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Leeder WM, Geyer FK, Göringer HU. Fuzzy RNA recognition by the Trypanosoma brucei editosome. Nucleic Acids Res 2022; 50:5818-5833. [PMID: 35580050 PMCID: PMC9178004 DOI: 10.1093/nar/gkac357] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/20/2022] [Accepted: 04/26/2022] [Indexed: 11/30/2022] Open
Abstract
The assembly of high molecular mass ribonucleoprotein complexes typically relies on the binary interaction of defined RNA sequences or precisely folded RNA motifs with dedicated RNA-binding domains on the protein side. Here we describe a new molecular recognition principle of RNA molecules by a high molecular mass protein complex. By chemically probing the solvent accessibility of mitochondrial pre-mRNAs when bound to the Trypanosoma brucei editosome, we identified multiple similar but non-identical RNA motifs as editosome contact sites. However, by treating the different motifs as mathematical graph objects we demonstrate that they fit a consensus 2D-graph consisting of 4 vertices (V) and 3 edges (E) with a Laplacian eigenvalue of 0.5477 (λ2). We establish that synthetic 4V(3E)-RNAs are sufficient to compete for the editosomal pre-mRNA binding site and that they inhibit RNA editing in vitro. Furthermore, we demonstrate that only two topological indices are necessary to predict the binding of any RNA motif to the editosome with a high level of confidence. Our analysis corroborates that the editosome has adapted to the structural multiplicity of the mitochondrial mRNA folding space by recognizing a fuzzy continuum of RNA folds that fit a consensus graph descriptor.
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Affiliation(s)
| | - Felix Klaus Geyer
- Molecular Genetics, Technical University Darmstadt, 64287 Darmstadt, Germany
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2
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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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Simpson RM, Bruno AE, Chen R, Lott K, Tylec BL, Bard JE, Sun Y, Buck MJ, Read LK. Trypanosome RNA Editing Mediator Complex proteins have distinct functions in gRNA utilization. Nucleic Acids Res 2017; 45:7965-7983. [PMID: 28535252 PMCID: PMC5737529 DOI: 10.1093/nar/gkx458] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 05/01/2017] [Accepted: 05/10/2017] [Indexed: 11/13/2022] Open
Abstract
Uridine insertion/deletion RNA editing is an essential process in kinetoplastid parasites whereby mitochondrial mRNAs are modified through the specific insertion and deletion of uridines to generate functional open reading frames, many of which encode components of the mitochondrial respiratory chain. The roles of numerous non-enzymatic editing factors have remained opaque given the limitations of conventional methods to interrogate the order and mechanism by which editing progresses and thus roles of individual proteins. Here, we examined whole populations of partially edited sequences using high throughput sequencing and a novel bioinformatic platform, the Trypanosome RNA Editing Alignment Tool (TREAT), to elucidate the roles of three proteins in the RNA Editing Mediator Complex (REMC). We determined that the factors examined function in the progression of editing through a gRNA; however, they have distinct roles and REMC is likely heterogeneous in composition. We provide the first evidence that editing can proceed through numerous paths within a single gRNA and that non-linear modifications are essential, generating commonly observed junction regions. Our data support a model in which RNA editing is executed via multiple paths that necessitate successive re-modification of junction regions facilitated, in part, by the REMC variant containing TbRGG2 and MRB8180.
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Affiliation(s)
- Rachel M. Simpson
- Department of Microbiology and Immunology, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, 3435 Main Street, Buffalo, NY 14214, USA
| | - Andrew E. Bruno
- Center for Computational Research, University at Buffalo, 701 Ellicott St., Buffalo, NY 14203, USA
| | - Runpu Chen
- Department of Computer Science and Engineering, New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott St., Buffalo, NY 14203, USA
| | - Kaylen Lott
- Department of Microbiology and Immunology, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, 3435 Main Street, Buffalo, NY 14214, USA
| | - Brianna L. Tylec
- Department of Microbiology and Immunology, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, 3435 Main Street, Buffalo, NY 14214, USA
| | - Jonathan E. Bard
- Genomics and Bioinformatics Core, University at Buffalo, 701 Ellicott St., Buffalo, NY 14203, USA
| | - Yijun Sun
- Department of Microbiology and Immunology, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, 3435 Main Street, Buffalo, NY 14214, USA
- Center for Computational Research, University at Buffalo, 701 Ellicott St., Buffalo, NY 14203, USA
| | - Michael J. Buck
- Department of Biochemistry, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, 701 Ellicott St., Buffalo, NY 14203, USA
| | - Laurie K. Read
- Department of Microbiology and Immunology, University at Buffalo Jacobs School of Medicine and Biomedical Sciences, 3435 Main Street, Buffalo, NY 14214, USA
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Abstract
Uridine insertion and deletion RNA editing generates functional mitochondrial mRNAs in Trypanosoma brucei Editing is catalyzed by three distinct ∼20S editosomes that have a common set of 12 proteins, but are typified by mutually exclusive RNase III endonucleases with distinct cleavage specificities and unique partner proteins. Previous studies identified a network of protein-protein interactions among a subset of common editosome proteins, but interactions among the endonucleases and their partner proteins, and their interactions with common subunits were not identified. Here, chemical cross-linking and mass spectrometry, comparative structural modeling, and genetic and biochemical analyses were used to define the molecular architecture and subunit organization of purified editosomes. We identified intra- and interprotein cross-links for all editosome subunits that are fully consistent with editosome protein structures and previously identified interactions, which we validated by genetic and biochemical studies. The results were used to create a highly detailed map of editosome protein domain proximities, leading to identification of molecular interactions between subunits, insights into the functions of noncatalytic editosome proteins, and a global understanding of editosome architecture.
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Aphasizheva I, Aphasizhev R. U-Insertion/Deletion mRNA-Editing Holoenzyme: Definition in Sight. Trends Parasitol 2015; 32:144-156. [PMID: 26572691 DOI: 10.1016/j.pt.2015.10.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 10/06/2015] [Accepted: 10/12/2015] [Indexed: 11/16/2022]
Abstract
RNA editing is a process that alters DNA-encoded sequences and is distinct from splicing, 5' capping, and 3' additions. In 30 years since editing was discovered in mitochondria of trypanosomes, several functionally and evolutionarily unrelated mechanisms have been described in eukaryotes, archaea, and viruses. Editing events are predominantly post-transcriptional and include nucleoside insertions and deletions, and base substitutions and modifications. Here, we review the mechanism of uridine insertion/deletion mRNA editing in kinetoplastid protists typified by Trypanosoma brucei. This type of editing corrects frameshifts, introduces translation punctuation signals, and often adds hundreds of uridines to create protein-coding sequences. We focus on protein complexes responsible for editing reactions and their interactions with other elements of the mitochondrial gene expression pathway.
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Affiliation(s)
- Inna Aphasizheva
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA 02118, USA.
| | - Ruslan Aphasizhev
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA 02118, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
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