1
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Dubey AP, Tylec BL, Mishra A, Sortino K, Chen R, Sun Y, Read LK. KREH1 RNA helicase activity promotes utilization of initiator gRNAs across multiple mRNAs in trypanosome RNA editing. Nucleic Acids Res 2023; 51:5791-5809. [PMID: 37140035 PMCID: PMC10287954 DOI: 10.1093/nar/gkad292] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/04/2023] [Accepted: 04/11/2023] [Indexed: 05/05/2023] Open
Abstract
Mitochondrial U-indel RNA editing in kinetoplastid protozoa is directed by trans-acting gRNAs and mediated by a holoenzyme with associated factors. Here, we examine the function of the holoenzyme-associated KREH1 RNA helicase in U-indel editing. We show that KREH1 knockout (KO) impairs editing of a small subset of mRNAs. Overexpression of helicase-dead mutants results in expanded impairment of editing across multiple transcripts, suggesting the existence of enzymes that can compensate for KREH1 in KO cells. In depth analysis of editing defects using quantitative RT-PCR and high-throughput sequencing reveals compromised editing initiation and progression in both KREH1-KO and mutant-expressing cells. In addition, these cells exhibit a distinct defect in the earliest stages of editing in which the initiator gRNA is bypassed, and a small number of editing events takes place just outside this region. Wild type KREH1 and a helicase-dead KREH1 mutant interact similarly with RNA and holoenzyme, and overexpression of both similarly disorders holoenzyme homeostasis. Thus, our data support a model in which KREH1 RNA helicase activity facilitates remodeling of initiator gRNA-mRNA duplexes to permit accurate utilization of initiating gRNAs on multiple transcripts.
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Affiliation(s)
- Ashutosh P Dubey
- Dept. of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Brianna L Tylec
- Dept. of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Amartya Mishra
- Dept. of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Katherine Sortino
- Dept. of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Runpu Chen
- Dept. of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Yijun Sun
- Dept. of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Laurie K Read
- Dept. of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
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2
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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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3
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Mapping the RNA Chaperone Activity of the T. brucei Editosome Using SHAPE Chemical Probing. Methods Mol Biol 2021; 2106:161-178. [PMID: 31889257 DOI: 10.1007/978-1-0716-0231-7_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Mitochondrial pre-mRNAs in African trypanosomes adopt intricately folded, highly stable 2D and 3D structures. The RNA molecules are substrates of a U-nucleotide-specific insertion/deletion-type RNA editing reaction, which is catalyzed by a 0.8 MDa protein complex known as the editosome. RNA binding to the editosome is followed by a chaperone-mediated RNA remodeling reaction. The reaction increases the dynamic of specifically U-nucleotides to lower their base-pairing probability and as a consequence generates a simplified RNA folding landscape that is critical for the progression of the editing reaction cycle. Here we describe a chemical mapping method to quantitatively monitor the chaperone-driven structural changes of pre-edited mRNAs upon editosome binding. The method is known as selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE). SHAPE is based on the differential electrophilic modification of ribose 2'-hydroxyl groups in structurally constraint (double-stranded) versus structurally unconstrained (single-stranded) nucleotides. Electrophilic anhydrides such as 1-methyl-7-nitroisatoic anhydride are used as probing reagents, and the ribose 2'-modified nucleotides are mapped as abortive cDNA synthesis products. As a result, SHAPE allows the identification of all single-stranded and base-paired regions in a given RNA, and the data are used to compute experimentally derived RNA 2D structures. A side-by-side comparison of the RNA 2D folds in the pre- and post-chaperone states finally maps the chaperone-induced dynamic of the different pre-mRNAs with single-nucleotide resolution.
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4
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Leeder WM, Kruse E, Göringer HU. Trypanosomatid, fluorescence-based in vitro U-insertion/U-deletion RNA-editing (FIDE). Bio Protoc 2021; 11:e3935. [PMID: 33796609 DOI: 10.21769/bioprotoc.3935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 11/02/2022] Open
Abstract
Gene expression within the mitochondria of African trypanosomes and other protozoan organisms relies on a nucleotide-specific RNA-editing reaction. In the process exclusively uridine (U)-nucleotides are site-specifically inserted into and deleted from sequence-deficient primary transcripts to convert them into translatable mRNAs. The reaction is catalyzed by a 0.8 MDa multiprotein complex termed the editosome. Here we describe an improved in vitro test to quantitatively explore the catalytic activity of the editosome. The assay uses synthetic, fluorophore-derivatized oligoribonucleotides as editing substrates, which enable the automated electrophoretic separation of the reaction products by capillary electrophoresis (CE) coupled to laser-induced fluorescence (LIF) detection systems. The assay is robust, it requires only nanogram amounts of materials and by using multicapillary CE/LIF-instruments it can be executed in a highly parallel layout. Further improvements include the usage of phosphorothioate-modified and thus RNase-resistant substrate RNAs as well as multiplex-type fluorophore labeling strategies to monitor the U-insertion and U-deletion reaction simultaneously. The assay is useful for investigating the mechanism and enzymology of the editosome. However, it can also be executed in high-throughput to screen for RNA editing-specific inhibitors. Graphic abstract: Characteristics of the fluorescence-based in vitro U-insertion/U-deletion RNA-editing (FIDE) assay.
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Affiliation(s)
| | - Elisabeth Kruse
- Molecular Genetics, Technical University Darmstadt, Darmstadt, Germany
| | - H Ulrich Göringer
- Molecular Genetics, Technical University Darmstadt, Darmstadt, Germany
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5
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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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6
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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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7
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Leeder WM, Voigt C, Brecht M, Göringer HU. The RNA chaperone activity of the Trypanosoma brucei editosome raises the dynamic of bound pre-mRNAs. Sci Rep 2016; 6:19309. [PMID: 26782631 PMCID: PMC4726059 DOI: 10.1038/srep19309] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 12/09/2015] [Indexed: 12/27/2022] Open
Abstract
Mitochondrial transcript maturation in African trypanosomes requires an RNA editing reaction that is characterized by the insertion and deletion of U-nucleotides into otherwise non-functional mRNAs. The reaction is catalyzed by editosomes and requires guide (g)RNAs as templates. Recent data demonstrate that the binding of pre-edited mRNAs to editosomes is followed by a chaperone-type RNA remodeling reaction. Here we map the changes in RNA folding using selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE). We demonstrate that pre-mRNAs in their free state adopt intricately folded, highly stable 2D-structures. Editosome binding renders the pre-mRNAs to adopt 2D-conformations of reduced stabilities. On average about 30% of the nucleotides in every pre-mRNA are affected with a prevalence for U-nucleotides. The data demonstrate that the chaperone activity acts by increasing the flexibility of U-residues to lower their base-pairing probability. This results in a simplified RNA folding landscape with a reduced energy barrier to facilitate the binding of gRNAs. The data provide a first rational for the enigmatic U-specificity of the editing reaction.
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MESH Headings
- G-Quadruplexes
- Genes, Mitochondrial
- Nucleic Acid Conformation
- Protein Binding
- Protozoan Proteins/metabolism
- RNA Editing
- RNA Precursors/chemistry
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA, Guide, Kinetoplastida/chemistry
- RNA, Guide, Kinetoplastida/genetics
- RNA, Guide, Kinetoplastida/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Protozoan
- RNA-Binding Proteins/metabolism
- Thermodynamics
- Trypanosoma brucei brucei/genetics
- Trypanosoma brucei brucei/metabolism
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Affiliation(s)
- W.-Matthias Leeder
- Molecular Genetics, Darmstadt University of Technology, Schnittspahnstraße 10, 64287 Darmstadt, Germany
| | - Christin Voigt
- Molecular Genetics, Darmstadt University of Technology, Schnittspahnstraße 10, 64287 Darmstadt, Germany
| | - Michael Brecht
- Molecular Genetics, Darmstadt University of Technology, Schnittspahnstraße 10, 64287 Darmstadt, Germany
| | - H. Ulrich Göringer
- Molecular Genetics, Darmstadt University of Technology, Schnittspahnstraße 10, 64287 Darmstadt, Germany
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8
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Szempruch AJ, Choudhury R, Wang Z, Hajduk SL. In vivo analysis of trypanosome mitochondrial RNA function by artificial site-specific RNA endonuclease-mediated knockdown. RNA (NEW YORK, N.Y.) 2015; 21:1781-1789. [PMID: 26264591 PMCID: PMC4574754 DOI: 10.1261/rna.052084.115] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 07/08/2015] [Indexed: 05/29/2023]
Abstract
Trypanosomes possess a unique mitochondrial genome called the kinetoplast DNA (kDNA). Many kDNA genes encode pre-mRNAs that must undergo guide RNA-directed editing. In addition, alternative mRNA editing gives rise to diverse mRNAs and several kDNA genes encode open reading frames of unknown function. To better understand the mechanism of RNA editing and the function of mitochondrial RNAs in trypanosomes, we have developed a reverse genetic approach using artificial site-specific RNA endonucleases (ASREs) to directly silence kDNA-encoded genes. The RNA-binding domain of an ASRE can be programmed to recognize unique 8-nucleotide sequences, allowing the design of ASREs to cleave any target RNA. Utilizing an ASRE containing a mitochondrial localization signal, we targeted the extensively edited mitochondrial mRNA for the subunit A6 of the F0F1 ATP synthase (A6) in the procyclic stage of Trypanosoma brucei. This developmental stage, found in the midgut of the insect vector, relies on mitochondrial oxidative phosphorylation for ATP production with A6 forming the critical proton half channel across the inner mitochondrial membrane. Expression of an A6-targeted ASRE in procyclic trypanosomes resulted in a 50% reduction in A6 mRNA levels after 24 h, a time-dependent decrease in mitochondrial membrane potential (ΔΨm), and growth arrest. Expression of the A6-ASRE, lacking the mitochondrial localization signal, showed no significant growth defect. The development of the A6-ASRE allowed the first in vivo functional analysis of an edited mitochondrial mRNA in T. brucei and provides a critical new tool to study mitochondrial RNA biology in trypanosomes.
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Affiliation(s)
- Anthony J Szempruch
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
| | - Rajarshi Choudhury
- Department of Pharmacology, University of North Carolina Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Zefeng Wang
- Department of Pharmacology, University of North Carolina Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Stephen L Hajduk
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA
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9
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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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10
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Leeder WM, Reuss AJ, Brecht M, Kratz K, Wachtveitl J, Göringer HU. Charge reduction and thermodynamic stabilization of substrate RNAs inhibit RNA editing. PLoS One 2015; 10:e0118940. [PMID: 25742417 PMCID: PMC4350841 DOI: 10.1371/journal.pone.0118940] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 01/07/2015] [Indexed: 01/04/2023] Open
Abstract
African trypanosomes cause a parasitic disease known as sleeping sickness. Mitochondrial transcript maturation in these organisms requires a RNA editing reaction that is characterized by the insertion and deletion of U-nucleotides into otherwise non-functional mRNAs. Editing represents an ideal target for a parasite-specific therapeutic intervention since the reaction cycle is absent in the infected host. In addition, editing relies on a macromolecular protein complex, the editosome, that only exists in the parasite. Therefore, all attempts to search for editing interfering compounds have been focused on molecules that bind to proteins of the editing machinery. However, in analogy to other RNA-driven biochemical pathways it should be possible to stall the reaction by targeting its substrate RNAs. Here we demonstrate inhibition of editing by specific aminoglycosides. The molecules bind into the major groove of the gRNA/pre-mRNA editing substrates thereby causing a stabilization of the RNA molecules through charge compensation and an increase in stacking. The data shed light on mechanistic details of the editing process and identify critical parameters for the development of new trypanocidal compounds.
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Affiliation(s)
- W.-Matthias Leeder
- Molecular Genetics, Darmstadt University of Technology, Darmstadt, Germany
| | - Andreas J. Reuss
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - Michael Brecht
- Molecular Genetics, Darmstadt University of Technology, Darmstadt, Germany
| | - Katja Kratz
- Molecular Genetics, Darmstadt University of Technology, Darmstadt, Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - H. Ulrich Göringer
- Molecular Genetics, Darmstadt University of Technology, Darmstadt, Germany
- * E-mail:
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11
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Molecular crowding inhibits U-insertion/deletion RNA editing in vitro: consequences for the in vivo reaction. PLoS One 2013; 8:e83796. [PMID: 24376749 PMCID: PMC3871654 DOI: 10.1371/journal.pone.0083796] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 11/16/2013] [Indexed: 01/02/2023] Open
Abstract
Mitochondrial pre-mRNAs in African trypanosomes are edited to generate functional transcripts. The reaction is typified by the insertion and deletion of U nucleotides and is catalyzed by a macromolecular complex, the editosome. Editosomes bind pre-edited mRNA/gRNA pairs and the reaction can be recapitulated in vitro by using pre-mRNA- and gRNA-mimicking oligoribonucleotides together with enriched editosome preparations. Although the in vitro assay has been instrumental in unraveling the basic steps of the editing cycle it is performed at dilute solvent conditions. This ignores the fact that editing takes place inside the highly crowded mitochondria. Here we investigate the effects of molecular crowding on RNA editing. By using neutral, macromolecular cosolutes we generate defined dilute, semidilute and crowded solvent properties and we demonstrate different thermodynamic stabilities of the pre-mRNA/gRNA hybrid RNAs at these conditions. Crowded conditions stabilize the RNAs by -30 kJ/mol. Furthermore, we show that the rate constants for the association and dissociation (kass/kdiss) of substrate RNAs to editosomes decrease, ultimately inhibiting the in vitro reaction. The data demonstrate that the current RNA editing in vitro system is sensitive to molecular crowding, which suggests that the in vivo reaction cannot rely on a diffusion-controlled, collision-based mechanism. Possible non-diffusional reaction pathways are discussed.
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12
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Kruse E, Voigt C, Leeder WM, Göringer HU. RNA helicases involved in U-insertion/deletion-type RNA editing. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1829:835-41. [PMID: 23587716 DOI: 10.1016/j.bbagrm.2013.04.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 04/04/2013] [Accepted: 04/08/2013] [Indexed: 12/20/2022]
Abstract
Mitochondrial pre-messenger RNAs in kinetoplastid protozoa such as the disease-causing African trypanosomes are substrates of a unique RNA editing reaction. The process is characterized by the site-specific insertion and deletion of exclusively U nucleotides and converts nonfunctional pre-mRNAs into translatable transcripts. Similar to other RNA-based metabolic pathways, RNA editing is catalyzed by a macromolecular protein complex, the editosome. Editosomes provide a reactive surface for the individual steps of the catalytic cycle and involve as key players a specific class of small, non-coding RNAs termed guide (g)RNAs. gRNAs basepair proximal to an editing site and act as quasi templates in the U-insertion/deletion reaction. Next to the editosome several accessory proteins and complexes have been identified, which contribute to different steps of the reaction. This includes matchmaking-type RNA/RNA annealing factors as well as RNA helicases of the archetypical DEAD- and DExH/D-box families. Here we summarize the current structural, genetic and biochemical knowledge of the two characterized "editing RNA helicases" and provide an outlook onto dynamic processes within the editing reaction cycle. This article is part of a Special Issue entitled: The Biology of RNA helicases - Modulation for life.
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13
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Multifunctional G-rich and RRM-containing domains of TbRGG2 perform separate yet essential functions in trypanosome RNA editing. EUKARYOTIC CELL 2012; 11:1119-31. [PMID: 22798390 DOI: 10.1128/ec.00175-12] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Efficient editing of Trypanosoma brucei mitochondrial RNAs involves the actions of multiple accessory factors. T. brucei RGG2 (TbRGG2) is an essential protein crucial for initiation and 3'-to-5' progression of editing. TbRGG2 comprises an N-terminal G-rich region containing GWG and RG repeats and a C-terminal RNA recognition motif (RRM)-containing domain. Here, we perform in vitro and in vivo separation-of-function studies to interrogate the mechanism of TbRGG2 action in RNA editing. TbRGG2 preferentially binds preedited mRNA in vitro with high affinity attributable to its G-rich region. RNA-annealing and -melting activities are separable, carried out primarily by the G-rich and RRM domains, respectively. In vivo, the G-rich domain partially complements TbRGG2 knockdown, but the RRM domain is also required. Notably, TbRGG2's RNA-melting activity is dispensable for RNA editing in vivo. Interactions between TbRGG2 and MRB1 complex proteins are mediated by both G-rich and RRM-containing domains, depending on the binding partner. Overall, our results are consistent with a model in which the high-affinity RNA binding and RNA-annealing activities of the G-rich domain are essential for RNA editing in vivo. The RRM domain may have key functions involving interactions with the MRB1 complex and/or regulation of the activities of the G-rich domain.
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