1
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Meehan J, Ivens A, Grote S, Rodshagen T, Chen Z, Goode C, Sharma SK, Kumar V, Frese A, Goodall Z, McCleskey L, Sechrist R, Zeng L, Savill NJ, Rouskin S, Schnaufer A, McDermott SM, Cruz-Reyes J. KREH2 helicase represses ND7 mRNA editing in procyclic-stage Trypanosoma brucei by opposite modulation of canonical and 'moonlighting' gRNA utilization creating a proposed mRNA structure. Nucleic Acids Res 2024:gkae699. [PMID: 39149912 DOI: 10.1093/nar/gkae699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 07/17/2024] [Accepted: 08/01/2024] [Indexed: 08/17/2024] Open
Abstract
Unknown factors regulate mitochondrial U-insertion/deletion (U-indel) RNA editing in procyclic-form (PCF) and bloodstream-form (BSF) T. brucei. This editing, directed by anti-sense gRNAs, creates canonical protein-encoding mRNAs and may developmentally control respiration. Canonical editing by gRNAs that specify protein-encoding mRNA sequences occurs amid massive non-canonical editing of unclear sources and biological significance. We found PCF-specific repression at a major early checkpoint in mRNA ND7, involving helicase KREH2-dependent opposite modulation of canonical and non-canonical 'terminator' gRNA utilization. Terminator-programmed editing derails canonical editing and installs proposed repressive structure in 30% of the ND7 transcriptome. BSF-to-PCF differentiation in vitro recreated this negative control. Remarkably, KREH2-RNAi knockdown relieved repression and increased editing progression by reverting canonical/terminator gRNA utilization. ND7 transcripts lacking early terminator-directed editing in PCF exhibited similar negative editing control along the mRNA sequence, suggesting global modulation of gRNA utilization fidelity. The terminator is a 'moonlighting' gRNA also associated with mRNA COX3 canonical editing, so the gRNA transcriptome seems multifunctional. Thus, KREH2 is the first identified repressor in developmental editing control. This and our prior work support a model whereby KREH2 activates or represses editing in a stage and substrate-specific manner. KREH2's novel dual role tunes mitochondrial gene expression in either direction during development.
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Affiliation(s)
- Joshua Meehan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Alasdair Ivens
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Scott Grote
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Tyler Rodshagen
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Zihao Chen
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Cody Goode
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Sunil K Sharma
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Vikas Kumar
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Addison Frese
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Zachary Goodall
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Laura McCleskey
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Rebecca Sechrist
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Lanying Zeng
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Nicholas J Savill
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Silvi Rouskin
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Achim Schnaufer
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Suzanne M McDermott
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Jorge Cruz-Reyes
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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2
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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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3
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Rostamighadi M, Mehta V, Hassan Khan R, Moses D, Salavati R. Hammerhead ribozyme-based U-insertion and deletion RNA editing assays for multiplexing in HTS applications. RNA (NEW YORK, N.Y.) 2023; 29:252-261. [PMID: 36456183 PMCID: PMC9891259 DOI: 10.1261/rna.079454.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/18/2022] [Indexed: 05/14/2023]
Abstract
Untranslatable mitochondrial transcripts in kinetoplastids are decrypted post-transcriptionally through an RNA editing process that entails uridine insertion/deletion. This unique stepwise process is mediated by the editosome, a multiprotein complex that is a validated drug target of considerable interest in addressing the unmet medical needs for kinetoplastid diseases. With that objective, several in vitro RNA editing assays have been developed, albeit with limited success in discovering potent inhibitors. This manuscript describes the development of three hammerhead ribozyme (HHR) FRET reporter-based RNA editing assays for precleaved deletion, insertion, and ligation assays that bypass the rate-limiting endonucleolytic cleavage step, providing information on U-deletion, U-insertion, and ligation activities. These assays exhibit higher editing efficiencies in shorter incubation times while requiring significantly less purified editosome and 10,000-fold less ATP than the previously published full round of in vitro RNA editing assay. Moreover, modifications in the reporter ribozyme sequence enable the feasibility of multiplexing a ribozyme-based insertion/deletion editing (RIDE) assay that simultaneously surveils U-insertion and deletion editing suitable for HTS. These assays can be used to find novel chemical compounds with chemotherapeutic applications or as probes for studying the editosome machinery.
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Affiliation(s)
- Mojtaba Rostamighadi
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec, Canada H9X 3V9
| | - Vaibhav Mehta
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec, Canada H9X 3V9
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada H3G 1Y6
| | - Rufaida Hassan Khan
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec, Canada H9X 3V9
| | - Daniel Moses
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec, Canada H9X 3V9
| | - Reza Salavati
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec, Canada H9X 3V9
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada H3G 1Y6
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4
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Current Status of Regulatory Non-Coding RNAs Research in the Tritryp. Noncoding RNA 2022; 8:ncrna8040054. [PMID: 35893237 PMCID: PMC9326685 DOI: 10.3390/ncrna8040054] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 07/01/2022] [Accepted: 07/02/2022] [Indexed: 11/23/2022] Open
Abstract
Trypanosomatids are protozoan parasites that cause devastating vector-borne human diseases. Gene expression regulation of these organisms depends on post-transcriptional control in responding to diverse environments while going through multiple developmental stages of their complex life cycles. In this scenario, non-coding RNAs (ncRNAs) are excellent candidates for a very efficient, quick, and economic strategy to regulate gene expression. The advent of high throughput RNA sequencing technologies show the presence and deregulation of small RNA fragments derived from canonical ncRNAs. This review seeks to depict the ncRNA landscape in trypanosomatids, focusing on the small RNA fragments derived from functional RNA molecules observed in RNA sequencing studies. Small RNA fragments derived from canonical ncRNAs (tsRNAs, snsRNAs, sdRNAs, and sdrRNAs) were identified in trypanosomatids. Some of these RNAs display changes in their levels associated with different environments and developmental stages, demanding further studies to determine their functional characterization and potential roles. Nevertheless, a comprehensive and detailed ncRNA annotation for most trypanosomatid genomes is still needed, allowing better and more extensive comparative and functional studies.
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How RNases Shape Mitochondrial Transcriptomes. Int J Mol Sci 2022; 23:ijms23116141. [PMID: 35682820 PMCID: PMC9181182 DOI: 10.3390/ijms23116141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 11/17/2022] Open
Abstract
Mitochondria are the power houses of eukaryote cells. These endosymbiotic organelles of prokaryote origin are considered as semi-autonomous since they have retained a genome and fully functional gene expression mechanisms. These pathways are particularly interesting because they combine features inherited from the bacterial ancestor of mitochondria with characteristics that appeared during eukaryote evolution. RNA biology is thus particularly diverse in mitochondria. It involves an unexpectedly vast array of factors, some of which being universal to all mitochondria and others being specific from specific eukaryote clades. Among them, ribonucleases are particularly prominent. They play pivotal functions such as the maturation of transcript ends, RNA degradation and surveillance functions that are required to attain the pool of mature RNAs required to synthesize essential mitochondrial proteins such as respiratory chain proteins. Beyond these functions, mitochondrial ribonucleases are also involved in the maintenance and replication of mitochondrial DNA, and even possibly in the biogenesis of mitochondrial ribosomes. The diversity of mitochondrial RNases is reviewed here, showing for instance how in some cases a bacterial-type enzyme was kept in some eukaryotes, while in other clades, eukaryote specific enzymes were recruited for the same function.
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Gao Y, Liu H, Zhang C, Su S, Chen Y, Chen X, Li Y, Shao Z, Zhang Y, Shao Q, Li J, Huang Z, Ma J, Gan J. Structural basis for guide RNA trimming by RNase D ribonuclease in Trypanosoma brucei. Nucleic Acids Res 2021; 49:568-583. [PMID: 33332555 PMCID: PMC7797062 DOI: 10.1093/nar/gkaa1197] [Citation(s) in RCA: 3] [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: 11/04/2020] [Accepted: 11/24/2020] [Indexed: 11/18/2022] Open
Abstract
Infection with kinetoplastid parasites, including Trypanosoma brucei (T. brucei), Trypanosoma cruzi (T. cruzi) and Leishmania can cause serious disease in humans. Like other kinetoplastid species, mRNAs of these disease-causing parasites must undergo posttranscriptional editing in order to be functional. mRNA editing is directed by gRNAs, a large group of small RNAs. Similar to mRNAs, gRNAs are also precisely regulated. In T. brucei, overexpression of RNase D ribonuclease (TbRND) leads to substantial reduction in the total gRNA population and subsequent inhibition of mRNA editing. However, the mechanisms regulating gRNA binding and cleavage by TbRND are not well defined. Here, we report a thorough structural study of TbRND. Besides Apo- and NMP-bound structures, we also solved one TbRND structure in complexed with single-stranded RNA. In combination with mutagenesis and in vitro cleavage assays, our structures indicated that TbRND follows the conserved two-cation-assisted mechanism in catalysis. TbRND is a unique RND member, as it contains a ZFD domain at its C-terminus. In addition to T. brucei, our studies also advanced our understanding on the potential gRNA degradation pathway in T. cruzi, Leishmania, as well for as other disease-associated parasites expressing ZFD-containing RNDs.
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Affiliation(s)
- Yanqing Gao
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Hehua Liu
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Chong Zhang
- College of Life Sciences, Sichuan University, Chengdu 610041, China
| | - Shichen Su
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yiqing Chen
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xi Chen
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yangyang Li
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Zhiwei Shao
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yixi Zhang
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Qiyuan Shao
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jixi Li
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Zhen Huang
- College of Life Sciences, Sichuan University, Chengdu 610041, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jianhua Gan
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200438, China
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7
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Non-Coding RNA Editing in Cancer Pathogenesis. Cancers (Basel) 2020; 12:cancers12071845. [PMID: 32650588 PMCID: PMC7408896 DOI: 10.3390/cancers12071845] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/05/2020] [Accepted: 07/06/2020] [Indexed: 12/19/2022] Open
Abstract
In the last two decades, RNA post-transcriptional modifications, including RNA editing, have been the subject of increasing interest among the scientific community. The efforts of the Human Genome Project combined with the development of new sequencing technologies and dedicated bioinformatic approaches created to detect and profile RNA transcripts have served to further our understanding of RNA editing. Investigators have determined that non-coding RNA (ncRNA) A-to-I editing is often deregulated in cancer. This discovery has led to an increased number of published studies in the field. However, the eventual clinical application for these findings remains a work in progress. In this review, we provide an overview of the ncRNA editing phenomenon in cancer. We discuss the bioinformatic strategies for RNA editing detection as well as the potential roles for ncRNA A to I editing in tumor immunity and as clinical biomarkers.
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Aphasizheva I, Alfonzo J, Carnes J, Cestari I, Cruz-Reyes J, Göringer HU, Hajduk S, Lukeš J, Madison-Antenucci S, Maslov DA, McDermott SM, Ochsenreiter T, Read LK, Salavati R, Schnaufer A, Schneider A, Simpson L, Stuart K, Yurchenko V, Zhou ZH, Zíková A, Zhang L, Zimmer S, Aphasizhev R. Lexis and Grammar of Mitochondrial RNA Processing in Trypanosomes. Trends Parasitol 2020; 36:337-355. [PMID: 32191849 PMCID: PMC7083771 DOI: 10.1016/j.pt.2020.01.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 01/19/2020] [Accepted: 01/22/2020] [Indexed: 12/15/2022]
Abstract
Trypanosoma brucei spp. cause African human and animal trypanosomiasis, a burden on health and economy in Africa. These hemoflagellates are distinguished by a kinetoplast nucleoid containing mitochondrial DNAs of two kinds: maxicircles encoding ribosomal RNAs (rRNAs) and proteins and minicircles bearing guide RNAs (gRNAs) for mRNA editing. All RNAs are produced by a phage-type RNA polymerase as 3' extended precursors, which undergo exonucleolytic trimming. Most pre-mRNAs proceed through 3' adenylation, uridine insertion/deletion editing, and 3' A/U-tailing. The rRNAs and gRNAs are 3' uridylated. Historically, RNA editing has attracted major research effort, and recently essential pre- and postediting processing events have been discovered. Here, we classify the key players that transform primary transcripts into mature molecules and regulate their function and turnover.
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Affiliation(s)
- Inna Aphasizheva
- Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, MA 02118, USA.
| | - Juan Alfonzo
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Jason Carnes
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Igor Cestari
- Institute of Parasitology, McGill University, 21,111 Lakeshore Road, Ste-Anne-de-Bellevue, H9X3V9, Québec, Canada
| | - Jorge Cruz-Reyes
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - H Ulrich Göringer
- Department of Molecular Genetics, Darmstadt University of Technology, 64287 Darmstadt, Germany
| | - Stephen Hajduk
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Susan Madison-Antenucci
- Parasitology Laboratory, Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
| | - Dmitri A Maslov
- Department of Molecular, Cell, and Systems Biology, University of California - Riverside, Riverside, CA 92521, USA
| | - Suzanne M McDermott
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Torsten Ochsenreiter
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, Bern CH-3012, Switzerland
| | - Laurie K Read
- Department of Microbiology and Immunology, University at Buffalo, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Reza Salavati
- Institute of Parasitology, McGill University, 21,111 Lakeshore Road, Ste-Anne-de-Bellevue, H9X3V9, Québec, Canada
| | - Achim Schnaufer
- Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - André Schneider
- Department of Chemistry and Biochemistry, University of Bern, Bern CH-3012, Switzerland
| | - Larry Simpson
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095, USA
| | - Kenneth Stuart
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA 98109, USA
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic; Martsinovsky Institute of Medical Parasitology, Sechenov University, Moscow, Russia
| | - Z Hong Zhou
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095, USA
| | - Alena Zíková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Liye Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Sara Zimmer
- University of Minnesota Medical School, Duluth campus, Duluth, MN 55812, USA
| | - Ruslan Aphasizhev
- Department of Molecular and Cell Biology, Boston University Medical Campus, Boston, MA 02118, USA
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Kumar V, Doharey PK, Gulati S, Meehan J, Martinez MG, Hughes K, Mooers BHM, Cruz-Reyes J. Protein features for assembly of the RNA editing helicase 2 subcomplex (REH2C) in Trypanosome holo-editosomes. PLoS One 2019; 14:e0211525. [PMID: 31034523 PMCID: PMC6488192 DOI: 10.1371/journal.pone.0211525] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 04/11/2019] [Indexed: 02/06/2023] Open
Abstract
Uridylate insertion/deletion RNA editing in Trypanosoma brucei is a complex system that is not found in humans, so there is interest in targeting this system for drug development. This system uses hundreds of small non-coding guide RNAs (gRNAs) to modify the mitochondrial mRNA transcriptome. This process occurs in holo-editosomes that assemble several macromolecular trans factors around mRNA including the RNA-free RNA editing core complex (RECC) and auxiliary ribonucleoprotein (RNP) complexes. Yet, the regulatory mechanisms of editing remain obscure. The enzymatic accessory RNP complex, termed the REH2C, includes mRNA substrates and products, the multi-domain 240 kDa RNA Editing Helicase 2 (REH2) and an intriguing 8-zinc finger protein termed REH2-Associated Factor 1 (H2F1). Both of these proteins are essential in editing. REH2 is a member of the DExH/RHA subfamily of RNA helicases with a conserved C-terminus that includes a regulatory OB-fold domain. In trypanosomes, H2F1 recruits REH2 to the editing apparatus, and H2F1 downregulation causes REH2 fragmentation. Our systematic mutagenesis dissected determinants in REH2 and H2F1 for the assembly of REH2C, the stability of REH2, and the RNA-mediated association of REH2C with other editing trans factors. We identified functional OB-fold amino acids in eukaryotic DExH/RHA helicases that are conserved in REH2 and that impact the assembly and interactions of REH2C. H2F1 upregulation stabilized REH2 in vivo. Mutation of the core cysteines or basic amino acids in individual zinc fingers affected the stabilizing property of H2F1 but not its interactions with other examined editing components. This result suggests that most, if not all, fingers may contribute to REH2 stabilization. Finally, a recombinant REH2 (240 kDa) established that the full-length protein is a bona fide RNA helicase with ATP-dependent unwinding activity. REH2 is the only DExH/RHA-type helicase in kinetoplastid holo-editosomes.
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Affiliation(s)
- Vikas Kumar
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Pawan K. Doharey
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Shelly Gulati
- Department of Biochemistry & Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Joshua Meehan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Mary G. Martinez
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Karrisa Hughes
- Department of Biochemistry & Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Blaine H. M. Mooers
- Department of Biochemistry & Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
- * E-mail: (JC); (BM)
| | - Jorge Cruz-Reyes
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
- * E-mail: (JC); (BM)
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Nikpour N, Salavati R. The RNA binding activity of the first identified trypanosome protein with Z-DNA-binding domains. Sci Rep 2019; 9:5904. [PMID: 30976048 PMCID: PMC6459835 DOI: 10.1038/s41598-019-42409-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 03/25/2019] [Indexed: 12/22/2022] Open
Abstract
RNA-binding proteins play a particularly important role in regulating gene expression in trypanosomes. A map of the network of protein complexes in Trypanosoma brucei uncovered an essential protein (Tb927.10.7910) that is postulated to be an RNA-binding protein implicated in the regulation of the mitochondrial post-transcriptional gene regulatory network by its association with proteins that participate in a multi-protein RNA editing complex. However, the mechanism by which this protein interacts with its multiple target transcripts remained unknown. Using sensitive database searches and experimental data, we identify Z-DNA-binding domains in T. brucei in the N- and C-terminal regions of Tb927.10.7910. RNA-binding studies of the wild-type protein, now referred to as RBP7910 (RNA binding protein 7910), and site-directed mutagenesis of residues important for the Z-DNA binding domains show that it preferentially interacts with RNA molecules containing poly(U) and poly(AU)-rich sequences. The interaction of RBP7910 with these regions may be involved in regulation of RNA editing of mitochondrial transcripts.
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Affiliation(s)
- Najmeh Nikpour
- Institute of Parasitology, McGill University, Quebec, H9X3V9, Canada
| | - Reza Salavati
- Department of Biochemistry, McGill University, McIntyre Medical Building, 3655 Promenade Sir William Osler, Montreal, Quebec, H3G 1Y6, Canada.
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11
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Cruz-Reyes J, Mooers BHM, Doharey PK, Meehan J, Gulati S. Dynamic RNA holo-editosomes with subcomplex variants: Insights into the control of trypanosome editing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1502. [PMID: 30101566 DOI: 10.1002/wrna.1502] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 07/03/2018] [Accepted: 07/09/2018] [Indexed: 12/14/2022]
Abstract
RNA editing causes massive remodeling of the mitochondrial mRNA transcriptome in trypanosomes and related kinetoplastid protozoa. This type of editing involves the specific insertion or deletion of uridylates (U) directed by small noncoding guide RNAs (gRNAs). Because U-insertion exceeds U-deletion by a factor of 10, editing increases the nascent mRNA size by up to 55%. In Trypanosoma brucei, the editing apparatus uses ~40 proteins and >1,200 gRNAs to create the functional open reading frame in 12 mRNAs. Thousands of sites are specifically recognized in the pre-edited mRNAs and a myriad of partially edited transcript intermediates accumulates in mitochondria. The control of editing is poorly understood, but past work suggests that it occurs during substrate recognition, the initiation and progression of editing, and during the life-cycle in different hosts. The growing understanding of the editing proteins offers clues about editing control. Most editing proteins reside in the "RNA-free" RNA editing core complex (RECC) and in the accessory RNA editing substrate complex (RESC) that contains gRNA. Two accessory RNA helicases are known, including one in the RNA editing helicase 2 complex (REH2C). Both the RESC and the REH2C associate with mRNA, providing a rationale for the assembly of mRNA or its mRNPs, RESC, and the RECC enzyme. Identified variants of the canonical editing complexes further complicate the model of RNA editing. We examine specific examples of complex variants, differential effects of editing proteins on the mRNAs within and between T. brucei life stages, and possible control points in RNA holo-editosomes. This article is categorized under: RNA Processing > RNA Editing and Modification RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Jorge Cruz-Reyes
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Blaine H M Mooers
- Department of Biochemistry & Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
| | - Pawan K Doharey
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Joshua Meehan
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Shelly Gulati
- Department of Biochemistry & Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma
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Recent advances in trypanosomatid research: genome organization, expression, metabolism, taxonomy and evolution. Parasitology 2018; 146:1-27. [PMID: 29898792 DOI: 10.1017/s0031182018000951] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Unicellular flagellates of the family Trypanosomatidae are obligatory parasites of invertebrates, vertebrates and plants. Dixenous species are aetiological agents of a number of diseases in humans, domestic animals and plants. Their monoxenous relatives are restricted to insects. Because of the high biological diversity, adaptability to dramatically different environmental conditions, and omnipresence, these protists have major impact on all biotic communities that still needs to be fully elucidated. In addition, as these organisms represent a highly divergent evolutionary lineage, they are strikingly different from the common 'model system' eukaryotes, such as some mammals, plants or fungi. A number of excellent reviews, published over the past decade, were dedicated to specialized topics from the areas of trypanosomatid molecular and cell biology, biochemistry, host-parasite relationships or other aspects of these fascinating organisms. However, there is a need for a more comprehensive review that summarizing recent advances in the studies of trypanosomatids in the last 30 years, a task, which we tried to accomplish with the current paper.
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Cultured bloodstream Trypanosoma brucei adapt to life without mitochondrial translation release factor 1. Sci Rep 2018; 8:5135. [PMID: 29572512 PMCID: PMC5865105 DOI: 10.1038/s41598-018-23472-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 03/13/2018] [Indexed: 01/07/2023] Open
Abstract
Trypanosoma brucei is an extracellular parasite that alternates between an insect vector (procyclic form) and the bloodstream of a mammalian host (bloodstream form). While it was previously reported that mitochondrial release factor 1 (TbMrf1) is essential in cultured procyclic form cells, we demonstrate here that in vitro bloodstream form cells can tolerate the elimination of TbMrf1. Therefore, we explored if this discrepancy is due to the unique bioenergetics of the parasite since procyclic form cells rely on oxidative phosphorylation; whereas bloodstream form cells utilize glycolysis for ATP production and FoF1-ATPase to maintain the essential mitochondrial membrane potential. The observed disruption of intact bloodstream form FoF1-ATPases serves as a proxy to indicate that the translation of its mitochondrially encoded subunit A6 is impaired without TbMrf1. While these null mutants have a decreased mitochondrial membrane potential, they have adapted by increasing their dependence on the electrogenic contributions of the ADP/ATP carrier to maintain the mitochondrial membrane potential above the minimum threshold required for T. brucei viability in vitro. However, this inefficient compensatory mechanism results in avirulent mutants in mice. Finally, the depletion of the codon-independent release factor TbPth4 in the TbMrf1 knockouts further exacerbates the characterized mitchondrial phenotypes.
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Aphasizhev R, Suematsu T, Zhang L, Aphasizheva I. Constructive edge of uridylation-induced RNA degradation. RNA Biol 2016; 13:1078-1083. [PMID: 27715485 PMCID: PMC5100348 DOI: 10.1080/15476286.2016.1229736] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 08/06/2016] [Accepted: 08/24/2016] [Indexed: 12/18/2022] Open
Abstract
RNA uridylation is a significant transcriptome-shaping factor in protists, fungi, metazoans, and plants. The 3' U-additions are catalyzed by terminal uridyltransferases (TUTases), a diverse group of enzymes that along with non-canonical poly(A) polymerases form a distinct group in the superfamily of DNA polymerase β-like nucleotidyl transferases. Within and across studied organisms and subcellular compartments, TUTases differ in nucleotide triphosphate selectivity, interacting partners, and RNA targets. A general premise linking RNA uridylation to 3'-5' degradation received support from several studies of small RNAs and mRNA turnover. However, recent work on kinetoplastid protists typified by Trypanosoma brucei provides evidence that RNA uridylation may play a more nuanced role in generating functional small RNAs. In this pathogen's mitochondrion, most mRNAs are internally edited by U-insertions and deletions, and subjected to 3' adenylation/uridylation; guide RNAs (gRNAs) required for editing are U-tailed. The prominent role of uridylation in mitochondrial RNA metabolism stimulated identification of the first TUTase, RNA editing TUTase 1 (RET1). Here we discuss functional studies of mitochondrial uridylation in trypanosomes that have revealed an unorthodox pathway of small RNA biogenesis. The current model accentuates physical coupling of RET1 and 3'-5' RNase II/RNB-type exonuclease DSS1 within a stable complex termed the mitochondrial 3' processome (MPsome). In the confines of this complex, RET1 initially uridylates a long precursor to activate its 3'-5' degradation by DSS1, and then uridylates trimmed guide RNA to disengage the processing complex from the mature molecule. We also discuss a potential role of antisense transcription in the MPsome pausing at a fixed distance from gRNA's 5' end. This step likely defines the mature 3' end by enabling kinetic competition between TUTase and exonuclease activities.
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Affiliation(s)
- Ruslan Aphasizhev
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA, USA
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA
| | - Takuma Suematsu
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA, USA
| | - Liye Zhang
- Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA
| | - Inna Aphasizheva
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA, USA
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16
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Cruz-Reyes J, Mooers BHM, Abu-Adas Z, Kumar V, Gulati S. DEAH-RHA helicase•Znf cofactor systems in kinetoplastid RNA editing and evolutionarily distant RNA processes. RNA & DISEASE 2016; 3. [PMID: 27540585 PMCID: PMC4987287 DOI: 10.14800/rd.1336] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Multi-zinc finger proteins are an emerging class of cofactors in DEAH-RHA RNA helicases across highly divergent eukaryotic lineages. DEAH-RHA helicase•zinc finger cofactor partnerships predate the split of kinetoplastid protozoa, which include several human pathogens, from other eukaryotic lineages 100-400 Ma. Despite a long evolutionary history, the prototypical DEAH-RHA domains remain highly conserved. This short review focuses on a recently identified DEAH-RHA helicase•zinc finger cofactor system in kinetoplastid RNA editing, and its potential functional parallels with analogous systems in embryogenesis control in nematodes and antivirus protection in humans.
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Affiliation(s)
- Jorge Cruz-Reyes
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Blaine H M Mooers
- Department of Biochemistry & Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Zakaria Abu-Adas
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Vikas Kumar
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Shelly Gulati
- Department of Biochemistry & Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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Suematsu T, Zhang L, Aphasizheva I, Monti S, Huang L, Wang Q, Costello CE, Aphasizhev R. Antisense Transcripts Delimit Exonucleolytic Activity of the Mitochondrial 3' Processome to Generate Guide RNAs. Mol Cell 2016; 61:364-378. [PMID: 26833087 PMCID: PMC4744118 DOI: 10.1016/j.molcel.2016.01.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 11/16/2015] [Accepted: 12/24/2015] [Indexed: 12/21/2022]
Abstract
Small, noncoding RNA biogenesis typically involves cleavage of structured precursor by RNase III-like endonucleases. However, guide RNAs (gRNAs) that direct U-insertion/deletion mRNA editing in mitochondria of trypanosomes maintain 5' triphosphate characteristic of the transcription initiation and possess a U-tail indicative of 3' processing and uridylation. Here, we identified a protein complex composed of RET1 TUTase, DSS1 3'-5' exonuclease, and three additional subunits. This complex, termed mitochondrial 3' processome (MPsome), is responsible for primary uridylation of ∼800 nt gRNA precursors, their processive degradation to a mature size of 40-60 nt, and secondary U-tail addition. Both strands of the gRNA gene are transcribed into sense and antisense precursors of similar lengths. Head-to-head hybridization of these transcripts blocks symmetrical 3'-5' degradation at a fixed distance from the double-stranded region. Together, our findings suggest a model in which gRNA is derived from the 5' extremity of a primary molecule by uridylation-induced, antisense transcription-controlled 3'-5' exonucleolytic degradation.
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Affiliation(s)
- Takuma Suematsu
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA 02118, USA
| | - Liye Zhang
- Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Inna Aphasizheva
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, Boston, MA 02118, USA
| | - Stefano Monti
- Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Lan Huang
- Department of Physiology & Biophysics, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA
| | - Qi Wang
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Catherine E Costello
- Department of Biochemistry, Boston University School of 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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18
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Dietrich A, Wallet C, Iqbal RK, Gualberto JM, Lotfi F. Organellar non-coding RNAs: Emerging regulation mechanisms. Biochimie 2015; 117:48-62. [DOI: 10.1016/j.biochi.2015.06.027] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 06/29/2015] [Indexed: 02/06/2023]
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19
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Mooers BHM. Fusion RNAs in crystallographic studies of double-stranded RNA from trypanosome RNA editing. Methods Mol Biol 2015; 1240:191-216. [PMID: 25352146 DOI: 10.1007/978-1-4939-1896-6_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Head-to-head fusions of two identical double-stranded fragments of RNA can be designed to self-assemble from a single RNA species and form a double-stranded helix with a twofold rotation axis relating the two strands. These symmetrical RNA molecules are more likely to crystallize without end-on-end statistical packing disorder because the two halves of the molecule are identical. This approach can be used to study many fragments of double-stranded RNA or many isolated helical domains from large single-stranded RNAs that may not yet be amenable to high-resolution studies by crystallography or NMR. We used fusion RNAs to study one (the U-helix) of three functional domains formed when guide RNA binds to its cognate pre-edited mRNA from the trypanosome RNA editing system. The U-helix forms when the 3' oligo(U) tail of the guide RNA (gRNA) binds to the purine-rich, pre-edited mRNA upstream from the current RNA editing site. Fusion RNAs 16-and 32-base pairs in length formed crystals that gave diffraction to 1.37 and 1.05 Å respectively. We provide the composition of a fusion RNA crystallization screen and describe the X-ray data collection, structure determination, and refinement of the crystal structures of fusion RNAs.
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Affiliation(s)
- Blaine H M Mooers
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, 975 NE 10th St., Stanton L. Young Biomedical Research Center Rm. 466, Oklahoma City, OK, 73104-5419, USA,
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20
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Polyuridylation in Eukaryotes: A 3'-End Modification Regulating RNA Life. BIOMED RESEARCH INTERNATIONAL 2015; 2015:968127. [PMID: 26078976 PMCID: PMC4442281 DOI: 10.1155/2015/968127] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 03/23/2015] [Accepted: 04/15/2015] [Indexed: 12/22/2022]
Abstract
In eukaryotes, mRNA polyadenylation is a well-known modification that is essential for many aspects of the protein-coding RNAs life cycle. However, modification of the 3′ terminal nucleotide within various RNA molecules is a general and conserved process that broadly modulates RNA function in all kingdoms of life. Numerous types of modifications have been characterized, which are generally specific for a given type of RNA such as the CCA addition found in tRNAs. In recent years, the addition of nontemplated uridine nucleotides or uridylation has been shown to occur in various types of RNA molecules and in various cellular compartments with significantly different outcomes. Indeed, uridylation is able to alter RNA half-life both in positive and in negative ways, highlighting the importance of the enzymes in charge of performing this modification. The present review aims at summarizing the current knowledge on the various processes leading to RNA 3′-end uridylation and on their potential impacts in various diseases.
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21
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Aphasizheva I, Zhang L, Wang X, Kaake RM, Huang L, Monti S, Aphasizhev R. RNA binding and core complexes constitute the U-insertion/deletion editosome. Mol Cell Biol 2014; 34:4329-42. [PMID: 25225332 PMCID: PMC4248751 DOI: 10.1128/mcb.01075-14] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 09/02/2014] [Accepted: 09/11/2014] [Indexed: 12/19/2022] Open
Abstract
Enzymes embedded into the RNA editing core complex (RECC) catalyze the U-insertion/deletion editing cascade to generate open reading frames in trypanosomal mitochondrial mRNAs. The sequential reactions of mRNA cleavage, U-addition or removal, and ligation are directed by guide RNAs (gRNAs). We combined proteomic, genetic, and functional studies with sequencing of total and complex-bound RNAs to define a protein particle responsible for the recognition of gRNAs and pre-mRNA substrates, editing intermediates, and products. This approximately 23-polypeptide tripartite assembly, termed the RNA editing substrate binding complex (RESC), also functions as the interface between mRNA editing, polyadenylation, and translation. Furthermore, we found that gRNAs represent only a subset of small mitochondrial RNAs, and yet an inexplicably high fraction of them possess 3' U-tails, which correlates with gRNA's enrichment in the RESC. Although both gRNAs and mRNAs are associated with the RESC, their metabolic fates are distinct: gRNAs are degraded in an editing-dependent process, whereas edited mRNAs undergo 3' adenylation/uridylation prior to translation. Our results demonstrate that the well-characterized editing core complex (RECC) and the RNA binding particle defined in this study (RESC) typify enzymatic and substrate binding macromolecular constituents, respectively, of the ∼40S RNA editing holoenzyme, the editosome.
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MESH Headings
- Base Sequence
- Mitochondria/genetics
- Open Reading Frames/genetics
- Peptide Chain Elongation, Translational/genetics
- Polyadenylation/genetics
- Protozoan Proteins/metabolism
- RNA/genetics
- RNA Editing/genetics
- RNA Interference
- RNA, Catalytic/genetics
- RNA, Guide, Kinetoplastida/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Mitochondrial
- RNA, Protozoan/genetics
- RNA, Small Interfering
- RNA-Binding Proteins/genetics
- Sequence Analysis, RNA
- Trypanosoma brucei brucei/genetics
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Affiliation(s)
- Inna Aphasizheva
- Department of Molecular and Cell Biology, Boston University Goldman School of Dental Medicine, Boston, Massachusetts, USA
| | - Liye Zhang
- Section of Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Xiaorong Wang
- Department of Physiology & Biophysics, School of Medicine, University of California, Irvine, Irvine, California, USA
| | - Robyn M Kaake
- Department of Physiology & Biophysics, School of Medicine, University of California, Irvine, Irvine, California, USA
| | - Lan Huang
- Department of Physiology & Biophysics, School of Medicine, University of California, Irvine, Irvine, California, USA
| | - Stefano Monti
- Section of Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Ruslan Aphasizhev
- Department of Molecular and Cell Biology, Boston University Goldman School of Dental Medicine, Boston, Massachusetts, USA Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts, USA
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22
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Moshiri H, Mehta V, Yip CW, Salavati R. Pilot-scale compound screening against RNA editing identifies trypanocidal agents. ACTA ACUST UNITED AC 2014; 20:92-100. [PMID: 25170016 DOI: 10.1177/1087057114548833] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Most mitochondrial messenger RNAs in trypanosomatid pathogens undergo a unique type of posttranscriptional modification involving insertion and/or deletion of uridylates. This process, RNA editing, is catalyzed by a multiprotein complex (~1.6 MDa), the editosome. Knockdown of core editosome proteins compromises mitochondrial function and, ultimately, parasite viability. Hence, because the editosome is restricted to trypanosomatids, it serves as a unique drug target in these pathogens. Currently, there is a lack of editosome inhibitors for antitrypanosomatid drug development or that could serve as unique tools for perturbing and characterizing editosome interactions or RNA editing reaction stages. Here, we screened a library of pharmacologically active compounds (LOPAC1280) using high-throughput screening to identify RNA editing inhibitors. We report that aurintricarboxylic acid, mitoxantrone, PPNDS, and NF449 are potent inhibitors of deletion RNA editing (IC50 range, 1-5 µM). However, none of these compounds could specifically inhibit the catalytic steps of RNA editing. Mitoxantrone blocked editing by inducing RNA-protein aggregates, whereas the other three compounds interfered with editosome-RNA interactions to varying extents. Furthermore, NF449, a suramin analogue, was effective at killing Trypanosoma brucei in vitro. Thus, new tools for editosome characterization and downstream RNA editing inhibitor have been identified.
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Affiliation(s)
- Houtan Moshiri
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada Institute of Parasitology, McGill University, Montreal, Quebec, Canada
| | - Vaibhav Mehta
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada Institute of Parasitology, McGill University, Montreal, Quebec, Canada
| | - Chun Wai Yip
- Institute of Parasitology, McGill University, Montreal, Quebec, Canada
| | - Reza Salavati
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada Institute of Parasitology, McGill University, Montreal, Quebec, Canada McGill Centre for Bioinformatics, McGill University, Montreal, Quebec, Canada
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23
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Moshiri H, Mehta V, Salavati R. RNA catalyst as a reporter for screening drugs against RNA editing in trypanosomes. J Vis Exp 2014. [PMID: 25079143 DOI: 10.3791/51712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Substantial progress has been made in determining the mechanism of mitochondrial RNA editing in trypanosomes. Similarly, considerable progress has been made in identifying the components of the editosome complex that catalyze RNA editing. However, it is still not clear how those proteins work together. Chemical compounds obtained from a high-throughput screen against the editosome may block or affect one or more steps in the editing cycle. Therefore, the identification of new chemical compounds will generate valuable molecular probes for dissecting the editosome function and assembly. In previous studies, in vitro editing assays were carried out using radio-labeled RNA. These assays are time consuming, inefficient and unsuitable for high-throughput purposes. Here, a homogenous fluorescence-based "mix and measure" hammerhead ribozyme in vitro reporter assay to monitor RNA editing, is presented. Only as a consequence of RNA editing of the hammerhead ribozyme a fluorescence resonance energy transfer (FRET) oligoribonucleotide substrate undergoes cleavage. This in turn results in separation of the fluorophore from the quencher thereby producing a signal. In contrast, when the editosome function is inhibited, the fluorescence signal will be quenched. This is a highly sensitive and simple assay that should be generally applicable to monitor in vitro RNA editing or high throughput screening of chemicals that can inhibit the editosome function.
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Affiliation(s)
- Houtan Moshiri
- Department of Biochemistry, McGill University; Institute of Parasitology, McGill University
| | - Vaibhav Mehta
- Department of Biochemistry, McGill University; Institute of Parasitology, McGill University
| | - Reza Salavati
- Department of Biochemistry, McGill University; Institute of Parasitology, McGill University; McGill Centre for Bioinformatics, McGill University;
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Aphasizhev R, Aphasizheva I. Mitochondrial RNA editing in trypanosomes: small RNAs in control. Biochimie 2014; 100:125-31. [PMID: 24440637 PMCID: PMC4737708 DOI: 10.1016/j.biochi.2014.01.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 01/06/2014] [Indexed: 12/29/2022]
Abstract
Mitochondrial mRNA editing in trypanosomes is a posttranscriptional processing pathway thereby uridine residues (Us) are inserted into, or deleted from, messenger RNA precursors. By correcting frameshifts, introducing start and stop codons, and often adding most of the coding sequence, editing restores open reading frames for mitochondrially-encoded mRNAs. There can be hundreds of editing events in a single pre-mRNA, typically spaced by few nucleotides, with U-insertions outnumbering U-deletions by approximately 10-fold. The mitochondrial genome is composed of ∼50 maxicircles and thousands of minicircles. Catenated maxi- and minicircles are packed into a dense structure called the kinetoplast; maxicircles yield rRNA and mRNA precursors while guide RNAs (gRNAs) are produced predominantly from minicircles, although varying numbers of maxicircle-encoded gRNAs have been identified in kinetoplastids species. Guide RNAs specify positions and the numbers of inserted or deleted Us by hybridizing to pre-mRNA and forming series of mismatches. These 50-60 nucleotide (nt) molecules are 3' uridylated by RET1 TUTase and stabilized via association with the gRNA binding complex (GRBC). Editing reactions of mRNA cleavage, U-insertion or deletion, and ligation are catalyzed by the RNA editing core complex (RECC). To function in mitochondrial translation, pre-mRNAs must further undergo post-editing 3' modification by polyadenylation/uridylation. Recent studies revealed a highly compound nature of mRNA editing and polyadenylation complexes and their interactions with the translational machinery. Here we focus on mechanisms of RNA editing and its functional coupling with pre- and post-editing 3' mRNA modification and gRNA maturation pathways.
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Affiliation(s)
- Ruslan Aphasizhev
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, 72 East Concord Street, Evans 4th Floor, E426, Boston, MA 02118, USA.
| | - Inna Aphasizheva
- Department of Molecular and Cell Biology, Boston University School of Dental Medicine, 72 East Concord Street, Evans 4th Floor, E426, Boston, MA 02118, USA
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25
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Aphasizheva I, Maslov DA, Aphasizhev R. Kinetoplast DNA-encoded ribosomal protein S12: a possible functional link between mitochondrial RNA editing and translation in Trypanosoma brucei. RNA Biol 2013; 10:1679-88. [PMID: 24270388 DOI: 10.4161/rna.26733] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Mitochondrial ribosomes of Trypanosoma brucei are composed of 9S and 12S rRNAs, which are encoded by the kinetoplast genome, and more than 150 proteins encoded in the nucleus and imported from the cytoplasm. However, a single ribosomal protein RPS12 is encoded by the kinetoplast DNA (kDNA) in all trypanosomatid species examined. As typical for these organisms, the gene itself is cryptic and its transcript undergoes an extensive U-insertion/deletion editing. An evolutionary trend to reduce or eliminate RNA editing could be traced with other cryptogenes, but the invariably pan-edited RPS12 cryptogene is apparently spared. Here we inquired whether editing of RPS12 mRNA is essential for mitochondrial translation. By RNAi-mediated knockdowns of RNA editing complexes and inducible knock-in of a key editing enzyme in procyclic parasites, we could reversibly downregulate production of edited RPS12 mRNA and, by inference, synthesis of this protein. While inhibition of editing decreased edited mRNA levels, the translation of edited (Cyb) and unedited (COI) mRNAs was blocked. Furthermore, the population of SSU-related 45S complexes declined upon inactivation of editing and so did the amount of mRNA-bound ribosomes. In bloodstream parasites, which lack active electron transport chain but still require translation of ATP synthase subunit 6 mRNA (A6), both edited RPS12 and A6 mRNAs were detected in translation complexes. Collectively, our results indicate that a single ribosomal protein gene retained by the kinetoplast mitochondrion serves as a possible functional link between editing and translation processes and provide the rationale for the evolutionary conservation of RPS12 pan-editing.
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Affiliation(s)
- Inna Aphasizheva
- Department of Molecular and Cell Biology; Boston University Goldman School of Dental Medicine; Boston, MA USA
| | - Dmitri A Maslov
- Department of Biology; University of California at Riverside; Riverside, CA USA
| | - Ruslan Aphasizhev
- Department of Molecular and Cell Biology; Boston University Goldman School of Dental Medicine; Boston, MA USA
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Kolesnikov AA, Gerasimov ES. Diversity of mitochondrial genome organization. BIOCHEMISTRY (MOSCOW) 2013; 77:1424-35. [PMID: 23379519 DOI: 10.1134/s0006297912130020] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In this review, we discuss types of mitochondrial genome structural organization (architecture), which includes the following characteristic features: size and the shape of DNA molecule, number of encoded genes, presence of cryptogenes, and editing of primary transcripts.
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Affiliation(s)
- A A Kolesnikov
- Biological Faculty, Lomonosov Moscow State University, Moscow, 119234, Russia.
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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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Abstract
RNA editing describes a chemically diverse set of biomolecular reactions in which the nucleotide sequence of RNA molecules is altered. Editing reactions have been identified in many organisms and frequently contribute to the maturation of organellar transcripts. A special editing reaction has evolved within the mitochondria of the kinetoplastid protozoa. The process is characterized by the insertion and deletion of uridine nucleotides into otherwise nontranslatable messenger RNAs. Kinetoplastid RNA editing involves an exclusive class of small, noncoding RNAs known as guide RNAs. Furthermore, a unique molecular machinery, the editosome, catalyzes the process. Editosomes are megadalton multienzyme assemblies that provide a catalytic surface for the individual steps of the reaction cycle. Here I review the current mechanistic understanding and molecular inventory of kinetoplastid RNA editing and the editosome machinery. Special emphasis is placed on the molecular morphology of the editing complex in order to correlate structural features with functional characteristics.
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Affiliation(s)
- H Ulrich Göringer
- Department of Genetics, Darmstadt University of Technology, Germany.
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Kala S, Moshiri H, Mehta V, Yip CW, Salavati R. The oligonucleotide binding (OB)-fold domain of KREPA4 is essential for stable incorporation into editosomes. PLoS One 2012; 7:e46864. [PMID: 23056494 PMCID: PMC3464273 DOI: 10.1371/journal.pone.0046864] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 09/06/2012] [Indexed: 12/28/2022] Open
Abstract
Most mitochondrial mRNAs in trypanosomatid parasites require uridine insertion/deletion RNA editing, a process mediated by guide RNA (gRNA) and catalyzed by multi-protein complexes called editosomes. The six oligonucleotide/oligosaccharide binding (OB)-fold proteins (KREPA1-A6), are a part of the common core of editosomes. They form a network of interactions among themselves as well as with the insertion and deletion sub-complexes and are essential for the stability of the editosomes. KREPA4 and KREPA6 proteins bind gRNA in vitro and are known to interact directly in yeast two-hybrid analysis. In this study, using several approaches we show a minimal interaction surface of the KREPA4 protein that is required for this interaction. By screening a series of N- and C-terminally truncated KREPA4 fragments, we show that a predicted α-helix of KREPA4 OB-fold is required for its interaction with KREPA6. An antibody against the KREPA4 α-helix or mutations of this region can eliminate association with KREPA6; while a peptide fragment corresponding to the α-helix can independently interact with KREPA6, thereby supporting the identification of KREPA4-KREPA6 interface. We also show that the predicted OB-fold of KREPA4; independent of its interaction with gRNA, is responsible for the stable integration of KREPA4 in the editosomes, and editing complexes co-purified with the tagged OB-fold can catalyze RNA editing. Therefore, we conclude that while KREPA4 interacts with KREPA6 through the α-helix region of its OB-fold, the entire OB-fold is required for its integration in the functional editosome, through additional protein-protein interactions.
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Affiliation(s)
- Smriti Kala
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec, Canada
| | - Houtan Moshiri
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec, Canada
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Vaibhav Mehta
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec, Canada
| | - Chun Wai Yip
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec, Canada
| | - Reza Salavati
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec, Canada
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- McGill Centre for Bioinformatics, McGill University, Montreal, Quebec, Canada
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Carnes J, Schnaufer A, McDermott SM, Domingo G, Proff R, Steinberg AG, Kurtz I, Stuart K. Mutational analysis of Trypanosoma brucei editosome proteins KREPB4 and KREPB5 reveals domains critical for function. RNA (NEW YORK, N.Y.) 2012; 18:1897-1909. [PMID: 22919050 PMCID: PMC3446712 DOI: 10.1261/rna.035048.112] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 07/16/2012] [Indexed: 05/29/2023]
Abstract
The transcriptome of kinetoplastid mitochondria undergoes extensive RNA editing that inserts and deletes uridine residues (U's) to produce mature mRNAs. The editosome is a multiprotein complex that provides endonuclease, TUTase, exonuclease, and ligase activities required for RNA editing. The editosome's KREPB4 and KREPB5 proteins are essential for editosome integrity and parasite viability and contain semi-conserved motifs corresponding to zinc finger, RNase III, and PUF domains, but to date no functional analysis of these domains has been reported. We show here that various point mutations to KREPB4 and KREPB5 identify essential domains, and suggest that these proteins do not themselves perform RNase III catalysis. The zinc finger of KREPB4 but not KREPB5 is essential for editosome integrity and parasite viability, and mutation of the RNase III signature motif in KREPB5 prevents integration into editosomes, which is lethal. Isolated TAP-tagged KREPB4 and KREPB5 complexes preferentially associate with components of the deletion subcomplex, providing additional insights into editosome architecture. A new alignment of editosome RNase III sequences from several kinetoplastid species implies that KREPB4 and KREPB5 lack catalytic activity and reveals that the PUF motif is present in the editing endonucleases KREN1, KREN2, and KREN3. The data presented here are consistent with the hypothesis that KREPB4 and KREPB5 form intermolecular heterodimers with the catalytically active editing endonucleases, which is unprecedented among known RNase III proteins.
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Affiliation(s)
- Jason Carnes
- Seattle Biomedical Research Institute, Seattle, Washington 98109, USA
| | - Achim Schnaufer
- Seattle Biomedical Research Institute, Seattle, Washington 98109, USA
| | | | - Gonzalo Domingo
- Seattle Biomedical Research Institute, Seattle, Washington 98109, USA
| | - Rose Proff
- Seattle Biomedical Research Institute, Seattle, Washington 98109, USA
| | | | - Irina Kurtz
- Seattle Biomedical Research Institute, Seattle, Washington 98109, USA
| | - Kenneth Stuart
- Seattle Biomedical Research Institute, Seattle, Washington 98109, USA
- Department of Global Health, University of Washington, Seattle, Washington 98195, USA
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Editosome accessory factors KREPB9 and KREPB10 in Trypanosoma brucei. EUKARYOTIC CELL 2012; 11:832-43. [PMID: 22562468 DOI: 10.1128/ec.00046-12] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Multiprotein complexes, called editosomes, catalyze the uridine insertion and deletion RNA editing that forms translatable mitochondrial mRNAs in kinetoplastid parasites. We have identified here two new U1-like zinc finger proteins that associate with editosomes and have shown that they are related to KREPB6, KREPB7, and KREPB8, and thus we have named them Kinetoplastid RNA Editing Proteins, KREPB9 and KREPB10. They are conserved and syntenic in trypanosomatids although KREPB10 is absent in Trypanosoma vivax and both are absent in Leishmania. Tandem affinity purification (TAP)-tagged KREPB9 and KREPB10 incorporate into ~20S editosomes and/or subcomplexes thereof and preferentially associate with deletion subcomplexes, as do KREPB6, KREPB7, and KREPB8. KREPB10 also associates with editosomes that are isolated via a chimeric endonuclease, KREN1 in KREPB8 RNA interference (RNAi) cells, or MEAT1. The purified complexes have precleaved editing activities and endonuclease cleavage activity that appears to leave a 5' OH on the 3' product. RNAi knockdowns did not affect growth but resulted in relative reductions of both edited and unedited mitochondrial mRNAs. The similarity of KREPB9 and KREPB10 to KREPB6, KREPB7, and KREPB8 suggests they may be accessory factors that affect editing endonuclease activity and as a consequence may affect mitochondrial mRNA stability. KREPB9 and KREPB10, along with KREPB6, KREPB7, and KREPB8, may enable the endonucleases to discriminate among and accurately cleave hundreds of different editing sites and may be involved in the control of differential editing during the life cycle of T. brucei.
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mRNA 3' tagging is induced by nonsense-mediated decay and promotes ribosome dissociation. Mol Cell Biol 2012; 32:2585-95. [PMID: 22547684 DOI: 10.1128/mcb.00316-12] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
For a range of eukaryote transcripts, the initiation of degradation is coincident with the addition of a short pyrimidine tag at the 3' end. Previously, cytoplasmic mRNA tagging has been observed for human and fungal transcripts. We now report that Arabidopsis thaliana mRNA is subject to 3' tagging with U and C nucleotides, as in Aspergillus nidulans. Mutations that disrupt tagging, including A. nidulans cutA and a newly characterized gene, cutB, retard transcript degradation. Importantly, nonsense-mediated decay (NMD), a major checkpoint for transcript fidelity, elicits 3' tagging of transcripts containing a premature termination codon (PTC). Although PTC-induced transcript degradation does not require 3' tagging, subsequent dissociation of mRNA from ribosomes is retarded in tagging mutants. Additionally, tagging of wild-type and NMD-inducing transcripts is greatly reduced in strains lacking Upf1, a conserved NMD factor also required for human histone mRNA tagging. We argue that PTC-induced translational termination differs fundamentally from normal termination in polyadenylated transcripts, as it leads to transcript degradation and prevents rather than facilitates further translation. Furthermore, transcript deadenylation and the consequent dissociation of poly(A) binding protein will result in PTC-like termination events which recruit Upf1, resulting in mRNA 3' tagging, ribosome clearance, and transcript degradation.
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Carnes J, Lewis Ernst N, Wickham C, Panicucci B, Stuart K. KREX2 is not essential for either procyclic or bloodstream form Trypanosoma brucei. PLoS One 2012; 7:e33405. [PMID: 22438925 PMCID: PMC3305318 DOI: 10.1371/journal.pone.0033405] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 02/13/2012] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Most mitochondrial mRNAs in Trypanosoma brucei require RNA editing for maturation and translation. The edited RNAs primarily encode proteins of the oxidative phosphorylation system. These parasites undergo extensive changes in energy metabolism between the insect and bloodstream stages which are mirrored by alterations in RNA editing. Two U-specific exonucleases, KREX1 and KREX2, are both present in protein complexes (editosomes) that catalyze RNA editing but the relative roles of each protein are not known. METHODOLOGY/PRINCIPAL FINDINGS The requirement for KREX2 for RNA editing in vivo was assessed in both procyclic (insect) and bloodstream form parasites by methods that use homologous recombination for gene elimination. These studies resulted in null mutant cells in which both alleles were eliminated. The viability of these cells demonstrates that KREX2 is not essential in either life cycle stage, despite certain defects in RNA editing in vivo. Furthermore, editosomes isolated from KREX2 null cells require KREX1 for in vitro U-specific exonuclease activity. CONCLUSIONS KREX2 is a U-specific exonuclease that is dispensable for RNA editing in vivo in T. brucei BFs and PFs. This result suggests that the U deletion activity, which is required for RNA editing, is primarily mediated in vivo by KREX1 which is normally found associated with only one type of editosome. The retention of the KREX2 gene implies a non-essential role or a role that is essential in other life cycle stages or conditions.
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Affiliation(s)
- Jason Carnes
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Nancy Lewis Ernst
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Carey Wickham
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Brian Panicucci
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Kenneth Stuart
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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Guo X, Carnes J, Ernst NL, Winkler M, Stuart K. KREPB6, KREPB7, and KREPB8 are important for editing endonuclease function in Trypanosoma brucei. RNA (NEW YORK, N.Y.) 2012; 18:308-20. [PMID: 22184461 PMCID: PMC3264917 DOI: 10.1261/rna.029314.111] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Accepted: 10/31/2011] [Indexed: 05/19/2023]
Abstract
Three distinct editosomes are required for the uridine insertion/deletion editing that creates translatable mitochondrial mRNAs in Trypanosoma brucei. They contain KREPB6, KREPB7, or KREPB8 proteins and their respective endonucleases KREN3, KREN2, or KREN1. RNAi knockdowns of KREPB6, KREPB7, and KREPB8 variably affect growth and RNA editing. KREPB6 and KREPB7 knockdowns substantially reduced in vitro insertion site cleavage activity of their respective editosomes, while KREPB8 knockdown did not affect its editosome deletion site cleavage activity despite inhibition of growth and editing. KREPB6, KREPB7, and KREPB8 knockdowns disrupted tagged KREN3, KREN2, or KREN1 editosomes, respectively, to varying degrees, and in the case of KREN1 editosomes, the deletion editing site cleavage activity shifted to a smaller S value. The varying effects correlate with a combination of the relative abundances of the KREPB6-8 proteins and of the different insertion and deletion sites. Tagged KREPB6-8 were physically associated with deletion subcomplexes upon knockdown of the centrally interactive KREPA3 protein, while KREN1-3 endonucleases were associated with insertion subcomplexes. The results indicate that KREPB6-8 occupy similar positions in editosomes and are important for the activity and specificity of their respective endonucleases. This suggests that they contribute to the accurate recognition of the numerous similar but diverse editing site substrates.
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Affiliation(s)
- Xuemin Guo
- Seattle Biomedical Research Institute, Seattle, Washington 98109, USA
| | - Jason Carnes
- Seattle Biomedical Research Institute, Seattle, Washington 98109, USA
| | - Nancy Lewis Ernst
- Seattle Biomedical Research Institute, Seattle, Washington 98109, USA
| | - Matt Winkler
- Seattle Biomedical Research Institute, Seattle, Washington 98109, USA
| | - Kenneth Stuart
- Seattle Biomedical Research Institute, Seattle, Washington 98109, USA
- Department of Global Health, University of Washington, Seattle, Washington 98195, USA
- Corresponding author.E-mail .
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Salavati R, Moshiri H, Kala S, Shateri Najafabadi H. Inhibitors of RNA editing as potential chemotherapeutics against trypanosomatid pathogens. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2011; 2:36-46. [PMID: 24533263 DOI: 10.1016/j.ijpddr.2011.10.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 10/17/2011] [Accepted: 10/21/2011] [Indexed: 01/14/2023]
Abstract
The related trypanosomatid pathogens, Trypanosoma brucei spp., Trypanosoma cruzi and Leishmania spp. cause devastating diseases in humans and animals and continue to pose a major challenge in drug development. Mitochondrial RNA editing, catalyzed by multi-protein complexes known as editosomes, has provided an opportunity for development of efficient and specific chemotherapeutic targets against trypanosomatid pathogens. This review will discuss both methods for discovery of RNA editing inhibitors, as well as inhibitors against the T. brucei editosome that were recently discovered through creative virtual and high throughput screening methods. In addition, the use of these inhibitors as agents that can block or perturb one or more steps of the RNA editing process will be discussed. These inhibitors can potentially be used to study the dynamic processing and assembly of the editosome proteins. A thorough understanding of the mechanisms and specificities of these new inhibitors is needed in order to contribute to both the functional studies of an essential gene expression mechanism and to the possibility of future drug development against the trypanosomatid pathogens.
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Affiliation(s)
- Reza Salavati
- Department of Biochemistry, McGill University, McIntyre Medical Building, 3655 Promenade Sir William Osler, Montreal, Quebec, Canada H3G1Y6 ; Institute of Parasitology, McGill University, 21111 Lakeshore Road, Ste. Anne de Bellevue, Quebec, Canada H9X3V9 ; McGill Centre for Bioinformatics, McGill University, Bellini Building, 3649 Promenade Sir William Osler, Montreal, Quebec, Canada H3G0B1
| | - Houtan Moshiri
- Department of Biochemistry, McGill University, McIntyre Medical Building, 3655 Promenade Sir William Osler, Montreal, Quebec, Canada H3G1Y6 ; Institute of Parasitology, McGill University, 21111 Lakeshore Road, Ste. Anne de Bellevue, Quebec, Canada H9X3V9
| | - Smriti Kala
- Institute of Parasitology, McGill University, 21111 Lakeshore Road, Ste. Anne de Bellevue, Quebec, Canada H9X3V9
| | - Hamed Shateri Najafabadi
- Institute of Parasitology, McGill University, 21111 Lakeshore Road, Ste. Anne de Bellevue, Quebec, Canada H9X3V9 ; McGill Centre for Bioinformatics, McGill University, Bellini Building, 3649 Promenade Sir William Osler, Montreal, Quebec, Canada H3G0B1
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Mooers BHM, Singh A. The crystal structure of an oligo(U):pre-mRNA duplex from a trypanosome RNA editing substrate. RNA (NEW YORK, N.Y.) 2011; 17:1870-1883. [PMID: 21878548 PMCID: PMC3185919 DOI: 10.1261/rna.2880311] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 07/30/2011] [Indexed: 05/31/2023]
Abstract
Guide RNAs bind antiparallel to their target pre-mRNAs to form editing substrates in reaction cycles that insert or delete uridylates (Us) in most mitochondrial transcripts of trypanosomes. The 5' end of each guide RNA has an anchor sequence that binds to the pre-mRNA by base-pair complementarity. The template sequence in the middle of the guide RNA directs the editing reactions. The 3' ends of most guide RNAs have ∼15 contiguous Us that bind to the purine-rich unedited pre-mRNA upstream of the editing site. The resulting U-helix is rich in G·U wobble base pairs. To gain insights into the structure of the U-helix, we crystallized 8 bp of the U-helix in one editing substrate for the A6 mRNA of Trypanosoma brucei. The fragment provides three samples of the 5'-AGA-3'/5'-UUU-3' base-pair triple. The fusion of two identical U-helices head-to-head promoted crystallization. We obtained X-ray diffraction data with a resolution limit of 1.37 Å. The U-helix had low and high twist angles before and after each G·U wobble base pair; this variation was partly due to shearing of the wobble base pairs as revealed in comparisons with a crystal structure of a 16-nt RNA with all Watson-Crick base pairs. Both crystal structures had wider major grooves at the junction between the poly(U) and polypurine tracts. This junction mimics the junction between the template helix and the U-helix in RNA-editing substrates and may be a site of major groove invasion by RNA editing proteins.
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Affiliation(s)
- Blaine H M Mooers
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104-5419, USA.
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Aphasizhev R, Aphasizheva I. Uridine insertion/deletion editing in trypanosomes: a playground for RNA-guided information transfer. WILEY INTERDISCIPLINARY REVIEWS. RNA 2011; 2:669-85. [PMID: 21823228 PMCID: PMC3154072 DOI: 10.1002/wrna.82] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
RNA editing is a collective term referring to enzymatic processes that change RNA sequence apart from splicing, 5' capping or 3' extension. In this article, we focus on uridine insertion/deletion mRNA editing found exclusively in mitochondria of kinetoplastid protists. This type of editing corrects frameshifts, introduces start and stops codons, and often adds much of the coding sequence to create an open reading frame. The mitochondrial genome of trypanosomatids, the most extensively studied clade within the order Kinetoplastida, is composed of ∼50 maxicircles with limited coding capacity and thousands of minicircles. To produce functional mRNAs, a multitude of nuclear-encoded factors mediate interactions of maxicircle-encoded pre-mRNAs with a vast repertoire of minicircle-encoded guide RNAs. Editing reactions of mRNA cleavage, U-insertions or U-deletions, and ligation are catalyzed by the RNA editing core complex (RECC, the 20S editosome) while each step of this enzymatic cascade is directed by guide RNAs. These 50-60 nucleotide (nt) molecules are 3' uridylated by RET1 TUTase and stabilized via association with the gRNA binding complex (GRBC). Remarkably, the information transfer between maxicircle and minicircle transcriptomes does not rely on template-dependent polymerization of nucleic acids. Instead, intrinsic substrate specificities of key enzymes are largely responsible for the fidelity of editing. Conversely, the efficiency of editing is enhanced by assembling enzymes and RNA binding proteins into stable multiprotein complexes. WIREs RNA 2011 2 669-685 DOI: 10.1002/wrna.82 For further resources related to this article, please visit the WIREs website.
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MESH Headings
- Endonucleases/chemistry
- Endonucleases/genetics
- Endonucleases/metabolism
- Models, Biological
- Models, Molecular
- Protozoan Proteins/chemistry
- Protozoan Proteins/genetics
- Protozoan Proteins/metabolism
- RNA Editing/genetics
- RNA Editing/physiology
- RNA Helicases/chemistry
- RNA Helicases/genetics
- RNA Helicases/metabolism
- RNA, Guide, Kinetoplastida/genetics
- RNA, Guide, Kinetoplastida/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Protozoan/chemistry
- RNA, Protozoan/genetics
- RNA, Protozoan/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Trypanosoma/genetics
- Trypanosoma/metabolism
- Uridine/chemistry
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Affiliation(s)
- Ruslan Aphasizhev
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, USA.
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Aphasizheva I, Maslov D, Wang X, Huang L, Aphasizhev R. Pentatricopeptide repeat proteins stimulate mRNA adenylation/uridylation to activate mitochondrial translation in trypanosomes. Mol Cell 2011; 42:106-17. [PMID: 21474072 DOI: 10.1016/j.molcel.2011.02.021] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2010] [Revised: 12/10/2010] [Accepted: 01/20/2011] [Indexed: 01/10/2023]
Abstract
The majority of trypanosomal mitochondrial pre-mRNAs undergo massive uridine insertion/deletion editing, which creates open reading frames. Although the pre-editing addition of short 3' A tails is known to stabilize transcripts during and after the editing, the processing event committing the fully edited mRNAs to translation remained unknown. Here, we show that a heterodimer of pentatricopeptide repeat-containing (PPR) proteins, termed kinetoplast polyadenylation/uridylation factors (KPAFs) 1 and 2, induces the postediting addition of A/U heteropolymers by KPAP1 poly(A) polymerase and RET1 terminal uridyltransferase. Edited transcripts bearing 200- to 300-nucleotide-long A/U tails, but not short A tails, were enriched in translating ribosomal complexes and affinity-purified ribosomal particles. KPAF1 repression led to a selective loss of A/U-tailed mRNAs and concomitant inhibition of protein synthesis. These results establish A/U extensions as the defining cis-elements of translation-competent mRNAs. Furthermore, we demonstrate that A/U-tailed mRNA preferentially interacts with the small ribosomal subunit, whereas edited substrates and complexes bind to the large subunit.
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Affiliation(s)
- Inna Aphasizheva
- Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, Irvine, CA 92697, USA
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Göringer HU, Katari VS, Böhm C. The structural landscape of native editosomes in African trypanosomes. WILEY INTERDISCIPLINARY REVIEWS. RNA 2011; 2:395-407. [PMID: 21957025 DOI: 10.1002/wrna.67] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The majority of mitochondrial pre-messenger RNAs in African trypanosomes are substrates of a U-nucleotide-specific insertion/deletion-type RNA editing reaction. The process converts nonfunctional pre-mRNAs into translation-competent molecules and can generate protein diversity by alternative editing. High molecular mass protein complexes termed editosomes catalyze the processing reaction. They stably interact with pre-edited mRNAs and small noncoding RNAs, known as guide RNAs (gRNAs), which act as templates in the reaction. Editosomes provide a molecular surface for the individual steps of the catalytic reaction cycle and although the protein inventory of the complexes has been studied in detail, a structural analysis of the processing machinery has only recently been accomplished. Electron microscopy in combination with single particle reconstruction techniques has shown that steady state isolates of editosomes contain ensembles of two classes of stable complexes with calculated apparent hydrodynamic sizes of 20S and 35-40S. 20S editosomes are free of substrate RNAs, whereas 35-40S editosomes are associated with endogenous mRNA and gRNA molecules. Both complexes are characterized by a diverse structural landscape, which include complexes that lack or possess defined subdomains. Here, we summarize the consensus models and structural landmarks of both complexes. We correlate structural features with functional characteristics and provide an outlook into dynamic aspects of the editing reaction cycle.
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Affiliation(s)
- H Ulrich Göringer
- Department of Microbiology and Genetics, Darmstadt University of Technology, Darmstadt, Germany.
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Carnes J, Soares CZ, Wickham C, Stuart K. Endonuclease associations with three distinct editosomes in Trypanosoma brucei. J Biol Chem 2011; 286:19320-30. [PMID: 21474442 DOI: 10.1074/jbc.m111.228965] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Three distinct editosomes, typified by mutually exclusive KREN1, KREN2, or KREN3 endonucleases, are essential for mitochondrial RNA editing in Trypanosoma brucei. The three editosomes differ in substrate endoribonucleolytic cleavage specificity, which may reflect the vast number of editing sites that need insertion or deletion of uridine nucleotides (Us). Each editosome requires the single RNase III domain in each endonuclease for catalysis. Studies reported here show that the editing endonucleases do not form homodimeric domains, and may therefore function as intermolecular heterodimers, perhaps with KREPB4 and/or KREPB5. Editosomes isolated via TAP tag fused to KREPB6, KREPB7, or KREPB8 have a common set of 12 proteins. In addition, KREN3 is only found in KREPB6 editosomes, KREN2 is only found in KREPB7 editosomes, and KREN1 is only found in KREPB8 editosomes. These are the same associations previously found in editosomes isolated via the TAP-tagged endonucleases KREN1, KREN2, or KREN3. Furthermore, TAP-tagged KREPB6, KREPB7, and KREPB8 complexes isolated from cells in which expression of their respective endonuclease were knocked down were disrupted and lacked the heterotrimeric insertion subcomplex (KRET2, KREPA1, and KREL2). These results and published data suggest that KREPB6, KREPB7, and KREPB8 associate with the deletion subcomplex, whereas the KREN1, KREN2, and KREN3 endonucleases associate with the insertion subcomplex.
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Affiliation(s)
- Jason Carnes
- Seattle Biomedical Research Institute, Seattle, Washington 98109, USA
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42
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Moshiri H, Acoca S, Kala S, Najafabadi HS, Hogues H, Purisima E, Salavati R. Naphthalene-based RNA editing inhibitor blocks RNA editing activities and editosome assembly in Trypanosoma brucei. J Biol Chem 2011; 286:14178-89. [PMID: 21378165 DOI: 10.1074/jbc.m110.199646] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
RNA editing, catalyzed by the multiprotein editosome complex, is an essential step for the expression of most mitochondrial genes in trypanosomatid pathogens. It has been shown previously that Trypanosoma brucei RNA editing ligase 1 (TbREL1), a core catalytic component of the editosome, is essential in the mammalian life stage of these parasitic pathogens. Because of the availability of its crystal structure and absence from human, the adenylylation domain of TbREL1 has recently become the focus of several studies for designing inhibitors that target its adenylylation pocket. Here, we have studied new and existing inhibitors of TbREL1 to better understand their mechanism of action. We found that these compounds are moderate to weak inhibitors of adenylylation of TbREL1 and in fact enhance adenylylation at higher concentrations of protein. Nevertheless, they can efficiently block deadenylylation of TbREL1 in the editosome and, consequently, result in inhibition of the ligation step of RNA editing. Further experiments directly showed that the studied compounds inhibit the interaction of the editosome with substrate RNA. This was supported by the observation that not only the ligation activity of TbREL1 but also the activities of other editosome proteins such as endoribonuclease, terminal RNA uridylyltransferase, and uridylate-specific exoribonuclease, all of which require the interaction of the editosome with the substrate RNA, are efficiently inhibited by these compounds. In addition, we found that these compounds can interfere with the integrity and/or assembly of the editosome complex, opening the exciting possibility of using them to study the mechanism of assembly of the editosome components.
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Affiliation(s)
- Houtan Moshiri
- Department of Biochemistry, McGill University, McIntyre Medical Building, 3655 Promenade Sir William Osler, Montreal, Quebec H3G1Y6, Canada
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43
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Knoop V. When you can't trust the DNA: RNA editing changes transcript sequences. Cell Mol Life Sci 2011; 68:567-86. [PMID: 20938709 PMCID: PMC11114842 DOI: 10.1007/s00018-010-0538-9] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Revised: 09/13/2010] [Accepted: 09/23/2010] [Indexed: 12/25/2022]
Abstract
RNA editing describes targeted sequence alterations in RNAs so that the transcript sequences differ from their DNA template. Since the original discovery of RNA editing in trypanosomes nearly 25 years ago more than a dozen such processes of nucleotide insertions, deletions, and exchanges have been identified in evolutionarily widely separated groups of the living world including plants, animals, fungi, protists, bacteria, and viruses. In many cases gene expression in mitochondria is affected, but RNA editing also takes place in chloroplasts and in nucleocytosolic genetic environments. While some RNA editing systems largely seem to repair defect genes (cryptogenes), others have obvious functions in modulating gene activities. The present review aims for an overview on the current states of research in the different systems of RNA editing by following a historic timeline along the respective original discoveries.
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Affiliation(s)
- Volker Knoop
- Abteilung Molekulare Evolution, Institut für Zelluläre und Molekulare Botanik (IZMB), Bonn, Germany.
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44
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Liang S, Connell GJ. Identification of specific inhibitors for a trypanosomatid RNA editing reaction. RNA (NEW YORK, N.Y.) 2010; 16:2435-2441. [PMID: 20940340 PMCID: PMC2995404 DOI: 10.1261/rna.2347310] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 09/02/2010] [Indexed: 05/27/2023]
Abstract
Several mitochondrial mRNAs of the trypanosomatid protozoa are edited through the post-transcriptional insertion and deletion of uridylates. The reaction has provided insights into basic cellular biology and is also important as a potential therapeutic target for the diseases caused by trypanosomatid pathogens. Despite this importance, the field has been hindered by the lack of specific inhibitors that could be used as probes of the reaction mechanism or developed into novel therapeutics. In this study, an electrochemiluminescent aptamer-switch was utilized in a high-throughput screen for inhibitors of a trypanosomatid RNA editing reaction. The screen identified GW5074, mitoxantrone, NF 023, protoporphyrin IX, and D-sphingosine as inhibitors of insertion editing, with IC(50) values ranging from 1 to 3 μM. GW5074 and protoporphyrin IX are demonstrated to inhibit at or before the endonuclease cleavage that initiates editing and will be valuable biochemical probes for the early events of the in vitro reaction. Since protoporphyrin IX and sphingosine are both naturally present within the trypanosomatids, their effectiveness as in vitro inhibitors is also suggestive of the potential for in vivo modulatory roles.
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Affiliation(s)
- Shuang Liang
- Department of Pharmacology, Medical School, University of Minnesota, Minneapolis, Minnesota 55455, USA
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45
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Kala S, Salavati R. OB-fold domain of KREPA4 mediates high-affinity interaction with guide RNA and possesses annealing activity. RNA (NEW YORK, N.Y.) 2010; 16:1951-67. [PMID: 20713467 PMCID: PMC2941104 DOI: 10.1261/rna.2124610] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Accepted: 07/19/2010] [Indexed: 05/29/2023]
Abstract
KREPA4, also called MP24, is an essential mitochondrial guide RNA (gRNA)-binding protein with a preference for the 3' oligo(U) tail in trypanosomes. Structural prediction and compositional analysis of KREPA4 have identified a conserved OB (oligonucleotide/oligosaccharide-binding)-fold at the C-terminal end and two low compositional complexity regions (LCRs) at its N terminus. Concurrent with these predictions, one or both of these regions in KREPA4 protein may be involved in gRNA binding. To test this possibility, deletion mutants of KREPA4 were made and the effects on the gRNA-binding affinities were measured by quantitative electrophoretic mobility shift assays. The gRNA-binding specificities of these mutants were evaluated by competition experiments using gRNAs with U-tail deletions or stem-loop modifications and uridylated nonguide RNAs or heterologous RNA. Our results identified the predicted OB-fold as the functional domain of KREPA4 that mediates a high-affinity interaction with the gRNA oligo(U) tail. An additional contribution toward RNA-binding function was localized to LCRs that further stabilize the binding through sequence-specific interactions with the guide secondary structure. In this study we also found that the predicted OB-fold has an RNA annealing activity, representing the first report of such activity for a core component of the RNA editing complex.
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MESH Headings
- Amino Acid Sequence
- Base Sequence
- Binding, Competitive
- Kinetics
- Models, Biological
- Molecular Sequence Data
- Nucleic Acid Conformation
- Protein Folding
- Protein Structure, Tertiary
- Protozoan Proteins/chemistry
- Protozoan Proteins/genetics
- 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, Protozoan/chemistry
- RNA, Protozoan/genetics
- RNA, Protozoan/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Sequence Deletion
- Trypanosoma brucei brucei/genetics
- Trypanosoma brucei brucei/metabolism
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Affiliation(s)
- Smriti Kala
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec, Canada
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46
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Moshiri H, Salavati R. A fluorescence-based reporter substrate for monitoring RNA editing in trypanosomatid pathogens. Nucleic Acids Res 2010; 38:e138. [PMID: 20444864 PMCID: PMC2910069 DOI: 10.1093/nar/gkq333] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
RNA editing regulates mitochondrial gene expression in trypanosomatid pathogens by creating functional mRNAs. It is catalyzed by a multi-protein complex (the editosome), and is found to be essential in both insect stage and mammalian blood stream form of Trypanosoma brucei. This particular form of RNA editing is unique to trypanosomatids, and thus provides a suitable drug target in trypanosomatid pathogens. Here, we demonstrate the feasibility of a rapid and sensitive fluorescence-based reporter assay to monitor RNA editing based on ribozyme activity. We could validate our new assay using previously identified inhibitors against the essential RNA editing ligase. The principle advantages of this assay are: (i) the use of non-radioactively labeled materials, (ii) sensitivity afforded by fluorescence instrumentation applicable to high-throughput screening of chemical inhibitors against the essential editosome and (iii) a rapid and convenient 'mix and measure' type of assay in low volume with a high signal to noise ratio. This assay should enhance rapid identification and characterization of the editosome inhibitors primarily based on the overall composition of the editosomes from T. brucei. These inhibitors could also be tested against the editosomes from the closely related pathogens including T. cruzi and Leishmania species.
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Affiliation(s)
- Houtan Moshiri
- Institute of Parasitology, McGill University, 21111 Lakeshore Road, Ste. Anne de Bellevue, Montreal, Quebec H9X3V9, Canada
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47
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Simpson L, Aphasizhev R, Lukes J, Cruz-Reyes J. Guide to the nomenclature of kinetoplastid RNA editing: a proposal. Protist 2009; 161:2-6. [PMID: 19945343 DOI: 10.1016/j.protis.2009.10.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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48
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Swift RV, Amaro RE. Discovery and design of DNA and RNA ligase inhibitors in infectious microorganisms. Expert Opin Drug Discov 2009; 4:1281-1294. [PMID: 20354588 DOI: 10.1517/17460440903373617] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
BACKGROUND: Members of the nucleotidyltransferase superfamily known as DNA and RNA ligases carry out the enzymatic process of polynucleotide ligation. These guardians of genomic integrity share a three-step ligation mechanism, as well as common core structural elements. Both DNA and RNA ligases have experienced a surge of recent interest as chemotherapeutic targets for the treatment of a range of diseases, including bacterial infection, cancer, and the diseases caused by the protozoan parasites known as trypanosomes. OBJECTIVE: In this review, we will focus on efforts targeting pathogenic microorganisms; specifically, bacterial NAD(+)-dependent DNA ligases, which are promising broad-spectrum antibiotic targets, and ATP-dependent RNA editing ligases from Trypanosoma brucei, the species responsible for the devastating neurodegenerative disease, African sleeping sickness. CONCLUSION: High quality crystal structures of both NAD(+)-dependent DNA ligase and the Trypanosoma brucei RNA editing ligase have facilitated the development of a number of promising leads. For both targets, further progress will require surmounting permeability issues and improving selectivity and affinity.
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Affiliation(s)
- Robert V Swift
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
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49
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Liang S, Connell GJ. An electrochemiluminescent aptamer switch for a high-throughput assay of an RNA editing reaction. RNA (NEW YORK, N.Y.) 2009; 15:1929-1938. [PMID: 19696159 PMCID: PMC2743045 DOI: 10.1261/rna.1720209] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2009] [Accepted: 07/20/2009] [Indexed: 05/27/2023]
Abstract
An RNA editing reaction that is both essential and specific to the trypanosomatid parasites is an attractive target for new drug development. Although high-throughput screening of chemical libraries is a powerful strategy often used to identify new drugs, the available in vitro editing assays do not have the necessary sensitivity and format for this approach to be feasible. A ruthenium labeled reporter RNA is described here that overcomes these limitations as it can both detect edited product in the low femtomole range and is ideal for high-throughput format. The reporter RNA consists of an RNA editing substrate linked to a streptavidin-binding aptamer that is initially held within an inactive conformation. An in vitro selection strategy optimized the linkage so that the streptavidin-binding aptamer is only activated by an editing-induced conformational change. An electrochemiluminescent signal results from the ruthenium label when the reporter is bound to the bottom of a streptavidin-coated microtiter plate where it can be stimulated by a carbon electrode. Chemical probing, mutagenesis, and binding affinity measurements were used to characterize the reporter. The highly sensitive assay could be adapted to a broad range of RNA processing reactions.
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Affiliation(s)
- Shuang Liang
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA
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50
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Structure of the core editing complex (L-complex) involved in uridine insertion/deletion RNA editing in trypanosomatid mitochondria. Proc Natl Acad Sci U S A 2009; 106:12306-10. [PMID: 19590014 DOI: 10.1073/pnas.0901754106] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Uridine insertion/deletion RNA editing is a unique form of posttranscriptional RNA processing that occurs in mitochondria of kinetoplastid protists. We have carried out 3D structural analyses of the core editing complex or "L (ligase)-complex" from Leishmania tarentolae mitochondria isolated by the tandem affinity purification procedure (TAP). The purified material, sedimented at 20-25S, migrated in a blue native gel at 1 MDa and exhibited both precleaved and full-cycle gRNA-mediated U-insertion and U-deletion in vitro activities. The purified L-complex was analyzed by electron tomography to determine the extent of heterogeneity. Three-dimensional structural comparisons of individual particles in the tomograms revealed that a majority of the complexes have a similar shape of a slender triangle. An independent single-particle reconstruction, using a featureless Gaussian ball as the initial model, converged to a similar triangular structure. Another single-particle reconstruction, using the averaged tomography structure as the initial model, yielded a similar structure. The REL1 ligase was localized on the model to the base of the apex by decoration with REL1-specific IgG. This structure should prove useful for a detailed analysis of the editing reaction.
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