1
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Mendoza HG, Matos VJ, Park S, Pham KM, Beal PA. Selective Inhibition of ADAR1 Using 8-Azanebularine-Modified RNA Duplexes. Biochemistry 2023; 62:1376-1387. [PMID: 36972568 PMCID: PMC10804918 DOI: 10.1021/acs.biochem.2c00686] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Adenosine deaminases acting on RNA (ADARs) are RNA editing enzymes that catalyze the hydrolytic deamination of adenosine (A) to inosine (I) in dsRNA. In humans, two catalytically active ADARs, ADAR1 and ADAR2, perform this A-to-I editing event. The growing field of nucleotide base editing has highlighted ADARs as promising therapeutic agents while multiple studies have also identified ADAR1's role in cancer progression. However, the potential for site-directed RNA editing as well as the rational design of inhibitors is being hindered by the lack of detailed molecular understanding of RNA recognition by ADAR1. Here, we designed short RNA duplexes containing the nucleoside analog, 8-azanebularine (8-azaN), to gain insight into molecular recognition by the human ADAR1 catalytic domain. From gel shift and in vitro deamination experiments, we validate ADAR1 catalytic domain's duplex secondary structure requirement and present a minimum duplex length for binding (14 bp, with 5 bp 5' and 8 bp 3' to editing site). These findings concur with predicted RNA-binding contacts from a previous structural model of the ADAR1 catalytic domain. Finally, we establish that neither 8-azaN as a free nucleoside nor a ssRNA bearing 8-azaN inhibits ADAR1 and demonstrate that the 8-azaN-modified RNA duplexes selectively inhibit ADAR1 and not the closely related ADAR2 enzyme.
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Affiliation(s)
- Herra G. Mendoza
- Department of Chemistry, University of California, Davis, CA 95616 USA
| | | | - SeHee Park
- Department of Chemistry, University of California, Davis, CA 95616 USA
| | - Kevin M. Pham
- Department of Chemistry, University of California, Davis, CA 95616 USA
| | - Peter A. Beal
- Department of Chemistry, University of California, Davis, CA 95616 USA
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2
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Hajji K, Sedmík J, Cherian A, Amoruso D, Keegan LP, O'Connell MA. ADAR2 enzymes: efficient site-specific RNA editors with gene therapy aspirations. RNA (NEW YORK, N.Y.) 2022; 28:1281-1297. [PMID: 35863867 PMCID: PMC9479739 DOI: 10.1261/rna.079266.122] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The adenosine deaminase acting on RNA (ADAR) enzymes are essential for neuronal function and innate immune control. ADAR1 RNA editing prevents aberrant activation of antiviral dsRNA sensors through editing of long, double-stranded RNAs (dsRNAs). In this review, we focus on the ADAR2 proteins involved in the efficient, highly site-specific RNA editing to recode open reading frames first discovered in the GRIA2 transcript encoding the key GLUA2 subunit of AMPA receptors; ADAR1 proteins also edit many of these sites. We summarize the history of ADAR2 protein research and give an up-to-date review of ADAR2 structural studies, human ADARBI (ADAR2) mutants causing severe infant seizures, and mouse disease models. Structural studies on ADARs and their RNA substrates facilitate current efforts to develop ADAR RNA editing gene therapy to edit disease-causing single nucleotide polymorphisms (SNPs). Artificial ADAR guide RNAs are being developed to retarget ADAR RNA editing to new target transcripts in order to correct SNP mutations in them at the RNA level. Site-specific RNA editing has been expanded to recode hundreds of sites in CNS transcripts in Drosophila and cephalopods. In Drosophila and C. elegans, ADAR RNA editing also suppresses responses to self dsRNA.
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Affiliation(s)
- Khadija Hajji
- CEITEC Masaryk University, Brno 62500, Czech Republic
| | - Jiří Sedmík
- CEITEC Masaryk University, Brno 62500, Czech Republic
| | - Anna Cherian
- CEITEC Masaryk University, Brno 62500, Czech Republic
| | | | - Liam P Keegan
- CEITEC Masaryk University, Brno 62500, Czech Republic
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3
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Zhai J, Koh JH, Soong TW. RNA editing of ion channels and receptors in physiology and neurological disorders. OXFORD OPEN NEUROSCIENCE 2022; 1:kvac010. [PMID: 38596706 PMCID: PMC11003377 DOI: 10.1093/oons/kvac010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/14/2022] [Accepted: 05/15/2022] [Indexed: 04/11/2024]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing is a post-transcriptional modification that diversifies protein functions by recoding RNA or alters protein quantity by regulating mRNA level. A-to-I editing is catalyzed by adenosine deaminases that act on RNA. Millions of editing sites have been reported, but they are mostly found in non-coding sequences. However, there are also several recoding editing sites in transcripts coding for ion channels or transporters that have been shown to play important roles in physiology and changes in editing level are associated with neurological diseases. These editing sites are not only found to be evolutionary conserved across species, but they are also dynamically regulated spatially, developmentally and by environmental factors. In this review, we discuss the current knowledge of A-to-I RNA editing of ion channels and receptors in the context of their roles in physiology and pathological disease. We also discuss the regulation of editing events and site-directed RNA editing approaches for functional study that offer a therapeutic pathway for clinical applications.
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Affiliation(s)
- Jing Zhai
- Department of Physiology, National University of Singapore, Singapore 117593, Singapore
| | - Joanne Huifen Koh
- Department of Physiology, National University of Singapore, Singapore 117593, Singapore
| | - Tuck Wah Soong
- Department of Physiology, National University of Singapore, Singapore 117593, Singapore
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore,
Singapore 117456, Singapore
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4
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Dutta N, Deb I, Sarzynska J, Lahiri A. Inosine and its methyl derivatives: Occurrence, biogenesis, and function in RNA. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 169-170:21-52. [PMID: 35065168 DOI: 10.1016/j.pbiomolbio.2022.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 12/11/2021] [Accepted: 01/11/2022] [Indexed: 05/21/2023]
Abstract
Inosine is one of the most common post-transcriptional modifications. Since its discovery, it has been noted for its ability to contribute to non-Watson-Crick interactions within RNA. Rapidly accumulating evidence points to the widespread generation of inosine through hydrolytic deamination of adenosine to inosine by different classes of adenosine deaminases. Three naturally occurring methyl derivatives of inosine, i.e., 1-methylinosine, 2'-O-methylinosine and 1,2'-O-dimethylinosine are currently reported in RNA modification databases. These modifications are expected to lead to changes in the structure, folding, dynamics, stability and functions of RNA. The importance of the modifications is indicated by the strong conservation of the modifying enzymes across organisms. The structure, binding and catalytic mechanism of the adenosine deaminases have been well-studied, but the underlying mechanism of the catalytic reaction is not very clear yet. Here we extensively review the existing data on the occurrence, biogenesis and functions of inosine and its methyl derivatives in RNA. We also included the structural and thermodynamic aspects of these modifications in our review to provide a detailed and integrated discussion on the consequences of A-to-I editing in RNA and the contribution of different structural and thermodynamic studies in understanding its role in RNA. We also highlight the importance of further studies for a better understanding of the mechanisms of the different classes of deamination reactions. Further investigation of the structural and thermodynamic consequences and functions of these modifications in RNA should provide more useful information about their role in different diseases.
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Affiliation(s)
- Nivedita Dutta
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata, 700009, West Bengal, India
| | - Indrajit Deb
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata, 700009, West Bengal, India
| | - Joanna Sarzynska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Ansuman Lahiri
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, Acharya Prafulla Chandra Road, Kolkata, 700009, West Bengal, India.
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5
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Rajendren S, Manning AC, Al-Awadi H, Yamada K, Takagi Y, Hundley HA. A protein-protein interaction underlies the molecular basis for substrate recognition by an adenosine-to-inosine RNA-editing enzyme. Nucleic Acids Res 2019; 46:9647-9659. [PMID: 30202880 PMCID: PMC6182170 DOI: 10.1093/nar/gky800] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 08/27/2018] [Indexed: 01/06/2023] Open
Abstract
Adenosine deaminases that act on RNA (ADARs) convert adenosine to inosine within double-stranded regions of RNA, resulting in increased transcriptomic diversity, as well as protection of cellular double-stranded RNA (dsRNA) from silencing and improper immune activation. The presence of dsRNA-binding domains (dsRBDs) in all ADARs suggests these domains are important for substrate recognition; however, the role of dsRBDs in vivo remains largely unknown. Herein, our studies indicate the Caenorhabditis elegans ADAR enzyme, ADR-2, has low affinity for dsRNA, but interacts with ADR-1, an editing-deficient member of the ADAR family, which has a 100-fold higher affinity for dsRNA. ADR-1 uses one dsRBD to physically interact with ADR-2 and a second dsRBD to bind to dsRNAs, thereby tethering ADR-2 to substrates. ADR-2 interacts with >1200 transcripts in vivo, and ADR-1 is required for 80% of these interactions. Our results identify a novel mode of substrate recognition for ADAR enzymes and indicate that protein-protein interactions can guide substrate recognition for RNA editors.
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Affiliation(s)
- Suba Rajendren
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Aidan C Manning
- Medical Sciences Program, Indiana University, Bloomington, IN 47405, USA
| | - Haider Al-Awadi
- Medical Sciences Program, Indiana University, Bloomington, IN 47405, USA
| | - Kentaro Yamada
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yuichiro Takagi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Heather A Hundley
- Medical Sciences Program, Indiana University, Bloomington, IN 47405, USA
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6
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McMahon AC, Rahman R, Jin H, Shen JL, Fieldsend A, Luo W, Rosbash M. TRIBE: Hijacking an RNA-Editing Enzyme to Identify Cell-Specific Targets of RNA-Binding Proteins. Cell 2016; 165:742-53. [PMID: 27040499 DOI: 10.1016/j.cell.2016.03.007] [Citation(s) in RCA: 156] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 01/15/2016] [Accepted: 02/25/2016] [Indexed: 10/22/2022]
Abstract
RNA transcripts are bound and regulated by RNA-binding proteins (RBPs). Current methods for identifying in vivo targets of an RBP are imperfect and not amenable to examining small numbers of cells. To address these issues, we developed TRIBE (targets of RNA-binding proteins identified by editing), a technique that couples an RBP to the catalytic domain of the Drosophila RNA-editing enzyme ADAR and expresses the fusion protein in vivo. RBP targets are marked with novel RNA editing events and identified by sequencing RNA. We have used TRIBE to identify the targets of three RBPs (Hrp48, dFMR1, and NonA). TRIBE compares favorably to other methods, including CLIP, and we have identified RBP targets from as little as 150 specific fly neurons. TRIBE can be performed without an antibody and in small numbers of specific cells.
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Affiliation(s)
- Aoife C McMahon
- Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, MA 02453, USA
| | - Reazur Rahman
- Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, MA 02453, USA
| | - Hua Jin
- Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, MA 02453, USA
| | - James L Shen
- Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, MA 02453, USA
| | - Allegra Fieldsend
- Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, MA 02453, USA
| | - Weifei Luo
- Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, MA 02453, USA
| | - Michael Rosbash
- Department of Biology, Howard Hughes Medical Institute and National Center for Behavioral Genomics, Brandeis University, Waltham, MA 02453, USA.
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7
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Mannion N, Arieti F, Gallo A, Keegan LP, O'Connell MA. New Insights into the Biological Role of Mammalian ADARs; the RNA Editing Proteins. Biomolecules 2015; 5:2338-62. [PMID: 26437436 PMCID: PMC4693238 DOI: 10.3390/biom5042338] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 09/09/2015] [Accepted: 09/11/2015] [Indexed: 12/20/2022] Open
Abstract
The ADAR proteins deaminate adenosine to inosine in double-stranded RNA which is one of the most abundant modifications present in mammalian RNA. Inosine can have a profound effect on the RNAs that are edited, not only changing the base-pairing properties, but can also result in recoding, as inosine behaves as if it were guanosine. In mammals there are three ADAR proteins and two ADAR-related proteins (ADAD) expressed. All have a very similar modular structure; however, both their expression and biological function differ significantly. Only two of the ADAR proteins have enzymatic activity. However, both ADAR and ADAD proteins possess the ability to bind double-strand RNA. Mutations in ADARs have been associated with many diseases ranging from cancer, innate immunity to neurological disorders. Here, we will discuss in detail the domain structure of mammalian ADARs, the effects of RNA editing, and the role of ADARs in human diseases.
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Affiliation(s)
- Niamh Mannion
- Paul O'Gorman Leukaemia Research Centre, Institute of Cancer Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, 21 Shelley Road, Glasgow G12 0ZD, UK.
| | - Fabiana Arieti
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic.
| | - Angela Gallo
- Oncohaematoogy Department, Ospedale Pediatrico Bambino Gesù (IRCCS) Viale di San Paolo, Roma 15-00146, Italy.
| | - Liam P Keegan
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic.
| | - Mary A O'Connell
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic.
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8
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Phelps KJ, Tran K, Eifler T, Erickson AI, Fisher AJ, Beal PA. Recognition of duplex RNA by the deaminase domain of the RNA editing enzyme ADAR2. Nucleic Acids Res 2015; 43:1123-32. [PMID: 25564529 PMCID: PMC4333395 DOI: 10.1093/nar/gku1345] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Adenosine deaminases acting on RNA (ADARs) hydrolytically deaminate adenosines (A) in a wide variety of duplex RNAs and misregulation of editing is correlated with human disease. However, our understanding of reaction selectivity is limited. ADARs are modular enzymes with multiple double-stranded RNA binding domains (dsRBDs) and a catalytic domain. While dsRBD binding is understood, little is known about ADAR catalytic domain/RNA interactions. Here we use a recently discovered RNA substrate that is rapidly deaminated by the isolated human ADAR2 deaminase domain (hADAR2-D) to probe these interactions. We introduced the nucleoside analog 8-azanebularine (8-azaN) into this RNA (and derived constructs) to mechanistically trap the protein–RNA complex without catalytic turnover for EMSA and ribonuclease footprinting analyses. EMSA showed that hADAR2-D requires duplex RNA and is sensitive to 2′-deoxy substitution at nucleotides opposite the editing site, the local sequence and 8-azaN nucleotide positioning on the duplex. Ribonuclease V1 footprinting shows that hADAR2-D protects ∼23 nt on the edited strand around the editing site in an asymmetric fashion (∼18 nt on the 5′ side and ∼5 nt on the 3′ side). These studies provide a deeper understanding of the ADAR catalytic domain–RNA interaction and new tools for biophysical analysis of ADAR–RNA complexes.
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Affiliation(s)
- Kelly J Phelps
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Kiet Tran
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Tristan Eifler
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Anna I Erickson
- Department of Molecular and Cellular Biology, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Andrew J Fisher
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA Department of Molecular and Cellular Biology, University of California, One Shields Avenue, Davis, CA 95616, USA
| | - Peter A Beal
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA 95616, USA
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9
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Eifler T, Pokharel S, Beal PA. RNA-Seq analysis identifies a novel set of editing substrates for human ADAR2 present in Saccharomyces cerevisiae. Biochemistry 2013; 52:7857-69. [PMID: 24124932 DOI: 10.1021/bi4006539] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
ADAR2 is a member of a family of RNA editing enzymes found in metazoa that bind double helical RNAs and deaminate select adenosines. We find that when human ADAR2 is overexpressed in the budding yeast Saccharomyces cerevisiae it substantially reduces the rate of cell growth. This effect is dependent on the deaminase activity of the enzyme, suggesting yeast transcripts are edited by ADAR2. Characterization of this novel set of RNA substrates provided a unique opportunity to gain insight into ADAR2's site selectivity. We used RNA-Seq. to identify transcripts present in S. cerevisiae subject to ADAR2-catalyzed editing. From this analysis, we identified 17 adenosines present in yeast RNAs that satisfied our criteria for candidate editing sites. Substrates identified include both coding and noncoding RNAs. Subsequent Sanger sequencing of RT-PCR products from yeast total RNA confirmed efficient editing at a subset of the candidate sites including BDF2 mRNA, RL28 intron RNA, HAC1 3'UTR RNA, 25S rRNA, U1 snRNA, and U2 snRNA. Two adenosines within the U1 snRNA sequence not identified as substrates during the original RNA-Seq. screen were shown to be deaminated by ADAR2 during the follow-up analysis. In addition, examination of the RNA sequence surrounding each edited adenosine in this novel group of ADAR2 sites revealed a previously unrecognized sequence preference. Remarkably, rapid deamination at one of these sites (BDF2 mRNA) does not require ADAR2's dsRNA-binding domains (dsRBDs). Human glioma-associated oncogene 1 (GLI1) mRNA is a known ADAR2 substrate with similar flanking sequence and secondary structure to the yeast BDF2 site discovered here. As observed with the BDF2 site, rapid deamination at the GLI1 site does not require ADAR2's dsRBDs.
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Affiliation(s)
- Tristan Eifler
- Department of Chemistry, University of California , One Shields Avenue, Davis, California 95616, United States
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10
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Dahabieh MS, Samanta D, Brodovitch JC, Frech C, O'Neill MA, Pinto BM. Sequence-dependent structural dynamics of primate adenosine-to-inosine editing substrates. Chembiochem 2012. [PMID: 23193088 DOI: 10.1002/cbic.201200526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Humans have the highest level of adenosine-to-inosine (A-to-I) editing amongst primates, yet the reasons for this difference remain unclear. Sequence analysis of the Alu Sg elements (A-to-I RNA substrates) corresponding to the Nup50 gene in human, chimp, and rhesus reveals subtle sequence variations surrounding the edit sites. We have developed three constructs that represent human (HuAp5), chimp (ChAp5), and rhesus (RhAp5) Nup50 Alu Sg A-to-I editing substrates. Here, 2-aminopurine (2-Ap) was substituted for edited adenosine (A5) so as to monitor the fluorescence intensity with respect to temperature. UV and steady-state fluorescence (SSF) T(M) plots indicate that local and global unfolding are coincident, with the human construct displaying a T(M) of approximately 70°C, compared to 60°C for chimp and 54°C for rhesus. However, time-resolved fluorescence (TRF) resolves three different fluorescence lifetimes that we assign to folded, intermediate(s), and unfolded states. The TRF data fit well to a two-intermediate model, whereby both intermediates (M, J) are in equilibrium with each other, and the folded/unfolded states. Our model suggests that, at 37°C, human state J and the folded state will be the most heavily populated in comparison to the other primate constructs. In order for adenosine deaminase acting on RNA (ADAR) to efficiently dock, a stable duplex must be present that corresponds to the human construct, globally. Next, the enzyme must "flip out" the base of interest to facilitate the A-to-I conversion; a nucleotide in an intermediate-like position would enhance this conformational change. Our experiments demonstrate that subtle variations in RNA sequence might contribute to the high A-to-I editing levels found in humans.
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11
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Mizrahi RA, Phelps KJ, Ching AY, Beal PA. Nucleoside analog studies indicate mechanistic differences between RNA-editing adenosine deaminases. Nucleic Acids Res 2012; 40:9825-35. [PMID: 22885375 PMCID: PMC3479202 DOI: 10.1093/nar/gks752] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Adenosine deaminases acting on RNA (ADAR1 and ADAR2) are human RNA-editing adenosine deaminases responsible for the conversion of adenosine to inosine at specific locations in cellular RNAs. Since inosine is recognized during translation as guanosine, this often results in the expression of protein sequences different from those encoded in the genome. While our knowledge of the ADAR2 structure and catalytic mechanism has grown over the years, our knowledge of ADAR1 has lagged. This is due, at least in part, to the lack of well defined, small RNA substrates useful for mechanistic studies of ADAR1. Here, we describe an ADAR1 substrate RNA that can be prepared by a combination of chemical synthesis and enzymatic ligation. Incorporation of adenosine analogs into this RNA and analysis of the rate of ADAR1 catalyzed deamination revealed similarities and differences in the way the ADARs recognize the edited nucleotide. Importantly, ADAR1 is more dependent than ADAR2 on the presence of N7 in the edited base. This difference between ADAR1 and ADAR2 appears to be dependent on the identity of a single amino acid residue near the active site. Thus, this work provides an important starting point in defining mechanistic differences between two functionally distinct human RNA editing ADARs.
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Affiliation(s)
- Rena A Mizrahi
- Department of Chemistry, University of California, Davis, CA 95616, USA
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12
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The biochemistry of activation-induced deaminase and its physiological functions. Semin Immunol 2012; 24:255-63. [DOI: 10.1016/j.smim.2012.05.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Accepted: 05/18/2012] [Indexed: 01/26/2023]
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13
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Tariq A, Jantsch MF. Transcript diversification in the nervous system: a to I RNA editing in CNS function and disease development. Front Neurosci 2012; 6:99. [PMID: 22787438 PMCID: PMC3391646 DOI: 10.3389/fnins.2012.00099] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 06/14/2012] [Indexed: 12/16/2022] Open
Abstract
RNA editing by adenosine deaminases that act on RNA converts adenosines to inosines in coding and non-coding regions of mRNAs. Inosines are interpreted as guanosines and hence, this type of editing can change codons, alter splice patterns, or influence the fate of an RNA. A to I editing is most abundant in the central nervous system (CNS). Here, targets for this type of nucleotide modification frequently encode receptors and channels. In many cases, the editing-induced amino acid exchanges alter the properties of the receptors and channels. Consistently, changes in editing patterns are frequently found associated with diseases of the CNS. In this review we describe the mechanisms of RNA editing and focus on target mRNAs of editing that are functionally relevant to normal and aberrant CNS activity.
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Affiliation(s)
- Aamira Tariq
- Max F. Perutz Laboratories, Department of Chromosome Biology, University of Vienna Vienna, Austria
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14
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Posttranscriptional recoding by RNA editing. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2012; 86:193-224. [PMID: 22243585 DOI: 10.1016/b978-0-12-386497-0.00006-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The posttranscriptional recoding of nuclear RNA transcripts has emerged as an important regulatory mechanism during eukaryotic gene expression. In particular the deamination of adenosine to inosine (interpreted by the translational machinery as a guanosine) is a frequent event that can recode the meaning of amino acid codons in translated exons, lead to structural changes in the RNA fold, or may affect splice consensus or regulatory sequence sites in noncoding exons or introns and modulate the biogenesis of small RNAs. The molecular mechanism of how the RNA editing machinery and its substrates recognize and interact with each other is not understood well enough to allow for the ab initio delineation of bona fide RNA editing sites. However, progress in the identification of various physiological modification sites and their characterization has given important insights regarding molecular features and events critical for productive RNA editing reactions. In addition, structural studies using components of the RNA editing machinery and together with editing competent substrate molecules have provided information on the chemical mechanism of adenosine deamination within the context of RNA molecules. Here, I give an overview of the process of adenosine deamination RNA editing and describe its relationship to other RNA processing events and its currently established roles in gene regulation.
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15
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Abstract
Fluorescent sensors that make use of DNA structures have become widely useful in monitoring enzymatic activities. Early studies focused primarily on enzymes that naturally use DNA or RNA as the substrate. However, recent advances in molecular design have enabled the development of nucleic acid sensors for a wider range of functions, including enzymes that do not normally bind DNA or RNA. Nucleic acid sensors present some potential advantages over classical small-molecule sensors, including water solubility and ease of synthesis. An overview of the multiple strategies under recent development is presented in this critical review, and expected future developments in microarrays, single molecule analysis, and in vivo sensing are discussed (160 references).
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Affiliation(s)
- Nan Dai
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Eric T. Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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16
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Godfried Sie CP, Kuchka M. RNA Editing adds flavor to complexity. BIOCHEMISTRY (MOSCOW) 2011; 76:869-81. [DOI: 10.1134/s0006297911080025] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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17
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Dierckx A, Dinér P, El-Sagheer AH, Kumar JD, Brown T, Grøtli M, Wilhelmsson LM. Characterization of photophysical and base-mimicking properties of a novel fluorescent adenine analogue in DNA. Nucleic Acids Res 2011; 39:4513-24. [PMID: 21278417 PMCID: PMC3105426 DOI: 10.1093/nar/gkr010] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
To increase the diversity of fluorescent base analogues with improved properties, we here present the straightforward click-chemistry-based synthesis of a novel fluorescent adenine-analogue triazole adenine (AT) and its photophysical characterization inside DNA. AT shows promising properties compared to the widely used adenine analogue 2-aminopurine. Quantum yields reach >20% and >5% in single- and double-stranded DNA, respectively, and show dependence on neighbouring bases. Moreover, AT shows only a minor destabilization of DNA duplexes, comparable to 2-aminopurine, and circular dichroism investigations suggest that AT only causes minimal structural perturbations to normal B-DNA. Furthermore, we find that AT shows favourable base-pairing properties with thymine and more surprisingly also with normal adenine. In conclusion, AT shows strong potential as a new fluorescent adenine analogue for monitoring changes within its microenvironment in DNA.
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Affiliation(s)
- Anke Dierckx
- Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, University of Gothenburg, S-41296 Gothenburg, Sweden
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18
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Abstract
Since the discovery of the adenosine deaminase (ADA) acting on RNA (ADAR) family of proteins in 1988 (Bass and Weintraub, Cell 55:1089-1098, 1988) (Wagner et al. Proc Natl Acad Sci U S A 86:2647-2651, 1989), we have learned much about their structure and catalytic mechanism. However, much about these enzymes is still unknown, particularly regarding the selective recognition and processing of specific adenosines within substrate RNAs. While a crystal structure of the catalytic domain of human ADAR2 has been solved, we still lack structural data for an ADAR catalytic domain bound to RNA, and we lack any structural data for other ADARs. However, by analyzing the structural data that is available along with similarities to other deaminases, mutagenesis and other biochemical experiments, we have been able to advance the understanding of how these fascinating enzymes function.
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Pokharel S, Jayalath P, Maydanovych O, Goodman RA, Wang SC, Tantillo DJ, Beal PA. Matching active site and substrate structures for an RNA editing reaction. J Am Chem Soc 2009; 131:11882-91. [PMID: 19642681 DOI: 10.1021/ja9034076] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The RNA-editing adenosine deaminases (ADARs) catalyze deamination of adenosine to inosine in a double-stranded structure found in various RNA substrates, including mRNAs. Here we present recent efforts to define structure/activity relationships for the ADAR reaction. We describe the synthesis of new phosphoramidites for the incorporation of 7-substituted-8-aza-7-deazaadenosine derivatives into RNA. These reagents were used to introduce the analogues into mimics of the R/G-editing site found in the pre-mRNA for the human glutamate receptor B subunit (GluR B). Analysis of the kinetics of the ADAR2 reaction with analogue-containing RNAs indicated 8-aza-7-deazaadenosine is an excellent substrate for this enzyme with a deamination rate eight times greater than that for adenosine. However, replacing the C7 hydrogen in this analogue with bromine, iodine, or propargyl alcohol failed to increase the deamination rate further but rather decreased the rate. Modeling of nucleotide binding in the enzyme active site suggested amino acid residues that may be involved in nucleotide recognition. We carried out a functional screen of a library of ADAR2 mutants expressed in S. cerevisiae that varied the identity of these residues to identify active deaminases with altered active sites. One of these mutants (ADAR2 R455A) was able to substantially overcome the inhibitory effect of the bulky C7 substituents (-Br, -I, propargyl alcohol). These results advance our understanding of the importance of functional groups found in the edited nucleotide and the role of specific active site residues of ADAR2.
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Affiliation(s)
- Subhash Pokharel
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, USA
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20
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Nakano SI, Oka H, Uotani Y, Uenishi K, Fujii M, Sugimoto N. Dynamics and Energetics of the Base Flipping Conformation Studied with Base Pair-Mimic Nucleosides. Biochemistry 2009; 48:11304-11. [DOI: 10.1021/bi901496q] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Shu-ichi Nakano
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST)
- Frontier Institute for Biomolecular Engineering Research (FIBER)
| | - Hirohito Oka
- Department of Chemistry, Faculty of Science and Engineering
| | - Yuuki Uotani
- Department of Chemistry, Faculty of Science and Engineering
| | | | - Masayuki Fujii
- Molecular Engineering Institute (MEI)
- Department of Environmental and Biological Chemistry
| | - Naoki Sugimoto
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST)
- Frontier Institute for Biomolecular Engineering Research (FIBER)
- Department of Chemistry, Faculty of Science and Engineering
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Ensterö M, Daniel C, Wahlstedt H, Major F, Ohman M. Recognition and coupling of A-to-I edited sites are determined by the tertiary structure of the RNA. Nucleic Acids Res 2009; 37:6916-26. [PMID: 19740768 PMCID: PMC2777444 DOI: 10.1093/nar/gkp731] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Adenosine-to-inosine (A-to-I) editing has been shown to be an important mechanism that increases protein diversity in the brain of organisms from human to fly. The family of ADAR enzymes converts some adenosines of RNA duplexes to inosines through hydrolytic deamination. The adenosine recognition mechanism is still largely unknown. Here, to investigate it, we analyzed a set of selectively edited substrates with a cluster of edited sites. We used a large set of individual transcripts sequenced by the 454 sequencing technique. On average, we analyzed 570 single transcripts per edited region at four different developmental stages from embryogenesis to adulthood. To our knowledge, this is the first time, large-scale sequencing has been used to determine synchronous editing events. We demonstrate that edited sites are only coupled within specific distances from each other. Furthermore, our results show that the coupled sites of editing are positioned on the same side of a helix, indicating that the three-dimensional structure is key in ADAR enzyme substrate recognition. Finally, we propose that editing by the ADAR enzymes is initiated by their attraction to one principal site in the substrate.
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Affiliation(s)
- Mats Ensterö
- Department of Molecular Biology and Functional Genomics, Stockholm University, S-106 91 Stockholm, Sweden
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22
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The protein factors MBNL1 and U2AF65 bind alternative RNA structures to regulate splicing. Proc Natl Acad Sci U S A 2009; 106:9203-8. [PMID: 19470458 DOI: 10.1073/pnas.0900342106] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a genetic disorder linked to a (CTG)(n) repeat expansion in the 3' untranslated region of the DMPK gene. Upon transcription in the nucleus, the CUG repeats form a stable RNA stem-loop that sequesters the RNA-binding protein MBNL1 from its normal function in the cell. MBNL1 regulates the alternative splicing of many pre-mRNAs, and upon MBNL1's sequestration, the alternative splicing of many genes is mis-regulated, leading to disease symptoms. MBNL1 is known to bind directly to at least 3 of the pre-mRNAs that it regulates, but how MBNL1 binding mechanistically regulates alternative splicing is unclear. Here, we demonstrate that MBNL1 controls the splicing of exon 5 in the cardiac troponin T (cTNT) pre-mRNA by competing directly with the essential splicing factor U2AF65 for binding at the 3' end of intron 4. When U2AF65 is prevented from binding to the pre-mRNA, the U2 snRNP can no longer be recruited and the following exon is skipped. Furthermore, MBNL1 and U2AF65 appear to compete by binding to mutually exclusive RNA structures. When bound by splicing factors, the 3' end of intron 4 can form either a stem-loop or a single-stranded structure. MBNL1 binds a portion of the intron as a stem-loop, whereas U2AF65 binds the same region in a single-strand structure. Mutations that strengthen the stem-loop decrease U2AF65 binding affinity and also repress exon 5 inclusion, independently of MBNL1. Thus, U2AF65 binding can be blocked either by MBNL1 binding or by the stabilization of RNA secondary structure.
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23
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Ballin JD, Prevas JP, Bharill S, Gryczynski I, Gryczynski Z, Wilson GM. Local RNA conformational dynamics revealed by 2-aminopurine solvent accessibility. Biochemistry 2008; 47:7043-52. [PMID: 18543944 DOI: 10.1021/bi800487c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Acrylamide quenching is widely used to monitor the solvent exposure of fluorescent probes in vitro. Here, we tested the utility of this technique to discriminate local RNA secondary structures using the fluorescent adenine analogue 2-aminopurine (2-AP). Under native conditions, the solvent accessibilities of most 2-AP-labeled RNA substrates were poorly resolved by classical single-population models; rather, a two-state quencher accessibility algorithm was required to model acrylamide-dependent changes in 2-AP fluorescence in structured RNA contexts. Comparing 2-AP quenching parameters between structured and unstructured RNA substrates permitted the effects of local RNA structure on 2-AP solvent exposure to be distinguished from nearest neighbor effects or environmental influences on intrinsic 2-AP photophysics. Using this strategy, the fractional accessibility of 2-AP for acrylamide ( f a) was found to be highly sensitive to local RNA structure. Base-paired 2-AP exhibited relatively poor accessibility, consistent with extensive shielding by adjacent bases. 2-AP in a single-base bulge was uniformly accessible to solvent, whereas the fractional accessibility of 2-AP in a hexanucleotide loop was indistinguishable from that of an unstructured RNA. However, these studies also provided evidence that the f a parameter reflects local conformational dynamics in base-paired RNA. Enhanced base pair dynamics at elevated temperatures were accompanied by increased f a values, while restricting local RNA breathing by adding a C-G base pair clamp or positioning 2-AP within extended RNA duplexes significantly decreased this parameter. Together, these studies show that 2-AP quenching studies can reveal local RNA structural and dynamic features beyond those that can be measured by conventional spectroscopic approaches.
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Affiliation(s)
- Jeff D Ballin
- Department of Biochemistry and Molecular Biology and Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
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24
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Homann M. Editing Reactions from the Perspective of RNA Structure. NUCLEIC ACIDS AND MOLECULAR BIOLOGY 2008. [DOI: 10.1007/978-3-540-73787-2_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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25
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Maydanovych O, Easterwood LM, Cui T, Véliz EA, Pokharel S, Beal PA. Probing adenosine-to-inosine editing reactions using RNA-containing nucleoside analogs. Methods Enzymol 2007; 424:369-86. [PMID: 17662850 DOI: 10.1016/s0076-6879(07)24017-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Advances in chemical synthesis and characterization of nucleic acids allows for atom-specific modification of complex RNAs, such as present in RNA editing substrates. By preparing substrates for ADARs by chemical synthesis, it is possible to subtly alter the structure of the edited nucleotide. Evaluating the effect these changes have on the rate of enzyme-catalyzed deamination reveals features of the editing reaction and guides the design of inhibitors. We describe the synthesis of select nucleoside analog phosphoramidites and their incorporation into RNAs that mimic known editing sites by solid phase synthesis, and analyze the interaction of these synthetic RNAs with ADARs using deamination kinetics and quantitative gel mobility shift assays.
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Affiliation(s)
- Olena Maydanovych
- Department of Chemistry, University of Utah, Salt Lake City, Utah, USA
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26
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Affiliation(s)
- Olena Maydanovych
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, USA
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27
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28
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Chao PW, Chow CS. Monitoring aminoglycoside-induced conformational changes in 16S rRNA through acrylamide quenching. Bioorg Med Chem 2007; 15:3825-31. [PMID: 17399988 PMCID: PMC2001229 DOI: 10.1016/j.bmc.2007.03.025] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2007] [Revised: 02/27/2007] [Accepted: 03/08/2007] [Indexed: 11/25/2022]
Abstract
Fluorescence of 2-aminopurine (2AP)-substituted A-site and acrylamide quenching were used to study the interactions of paromomycin and neamine with the decoding region of 16S rRNA. The results reveal that paromomycin binding to the A-site RNA leads to increased exposure of residue A1492. In contrast, neamine has little effect on the solvent accessibility of A1492. Electrospray ionization mass spectrometry was used to compare the affinity of paromomycin with the A-site and 2-AP-substituted A-site RNAs.
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Affiliation(s)
- Pei-Wen Chao
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, MI 48202, USA
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29
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Pokharel S, Beal PA. High-throughput screening for functional adenosine to inosine RNA editing systems. ACS Chem Biol 2006; 1:761-5. [PMID: 17240974 DOI: 10.1021/cb6003838] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Deamination of adenosines within messenger RNAs catalyzed by adenosine deaminases that act on RNA (ADAR) enzymes generates inosines at the corresponding nucleotide positions. Because inosine is decoded as guanosine, this reaction can lead to codon changes and the introduction of amino acids into a gene product not encoded in the gene. Translation of the different coding strands created by this process leads to protein structural diversity in the parent organism and is necessary for nervous system function in metazoa. The basis for selective editing of adenosines within certain codons is not well understood at the structural/biochemical level. Here we describe a high-throughput screen for ADAR/substrate combinations capable of RNA editing that can be carried out in the yeast Saccharomyces cerevisiae growing on agar plates. Results from the screening of libraries of human ADAR2 mutants and libraries of RNA substrates shed light on structure-activity relationships in the ADAR-catalyzed adenosine to inosine RNA editing reaction.
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30
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Poulsen H, Jorgensen R, Heding A, Nielsen FC, Bonven B, Egebjerg J. Dimerization of ADAR2 is mediated by the double-stranded RNA binding domain. RNA (NEW YORK, N.Y.) 2006; 12:1350-60. [PMID: 16682559 PMCID: PMC1484439 DOI: 10.1261/rna.2314406] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Members of the family of adenosine deaminases acting on RNA (ADARs) can catalyze the hydrolytic deamination of adenosine to inosine and thereby change the sequence of specific mRNAs with highly double-stranded structures. The ADARs all contain one or more repeats of the double-stranded RNA binding motif (DRBM). By both in vitro and in vivo assays, we show that the DRBMs of rat ADAR2 are necessary and sufficient for dimerization of the enzyme. Bioluminescence resonance energy transfer (BRET) demonstrates that ADAR2 also exists as dimers in living mammalian cells and that mutation of DRBM1 lowers the dimerization affinity while mutation of DRBM2 does not. Nonetheless, the editing efficiency of the GluR2 Q/R site depends on a functional DRBM2. The ADAR2 DRBMs thus serve differential roles in RNA dimerization and GluR2 Q/R editing, and we propose a model for RNA editing that incorporates the new findings.
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Affiliation(s)
- Hanne Poulsen
- Department of Molecular Biology, University of Aarhus, Denmark.
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31
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MacElrevey C, Wedekind JE. Crystallization and X-ray diffraction analysis of the Trp/amber editing site of hepatitis delta virus (+)RNA: a case of rational design. Acta Crystallogr Sect F Struct Biol Cryst Commun 2005; 61:1049-53. [PMID: 16511232 PMCID: PMC1978144 DOI: 10.1107/s1744309105035888] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2005] [Accepted: 11/02/2005] [Indexed: 11/10/2022]
Abstract
RNA editing by mammalian ADAR1 (Adenosine Deaminase Acting on RNA) is required for the life cycle of the hepatitis delta virus (HDV). Editing extends the single viral open reading frame to yield two protein products of alternate length. ADARs are believed to recognize double-stranded RNA substrates via a ;structure-based' readout mechanism. Crystals of 10-mer duplexes representing the HDV RNA-editing site diffracted to 1.35 A resolution, but suffered from merohedral twinning and averaging of the base registry. Expansion of the construct to include two flanking 3 x 1 internal loops yielded crystals in the primitive tetragonal space group P4(1)2(1)2 or P4(3)2(1)2. X-ray diffraction data were collected to 2.8 A resolution, revealing a unit cell with parameters a = 62.5, c = 63.5 A. The crystallization and X-ray analysis of multiple forms of the HDV RNA-editing substrate, encounters with common RNA crystal-growth defects and a strategy to overcome these problems are reported.
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Affiliation(s)
- Celeste MacElrevey
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
| | - Joseph E. Wedekind
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
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32
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Affiliation(s)
- Peter A Beal
- University of Utah, Department of Chemistry, Salt Lake City, Utah 84112, USA.
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33
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Hart K, Nyström B, Ohman M, Nilsson L. Molecular dynamics simulations and free energy calculations of base flipping in dsRNA. RNA (NEW YORK, N.Y.) 2005; 11:609-618. [PMID: 15811914 PMCID: PMC1370749 DOI: 10.1261/rna.7147805] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2004] [Accepted: 01/26/2005] [Indexed: 05/24/2023]
Abstract
The family of adenosine deaminases acting on RNA (ADARs) targets adenosines in RNA that is mainly double stranded. Some substrates are promiscuously deaminated whereas others, such as the mammalian glutamate receptor B (gluR-B) pre-mRNA, are more selectively deaminated. Many DNA/RNA-base modification enzymes use a base flipping mechanism to be able to reach their target base and it is believed that ADARs function in a similar way. In this study we used molecular dynamics (MD) simulations to describe two sites on the gluR-B pre-mRNA, the selectively targeted R/G site and the nontargeted 46 site, in an attempt to explain the substrate specificity. We used regular MD and also a forced base flipping method with umbrella sampling to calculate the free energy of base opening. Spontaneous opening of the mismatched adenosine was observed for the R/G site but not for the 46 site.
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Affiliation(s)
- Katarina Hart
- Department of Biosciences at NOVUM, Center for Structural Biochemistry, Karolinska Institutet, SE-141 57 Huddinge, Sweden
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34
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Haudenschild BL, Maydanovych O, Véliz EA, Macbeth MR, Bass BL, Beal PA. A transition state analogue for an RNA-editing reaction. J Am Chem Soc 2005; 126:11213-9. [PMID: 15355102 PMCID: PMC1823040 DOI: 10.1021/ja0472073] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Deamination at C6 of adenosine in RNA catalyzed by the ADAR enzymes generates inosine at the corresponding position. Because inosine is decoded as guanosine during translation, this modification can lead to codon changes in messenger RNA. Hydration of 8-azanebularine across the C6-N1 double bond generates an excellent mimic of the transition state proposed for the hydrolytic deamination reaction catalyzed by ADARs. Here, we report the synthesis of a phosphoramidite of 8-azanebularine and its use in the preparation of RNAs mimicking the secondary structure found at a known editing site in the glutamate receptor B subunit pre-mRNA. The binding properties of analogue-containing RNAs indicate that a tight binding ligand for an ADAR can be generated by incorporation of 8-azanebularine. The observed high-affinity binding is dependent on a functional active site, the presence of one, but not the other, of ADAR2's two double-stranded RNA-binding motifs (dsRBMs), and the correct placement of the nucleoside analogue into the sequence/structural context of a known editing site. These results advance our understanding of substrate recognition during ADAR-catalyzed RNA editing and are important for structural studies of ADAR.RNA complexes.
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35
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Stephens OM, Haudenschild BL, Beal PA. The binding selectivity of ADAR2's dsRBMs contributes to RNA-editing selectivity. ACTA ACUST UNITED AC 2005; 11:1239-50. [PMID: 15380184 DOI: 10.1016/j.chembiol.2004.06.009] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2003] [Revised: 05/18/2004] [Accepted: 06/21/2004] [Indexed: 01/23/2023]
Abstract
ADAR2 is an RNA editing enzyme that deaminates adenosines in certain duplex structures. Here, we describe the role of its RNA binding domain, consisting of two copies of a common dsRNA binding motif (dsRBM), in editing site selectivity. ADAR2's dsRBMs bind selectively on a duplex RNA that mimics the Q/R editing site in the glutamate receptor B-subunit pre-mRNA. This selectivity is different from that of PKR's dsRBM I, indicating that dsRBMs from different proteins possess intrinsic binding selectivity. Using directed hydroxyl radical cleavage data, molecular models were developed that predict important recognition surfaces on the RNA for identified dsRBM binding sites. Blocking these surfaces by benzyl modification of guanosine 2-amino groups impeded RNA-editing, demonstrating a correlation between deamination efficiency by ADAR2 and selective binding by its dsRBMs. In addition, the editing activity of a mutant of ADAR2 lacking dsRBM I on N(2)-benzylguanosine-modified RNA suggests the location of the dsRBM I binding site that leads to editing at the GluR-B Q/R site.
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Affiliation(s)
- Olen M Stephens
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
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36
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Valente L, Nishikura K. ADAR gene family and A-to-I RNA editing: diverse roles in posttranscriptional gene regulation. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2005; 79:299-338. [PMID: 16096031 DOI: 10.1016/s0079-6603(04)79006-6] [Citation(s) in RCA: 143] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Louis Valente
- The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
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37
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Abstract
Adenosine deaminases acting on RNA (ADARs), which are found in animals but are not known in other organisms, deaminate adenosines site-specifically within the coding sequences of transcripts encoding ion-channel subunits, increasing the diversity of these proteins in the central nervous system. Adenosine deaminases acting on RNA (ADARs) were discovered as a result of their ability extensively to deaminate adenosines in any long double-stranded RNA, converting them to inosines. Subsequently, ADARs were found to deaminate adenosines site-specifically within the coding sequences of transcripts encoding ion-channel subunits, increasing the diversity of these proteins in the central nervous system. ADAR1 is now known to be involved in defending the genome against viruses, and it may affect RNA interference. ADARs are found in animals but are not known in other organisms. It appears that ADARs evolved from a member of another family, adenosine deaminases acting on tRNAs (ADATs), by steps including fusion of two or more double-stranded-RNA binding domains to a common type of zinc-containing adenosine-deaminase domain.
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Affiliation(s)
- Liam P Keegan
- Medical Research Council Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK.
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38
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Dawson TR, Sansam CL, Emeson RB. Structure and sequence determinants required for the RNA editing of ADAR2 substrates. J Biol Chem 2003; 279:4941-51. [PMID: 14660658 DOI: 10.1074/jbc.m310068200] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
ADAR2 is a double-stranded RNA-specific adenosine deaminase involved in the editing of mammalian RNAs by the site-specific conversion of adenosine to inosine. We have demonstrated previously that ADAR2 can modify its own pre-mRNA, leading to the creation of a proximal 3'-splice junction containing a non-canonical adenosine-inosine (A-I) dinucleotide. Alternative splicing to this proximal acceptor shifts the reading frame of the mature mRNA transcript, resulting in the loss of functional ADAR2 expression. Both evolutionary sequence conservation and mutational analysis support the existence of an extended RNA duplex within the ADAR2 pre-mRNA formed by base-pairing interactions between regions approximately 1.3-kilobases apart in intron 4 and exon 5. Characterization of ADAR2 pre-mRNA transcripts isolated from adult rat brain identified 16 editing sites within this duplex region, and sites preferentially modified by ADAR1 and ADAR2 have been defined using both tissue culture and in vitro editing systems. Statistical analysis of nucleotide sequences surrounding edited and non-edited adenosine residues have identified a nucleotide sequence bias correlating with ADAR2 site preference and editing efficiency. Among a mixed population of ADAR substrates, ADAR2 preferentially favors its own transcript, yet mutation of a poor substrate to conform to the defined nucleotide bias increases the ability of that substrate to be modified by ADAR2. These data suggest that both sequence and structural elements are required to define adenosine moieties targeted for specific ADAR2-mediated deamination.
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Affiliation(s)
- T Renee Dawson
- Department of Molecular Physiology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
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39
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Carlson CB, Stephens OM, Beal PA. Recognition of double-stranded RNA by proteins and small molecules. Biopolymers 2003; 70:86-102. [PMID: 12925995 DOI: 10.1002/bip.10413] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Molecular recognition of double-stranded RNA (dsRNA) is a key event for numerous biological pathways including the trafficking, editing, and maturation of cellular RNA, the interferon antiviral response, and RNA interference. Over the past several years, our laboratory has studied proteins and small molecules that bind dsRNA with the goal of understanding and controlling the binding selectivity. In this review, we discuss members of the dsRBM class of proteins that bind dsRNA. The dsRBM is an approximately 70 amino acid sequence motif found in a variety of dsRNA-binding proteins. Recent results have led to a new appreciation of the ability of these proteins to bind selectivity to certain sites on dsRNA. This property is discussed in light of the RNA selectivity observed in the function of two proteins that contain dsRBMs, the RNA-dependent protein kinase (PKR) and an adenosine deaminase that acts on dsRNA (ADAR2). In addition, we introduce peptide-acridine conjugates (PACs), small molecules designed to control dsRBM-RNA interactions. These intercalating molecules bear variable peptide appendages at opposite edges of an acridine heterocycle. This design imparts the potential to exploit differences in groove characteristics and/or base-pair dynamics at binding sites to achieve selective binding.
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Affiliation(s)
- Coby B Carlson
- University of Utah, Department of Chemistry, 315 South 1400 East, Room 2020, Salt Lake City, UT 84112, USA
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Källman AM, Sahlin M, Ohman M. ADAR2 A-->I editing: site selectivity and editing efficiency are separate events. Nucleic Acids Res 2003; 31:4874-81. [PMID: 12907730 PMCID: PMC169957 DOI: 10.1093/nar/gkg681] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
ADAR enzymes, adenosine deaminases that act on RNA, form a family of RNA editing enzymes that convert adenosine to inosine within RNA that is completely or largely double-stranded. Site-selective A-->I editing has been detected at specific sites within a few structured pre-mRNAs of metazoans. We have analyzed the editing selectivity of ADAR enzymes and have chosen to study the naturally edited R/G site in the pre-mRNA of the glutamate receptor subunit B (GluR-B). A comparison of editing by ADAR1 and ADAR2 revealed differences in the specificity of editing. Our results show that ADAR2 selectively edits the R/G site, while ADAR1 edits more promiscuously at several other adenosines in the double-stranded stem. To further understand the mechanism of selective ADAR2 editing we have investigated the importance of internal loops in the RNA substrate. We have found that the immediate structure surrounding the editing site is important. A purine opposite to the editing site has a negative effect on both selectivity and efficiency of editing. More distant internal loops in the substrate were found to have minor effects on site selectivity, while efficiency of editing was found to be influenced. Finally, changes in the RNA structure that affected editing did not alter the binding abilities of ADAR2. Overall these findings suggest that binding and catalysis are independent events.
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Affiliation(s)
- Annika M Källman
- Department of Molecular Biology and Functional Genomics, Stockholm University, S-106 91 Stockholm, Sweden
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König J, Lotte K, Plessow R, Brockhinke A, Baier M, Dietz KJ. Reaction mechanism of plant 2-Cys peroxiredoxin. Role of the C terminus and the quaternary structure. J Biol Chem 2003; 278:24409-20. [PMID: 12702727 DOI: 10.1074/jbc.m301145200] [Citation(s) in RCA: 136] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Barley 2-cysteine peroxiredoxin (2-Cys Prx) was analyzed for peroxide reduction, quaternary structure, thylakoid attachment, and function as well as in vivo occurrence of the inactivated form, with emphasis on the role of specific amino acid residues. Data presented show the following. 1) 2-Cys Prx has a broad substrate specificity and reduces even complex lipid peroxides such as phosphatidylcholine dilineoyl hydroperoxide, although at low rates. 2) 2-Cys Prx partly becomes irreversibly oxidized by peroxide substrates during the catalytic cycle in a concentration-dependent manner, particularly by bulky hydroperoxides. 3) Using dithiothreitol and thioredoxin (Trx) as reductants, amino acids were identified that are important for peroxide reduction (Cys64, Arg140, and Arg163), regeneration by Trx (Cys185), and conformation changes from dimer to oligomer (Thr66, Trp99, and Trp189). 4) Oligomerization decreased the rate of Trx-dependent peroxide detoxification. 5) Comparison of PrxWT, W99L, and W189L using static and time-resolved LIF techniques demonstrated the contributions of the tryptophan residues and yielded information about their local environment. Data indicated protein dynamics in the catalytic site and the carboxyl terminus during the reduction-oxidation cycle. 6) Reduced and inactivated barley 2-Cys Prx oligomerized and attached to the thylakoid membrane in isolated chloroplasts. The in vivo relevance of inactivation was shown in leaves subjected to cold and wilting stress and during senescence. Based on these results, it is hypothesized that in addition to its function in peroxide detoxification, 2-Cys Prx may play a role as a structural redox sensor in chloroplasts.
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Affiliation(s)
- Janine König
- Biochemistry and Physiology of Plants, University of Bielefeld, Germany
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Klaue Y, Källman AM, Bonin M, Nellen W, Ohman M. Biochemical analysis and scanning force microscopy reveal productive and nonproductive ADAR2 binding to RNA substrates. RNA (NEW YORK, N.Y.) 2003; 9:839-846. [PMID: 12810917 PMCID: PMC1370450 DOI: 10.1261/rna.2167603] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2002] [Accepted: 03/28/2003] [Indexed: 05/24/2023]
Abstract
Scanning force microscopy (SFM) can be used to image biomolecules at high resolution. Here we demonstrate that single-molecule analysis by SFM complements biochemical data on RNA protein binding and can provide information that cannot be obtained by the usual biochemical methods. We have used this method to study the interaction between the RNA editing enzyme ADAR2 and RNA transcripts containing selective and nonselective editing sites. The natural selectively edited R/G site from glutamate receptor subunit B (GluR-B) was inserted into an RNA backbone molecule consisting of a completely double-stranded (ds) central part and incompletely paired ends derived from potato spindle tuber viroid (PSTVd). This molecule was efficiently edited at the R/G site, but promiscuous editing occurred at nonselective sites in the completely double-stranded region. The construct was also used to analyze binding of ADAR2 to wild-type and modified R/G editing sites in relation to binding at other nonselectively edited sites. Editing analysis together with SFM allow us to differentiate between binding and enzymatic activity. ADAR2 has been reported to have a general affinity to dsRNA. However, we show that there is a prominent bias for stable binding at sites selectively edited over other edited sites. On the other hand, promiscuous editing at nonselective sites apparently results from transient binding of the enzyme to the substrate. Furthermore, we find distinct sites with nonproductive binding of the enzyme.
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Affiliation(s)
- Yvonne Klaue
- Department of Genetics, University of Kassel, 34132 Kassel, Germany
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Doyle M, Jantsch MF. Distinct in vivo roles for double-stranded RNA-binding domains of the Xenopus RNA-editing enzyme ADAR1 in chromosomal targeting. J Cell Biol 2003; 161:309-19. [PMID: 12719472 PMCID: PMC2172894 DOI: 10.1083/jcb.200301034] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The RNA-editing enzyme adenosine deaminase that acts on RNA (ADAR1) deaminates adenosines to inosines in double-stranded RNA substrates. Currently, it is not clear how the enzyme targets and discriminates different substrates in vivo. However, it has been shown that the deaminase domain plays an important role in distinguishing various adenosines within a given substrate RNA in vitro. Previously, we could show that Xenopus ADAR1 is associated with nascent transcripts on transcriptionally active lampbrush chromosomes, indicating that initial substrate binding and possibly editing itself occurs cotranscriptionally. Here, we demonstrate that chromosomal association depends solely on the three double-stranded RNA-binding domains (dsRBDs) found in the central part of ADAR1, but not on the Z-DNA-binding domain in the NH2 terminus nor the catalytic deaminase domain in the COOH terminus of the protein. Most importantly, we show that individual dsRBDs are capable of recognizing different chromosomal sites in an apparently specific manner. Thus, our results not only prove the requirement of dsRBDs for chromosomal targeting, but also show that individual dsRBDs have distinct in vivo localization capabilities that may be important for initial substrate recognition and subsequent editing specificity.
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Affiliation(s)
- Michael Doyle
- Dept. of Cell Biology and Genetics, Institute of Botany, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
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Bratt E, Ohman M. Coordination of editing and splicing of glutamate receptor pre-mRNA. RNA (NEW YORK, N.Y.) 2003; 9:309-318. [PMID: 12592005 PMCID: PMC1370398 DOI: 10.1261/rna.2750803] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2002] [Accepted: 11/04/2002] [Indexed: 05/24/2023]
Abstract
Adenosine deaminase that acts on RNA, ADAR, catalyzes the conversion of adenosine into inosine within double-stranded RNA. This type of editing has mainly been found in genes involved in neurotransmission. Site-specific A to I modifications often require intronic sequences to create the double-stranded structure necessary for editing. A system was developed to investigate if editing and splicing of pre-mRNA are coordinated. We have focused on a selectively edited site (R/G) in the glutamate receptor subunit B pre-mRNA. This editing site is situated in close proximity to a 5' splice site. To ensure efficient splicing, the editing site, together with its natural 5' splice site, was fused to a 3' splice site of the major late transcript from adenovirus. In vitro, on a premade transcript, ADAR2 editing and splicing were found to interfere with each other. The stable stem-loop required for ADAR2 editing had a negative effect on in vitro splicing, possibly by sequestering the 5' splice site. Further, RNA helicase A was shown to overcome the splicing inhibition caused by ADAR2. In vivo, allowing cotranscriptional processing, the same construct was found to efficiently edit and splice without interference, suggesting that the two RNA processing events are coordinated.
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Affiliation(s)
- Eva Bratt
- Department of Molecular Biology and Functional Genomics, Stockholm University, 106 91 Stockholm, Sweden
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Jaikaran DCJ, Collins CH, MacMillan AM. Adenosine to inosine editing by ADAR2 requires formation of a ternary complex on the GluR-B R/G site. J Biol Chem 2002; 277:37624-9. [PMID: 12163487 DOI: 10.1074/jbc.m204126200] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
RNA editing by members of the ADAR (adenosine deaminase that acts on RNA) enzyme family involves hydrolytic deamination of adenosine to inosine within the context of a double-stranded pre-mRNA substrate. Editing of the human GluR-B transcript is catalyzed by the enzyme ADAR2 at the Q/R and R/G sites. We have established a minimal RNA substrate for editing based on the R/G site and have characterized the interaction of ADAR2 with this RNA by gel shift, kinetic, and cross-linking analyses. Gel shift analysis revealed that two complexes are formed on the RNA as protein concentration is increased; the ADAR monomers can be cross-linked to one another in an RNA-dependent fashion. We performed a detailed kinetic study of the editing reaction; the data from this study are consistent with a reaction scheme in which formation of an ADAR2.RNA ternary complex is required for efficient RNA editing and in which formation of this complex is rate determining. These observations suggest that RNA adenosine deaminases function as homodimers on their RNA substrates and may partially explain regulation of RNA editing in these systems.
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Affiliation(s)
- Dominic C J Jaikaran
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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Abstract
RNA editing is defined as a post-transcriptional change of a gene-encoded sequence at the RNA level, excluding alterations due to processes such as pre-mRNA splicing and 3'-end formation. RNA editing is found in many organisms and can occur either by the insertion or deletion of nucleotides or by the substitution of bases by modification. The nucleoside inosine (I) was first detected in cytoplasmic tRNA and was later found in messenger RNA precursors (pre-mRNAs) and in viral transcripts. It is formed by hydrolytic deamination of a genomically encoded adenosine (A) at C6 of the base and this reaction is catalysed by a family of related enzymes. ADARs (for adenosine deaminases acting on RNA) catalyse A to I conversion either promiscuously or site-specifically in pre-mRNAs, viral RNAs and synthetic double-stranded RNAs (dsRNAs), whereas ADATs (for adenosine deaminases acting on tRNA) are involved in inosine formation in tRNAs. ADAT1 generates I at position 37 (3' of the anticodon) in eukaryotic tRNA(Ala). ADAT2 and ADAT3 function as a heterodimer which catalyses inosine formation at the wobble position (position 34) in eukaryotic tRNAs. Here, we review the state of knowledge on ADARs and ADATs and their RNA substrates, with an emphasis on the developments over the past few years that have increased the understanding of the mechanism of action of these enzymes and of the functional consequences of the widespread modification they catalyse.
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Affiliation(s)
- Myriam Schaub
- Department of Cell Biology, Biozentrum, University of Basel, Klingelbergstrasse 70, 4056, Basel, Switzerland
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Abstract
ADARs are RNA editing enzymes that target double-stranded regions of nuclear-encoded RNA and viral RNA. These enzymes are particularly abundant in the nervous system, where they diversify the information encoded in the genome, for example, by altering codons in mRNAs. The functions of ADARs in known substrates suggest that the enzymes serve to fine-tune and optimize many biological pathways, in ways that we are only starting to imagine. ADARs are also interesting in regard to the remarkable double-stranded structures of their substrates and how enzyme specificity is achieved with little regard to sequence. This review summarizes ongoing investigations of the enzyme family and their substrates, focusing on biological function as well as biochemical mechanism.
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Affiliation(s)
- Brenda L Bass
- Department of Biochemistry and Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, Utah 84132, USA.
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Abstract
The availability of complete genome sequences has made it clear that gene number is not the sole determinant of the complexity of the proteome. Additional complexity that is not readily detected by genome analysis is present in the number and types of RNA transcript that can be derived from each locus. Although alternative splicing is a well-recognized method of generating diversity, the more subtle mechanism of RNA editing is less familiar.
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Affiliation(s)
- L P Keegan
- MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
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