast, thirty percent of the amino acid content of the editosome is intrinsically disordered, which includes most prominently proteins with OB-fold domains. Based on the data we suggest a functional model, in which the structurally disordered domains of the complex are correlated with the RNA binding and RNA unfolding activity of the T. brucei editosome.
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Affiliation(s)
- Anna Czerwoniec
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland.
| | - Joanna M Kasprzak
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, PL-02-109 Warsaw, Poland; Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland
| | - Patrycja Bytner
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland
| | - Mateusz Dobrychłop
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, PL-02-109 Warsaw, Poland; Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland.
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