101
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Drino A, Schaefer MR. RNAs, Phase Separation, and Membrane-Less Organelles: Are Post-Transcriptional Modifications Modulating Organelle Dynamics? Bioessays 2018; 40:e1800085. [PMID: 30370622 DOI: 10.1002/bies.201800085] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 09/25/2018] [Indexed: 12/24/2022]
Abstract
Membranous organelles allow sub-compartmentalization of biological processes. However, additional subcellular structures create dynamic reaction spaces without the need for membranes. Such membrane-less organelles (MLOs) are physiologically relevant and impact development, gene expression regulation, and cellular stress responses. The phenomenon resulting in the formation of MLOs is called liquid-liquid phase separation (LLPS), and is primarily governed by the interactions of multi-domain proteins or proteins harboring intrinsically disordered regions as well as RNA-binding domains. Although the presence of RNAs affects the formation and dissolution of MLOs, it remains unclear how the properties of RNAs exactly contribute to these effects. Here, the authors review this emerging field, and explore how particular RNA properties can affect LLPS and the behavior of MLOs. It is suggested that post-transcriptional RNA modification systems could be contributors for dynamically modulating the assembly and dissolution of MLOs.
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Affiliation(s)
- Aleksej Drino
- Division of Cell and Developmental Biology, Medical University Vienna, Center for Anatomy and Cell Biology, Schwarzspanierstrasse 17, A-1090, Vienna, Austria
| | - Matthias R Schaefer
- Division of Cell and Developmental Biology, Medical University Vienna, Center for Anatomy and Cell Biology, Schwarzspanierstrasse 17, A-1090, Vienna, Austria
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102
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Lobue PA, Yu N, Jora M, Abernathy S, Limbach PA. Improved application of RNAModMapper - An RNA modification mapping software tool - For analysis of liquid chromatography tandem mass spectrometry (LC-MS/MS) data. Methods 2018; 156:128-138. [PMID: 30366097 DOI: 10.1016/j.ymeth.2018.10.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 10/02/2018] [Accepted: 10/21/2018] [Indexed: 12/21/2022] Open
Abstract
Research into post-transcriptional processing and modification of RNA continues to speed forward, as their ever-emerging role in the regulation of gene expression in biological systems continues to unravel. Liquid chromatography tandem mass spectrometry (LC-MS/MS) has proven for over two decades to be a powerful ally in the elucidation of RNA modification identity and location, but the technique has not proceeded without its own unique technical challenges. The throughput of LC-MS/MS modification mapping experiments continues to be impeded by tedious and time-consuming spectral interpretation, particularly during for the analysis of complex RNA samples. RNAModMapper was recently developed as a tool to improve the interpretation and annotation of LC-MS/MS data sets from samples containing post-transcriptionally modified RNAs. Here, we delve deeper into the methodology and practice of RNAModMapper to provide greater insight into its utility, and remaining hurdles, in current RNA modification mapping experiments.
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Affiliation(s)
- Peter A Lobue
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, OH 45221-0172, United States
| | - Ningxi Yu
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, OH 45221-0172, United States
| | - Manasses Jora
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, OH 45221-0172, United States
| | - Scott Abernathy
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, OH 45221-0172, United States
| | - Patrick A Limbach
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, PO Box 210172, Cincinnati, OH 45221-0172, United States.
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103
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van Nues RW, Watkins NJ. Unusual C΄/D΄ motifs enable box C/D snoRNPs to modify multiple sites in the same rRNA target region. Nucleic Acids Res 2018; 45:2016-2028. [PMID: 28204564 PMCID: PMC5389607 DOI: 10.1093/nar/gkw842] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 09/08/2016] [Accepted: 09/12/2016] [Indexed: 11/13/2022] Open
Abstract
Eukaryotic box C/D small nucleolar (sno)RNPs catalyse the site-specific 2΄-O-methylation of ribosomal RNA. The RNA component (snoRNA) contains guide regions that base-pair with the target site to select the single nucleotide to be modified. The terminal C/D and internal C΄/D΄ motifs in the snoRNA, adjacent to the guide region, function as binding sites for the snoRNP proteins including the enzymatic subunit fibrillarin/Nop1. Four yeast snoRNAs are unusual in that they are predicted to methylate two nucleotides in a single target region. In each case, the internal C΄/D΄ motifs from these snoRNAs differ from the consensus. Our data indicate that the C΄/D΄ motifs in snR13, snR48 and U18 form two alternative structures that lead to differences in the position of the proteins bound to this motif. We propose that each snoRNA forms two different snoRNPs, subtly different in how the proteins are bound to the C΄/D΄ motif, leading to 2΄-O-methylation of different nucleotides in the target region. For snR48 and U18, the unusual C΄/D΄ alone is enough for the modification of two nucleotides. However, for the snR13 snoRNA the unusual C΄/D΄ motif and extra base-pairing, which stimulates rRNA 2΄-O-methylation, are both critical for multiple modifications in the target region.
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Affiliation(s)
- Robert Willem van Nues
- Institute for Cell and Molecular Biology, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Nicholas James Watkins
- Institute for Cell and Molecular Biology, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
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104
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Debnath TK, Okamoto A. Osmium Tag for Post-transcriptionally Modified RNA. Chembiochem 2018; 19:1653-1656. [PMID: 29799158 DOI: 10.1002/cbic.201800274] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Indexed: 12/19/2022]
Abstract
5-Methylcytidine (m5 C) and 5-methyluridine (m5 U) are highly abundant post-transcriptionally modified nucleotides that are observed in various natural RNAs. Such nucleotides were labeled through a chemical approach, as both underwent oxidation at the C5=C6 double bond, leading to the formation of osmium-bipyridine complexes, which could be identified by mass spectrometry. This osmium tag made it possible to distinguished m5 C and m5 U from their isomers, 2'-O-methylcytidine and 2'-O-methyluridine, respectively. Queuosine and 2-methylthio-N6 -isopentenyladenosine in tRNA were also tagged through complex formation.
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Affiliation(s)
- Turja Kanti Debnath
- Department of Advanced Interdisciplinary Studies, Graduate School of Engineering, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan
| | - Akimitsu Okamoto
- Department of Advanced Interdisciplinary Studies, Graduate School of Engineering, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan.,Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan
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105
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Structural insights into the stimulation of S. pombe Dnmt2 catalytic efficiency by the tRNA nucleoside queuosine. Sci Rep 2018; 8:8880. [PMID: 29892076 PMCID: PMC5995894 DOI: 10.1038/s41598-018-27118-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 05/24/2018] [Indexed: 01/16/2023] Open
Abstract
Dnmt2 methylates cytosine at position 38 of tRNAAsp in a variety of eukaryotic organisms. A correlation between the presence of the hypermodified nucleoside queuosine (Q) at position 34 of tRNAAsp and the Dnmt2 dependent C38 methylation was recently found in vivo for S. pombe and D. discoideum. We demonstrate a direct effect of the Q-modification on the methyltransferase catalytic efficiency in vitro, as Vmax/K0.5 of purified S. pombe Dnmt2 shows an increase for in vitro transcribed tRNAAsp containing Q34 to 6.27 ∗ 10–3 s−1 µM−1 compared to 1.51 ∗ 10–3 s−1 µM−1 for the unmodified substrate. Q34tRNAAsp exhibits an only slightly increased affinity for Dnmt2 in comparison to unmodified G34tRNA. In order to get insight into the structural basis for the Q-dependency, the crystal structure of S. pombe Dnmt2 was determined at 1.7 Å resolution. It closely resembles the known structures of human and E. histolytica Dnmt2, and contains the entire active site loop. The interaction with tRNA was analyzed by means of mass-spectrometry using UV cross-linked Dnmt2-tRNA complex. These cross-link data and computational docking of Dnmt2 and tRNAAsp reveal Q34 positioned adjacent to the S-adenosylmethionine occupying the active site, suggesting that the observed increase of Dnmt2 catalytic efficiency by queuine originates from optimal positioning of the substrate molecules and residues relevant for methyl transfer.
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106
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Leamy KA, Yennawar NH, Bevilacqua PC. Molecular Mechanism for Folding Cooperativity of Functional RNAs in Living Organisms. Biochemistry 2018; 57:2994-3002. [PMID: 29733204 PMCID: PMC6726375 DOI: 10.1021/acs.biochem.8b00345] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A diverse set of organisms has adapted to live under extreme conditions. The molecular origin of the stability is unclear, however. It is not known whether the adaptation of functional RNAs, which have intricate tertiary structures, arises from strengthening of tertiary or secondary structure. Herein we evaluate effects of sequence changes on the thermostability of tRNAphe using experimental and computational approaches. To separate out effects of secondary and tertiary structure on thermostability, we modify base pairing strength in the acceptor stem, which does not participate in tertiary structure. In dilute solution conditions, strengthening secondary structure leads to non-two-state thermal denaturation curves and has small effects on thermostability, or the temperature at which tertiary structure and function are lost. In contrast, under cellular conditions with crowding and Mg2+-chelated amino acids, where two-state cooperative unfolding is maintained, strengthening secondary structure enhances thermostability. Investigation of stabilities of each tRNA stem across 44 organisms with a range of optimal growing temperatures revealed that organisms that grow in warmer environments have more stable stems. We also used Shannon entropies to identify positions of higher and lower information content, or sequence conservation, in tRNAphe and found that secondary structures have modest information content allowing them to drive thermal adaptation, while tertiary structures have maximal information content hindering them from participating in thermal adaptation. Base-paired regions with no tertiary structure and modest information content thus offer a facile evolutionary route to enhancing the thermostability of functional RNA by the simple molecular rules of base pairing.
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Affiliation(s)
- Kathleen A Leamy
- Department of Chemistry , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
- Center for RNA Molecular Biology , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Neela H Yennawar
- Huck Institutes of the Life Sciences , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Philip C Bevilacqua
- Department of Chemistry , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
- Center for RNA Molecular Biology , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
- Department of Biochemistry and Molecular Biology , Pennsylvania State University , University Park , Pennsylvania 16802 , United States
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107
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Sabooh MF, Iqbal N, Khan M, Khan M, Maqbool HF. Identifying 5-methylcytosine sites in RNA sequence using composite encoding feature into Chou's PseKNC. J Theor Biol 2018; 452:1-9. [PMID: 29727634 DOI: 10.1016/j.jtbi.2018.04.037] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 04/24/2018] [Accepted: 04/27/2018] [Indexed: 02/02/2023]
Abstract
This study examines accurate and efficient computational method for identification of 5-methylcytosine sites in RNA modification. The occurrence of 5-methylcytosine (m5C) plays a vital role in a number of biological processes. For better comprehension of the biological functions and mechanism it is necessary to recognize m5C sites in RNA precisely. The laboratory techniques and procedures are available to identify m5C sites in RNA, but these procedures require a lot of time and resources. This study develops a new computational method for extracting the features of RNA sequence. In this method, first the RNA sequence is encoded via composite feature vector, then, for the selection of discriminate features, the minimum-redundancy-maximum-relevance algorithm was used. Secondly, the classification method used has been based on a support vector machine by using jackknife cross validation test. The suggested method efficiently identifies m5C sites from non- m5C sites and the outcome of the suggested algorithm is 93.33% with sensitivity of 90.0 and specificity of 96.66 on bench mark datasets. The result exhibits that proposed algorithm shown significant identification performance compared to the existing computational techniques. This study extends the knowledge about the occurrence sites of RNA modification which paves the way for better comprehension of the biological uses and mechanism.
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Affiliation(s)
- M Fazli Sabooh
- Department of Computer Science, Abdul Wali Khan University Mardan, Pakistan
| | - Nadeem Iqbal
- Department of Computer Science, Abdul Wali Khan University Mardan, Pakistan.
| | - Mukhtaj Khan
- Department of Computer Science, Abdul Wali Khan University Mardan, Pakistan
| | - Muslim Khan
- Department of Computer Science, Abdul Wali Khan University Mardan, Pakistan
| | - H F Maqbool
- University of Engineering & Technology Lahore, Pakistan
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108
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Angelova MT, Dimitrova DG, Dinges N, Lence T, Worpenberg L, Carré C, Roignant JY. The Emerging Field of Epitranscriptomics in Neurodevelopmental and Neuronal Disorders. Front Bioeng Biotechnol 2018; 6:46. [PMID: 29707539 PMCID: PMC5908907 DOI: 10.3389/fbioe.2018.00046] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 03/29/2018] [Indexed: 01/19/2023] Open
Abstract
Analogous to DNA methylation and histone modifications, RNA modifications represent a novel layer of regulation of gene expression. The dynamic nature and increasing number of RNA modifications offer new possibilities to rapidly alter gene expression upon specific environmental changes. Recent lines of evidence indicate that modified RNA molecules and associated complexes regulating and “reading” RNA modifications play key roles in the nervous system of several organisms, controlling both, its development and function. Mutations in several human genes that modify transfer RNA (tRNA) have been linked to neurological disorders, in particular to intellectual disability. Loss of RNA modifications alters the stability of tRNA, resulting in reduced translation efficiency and generation of tRNA fragments, which can interfere with neuronal functions. Modifications present on messenger RNAs (mRNAs) also play important roles during brain development. They contribute to neuronal growth and regeneration as well as to the local regulation of synaptic functions. Hence, potential combinatorial effects of RNA modifications on different classes of RNA may represent a novel code to dynamically fine tune gene expression during brain function. Here we discuss the recent findings demonstrating the impact of modified RNAs on neuronal processes and disorders.
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Affiliation(s)
- Margarita T Angelova
- Drosophila Genetics and Epigenetics, Sorbonne Université, Centre National de la Recherche Scientifique, Biologie du Développement-Institut de Biologie Paris Seine, Paris, France
| | - Dilyana G Dimitrova
- Drosophila Genetics and Epigenetics, Sorbonne Université, Centre National de la Recherche Scientifique, Biologie du Développement-Institut de Biologie Paris Seine, Paris, France
| | - Nadja Dinges
- Laboratory of RNA Epigenetics, Institute of Molecular Biology, Mainz, Germany
| | - Tina Lence
- Laboratory of RNA Epigenetics, Institute of Molecular Biology, Mainz, Germany
| | - Lina Worpenberg
- Laboratory of RNA Epigenetics, Institute of Molecular Biology, Mainz, Germany
| | - Clément Carré
- Drosophila Genetics and Epigenetics, Sorbonne Université, Centre National de la Recherche Scientifique, Biologie du Développement-Institut de Biologie Paris Seine, Paris, France
| | - Jean-Yves Roignant
- Laboratory of RNA Epigenetics, Institute of Molecular Biology, Mainz, Germany
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109
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Carlsson L, Clarke JC, Yen C, Gregoire F, Albery T, Billger M, Egnell AC, Gan LM, Jennbacken K, Johansson E, Linhardt G, Martinsson S, Sadiq MW, Witman N, Wang QD, Chen CH, Wang YP, Lin S, Ticho B, Hsieh PCH, Chien KR, Fritsche-Danielson R. Biocompatible, Purified VEGF-A mRNA Improves Cardiac Function after Intracardiac Injection 1 Week Post-myocardial Infarction in Swine. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2018; 9:330-346. [PMID: 30038937 PMCID: PMC6054703 DOI: 10.1016/j.omtm.2018.04.003] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 04/04/2018] [Indexed: 12/02/2022]
Abstract
mRNA can direct dose-dependent protein expression in cardiac muscle without genome integration, but to date has not been shown to improve cardiac function in a safe, clinically applicable way. Herein, we report that a purified and optimized mRNA in a biocompatible citrate-saline formulation is tissue specific, long acting, and does not stimulate an immune response. In small- and large-animal, permanent occlusion myocardial infarction models, VEGF-A 165 mRNA improves systolic ventricular function and limits myocardial damage. Following a single administration a week post-infarction in mini pigs, left ventricular ejection fraction, inotropy, and ventricular compliance improved, border zone arteriolar and capillary density increased, and myocardial fibrosis decreased at 2 months post-treatment. Purified VEGF-A mRNA establishes the feasibility of improving cardiac function in the sub-acute therapeutic window and may represent a new class of therapies for ischemic injury.
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Affiliation(s)
- Leif Carlsson
- Innovative Medicines and Early Development Biotech Unit, Cardiovascular, Renal and Metabolic Diseases, AstraZeneca, Mölndal 431 83, Sweden
| | - Jonathan C Clarke
- Integrated Cardiometabolic Center, Karolinska Institute, Huddinge 141 52, Sweden.,Department of Cell and Molecular Biology and Medicine, Karolinska Institute, Stockholm 171 77, Sweden
| | - Christopher Yen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | | | - Tamsin Albery
- Innovative Medicines and Early Development Biotech Unit, Cardiovascular, Renal and Metabolic Diseases, AstraZeneca, Mölndal 431 83, Sweden
| | - Martin Billger
- Drug Safety and Metabolism, Regulatory Safety, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Ann-Charlotte Egnell
- Innovative Medicines and Early Development Biotech Unit, Cardiovascular, Renal and Metabolic Diseases, AstraZeneca, Mölndal 431 83, Sweden
| | - Li-Ming Gan
- Innovative Medicines and Early Development Biotech Unit, Cardiovascular, Renal and Metabolic Diseases, AstraZeneca, Mölndal 431 83, Sweden
| | - Karin Jennbacken
- Innovative Medicines and Early Development Biotech Unit, Cardiovascular, Renal and Metabolic Diseases, AstraZeneca, Mölndal 431 83, Sweden
| | - Edvin Johansson
- Personalised Healthcare and Biomarkers, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Gunilla Linhardt
- Innovative Medicines and Early Development Biotech Unit, Cardiovascular, Renal and Metabolic Diseases, AstraZeneca, Mölndal 431 83, Sweden
| | - Sofia Martinsson
- Innovative Medicines and Early Development Biotech Unit, Cardiovascular, Renal and Metabolic Diseases, AstraZeneca, Mölndal 431 83, Sweden
| | - Muhammad Waqas Sadiq
- Innovative Medicines and Early Development Biotech Unit, Cardiovascular, Renal and Metabolic Diseases, AstraZeneca, Mölndal 431 83, Sweden
| | - Nevin Witman
- Department of Cell and Molecular Biology and Medicine, Karolinska Institute, Stockholm 171 77, Sweden
| | - Qing-Dong Wang
- Innovative Medicines and Early Development Biotech Unit, Cardiovascular, Renal and Metabolic Diseases, AstraZeneca, Mölndal 431 83, Sweden
| | - Chien-Hsi Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Ping Wang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Susan Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | | | - Patrick C H Hsieh
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan.,Institute of Medical Genomics and Proteomics, Institute of Clinical Medicine and Cardiovascular Surgery Division, National Taiwan University and Hospital, Taipei 100, Taiwan
| | - Kenneth R Chien
- Integrated Cardiometabolic Center, Karolinska Institute, Huddinge 141 52, Sweden.,Department of Cell and Molecular Biology and Medicine, Karolinska Institute, Stockholm 171 77, Sweden
| | - Regina Fritsche-Danielson
- Innovative Medicines and Early Development Biotech Unit, Cardiovascular, Renal and Metabolic Diseases, AstraZeneca, Mölndal 431 83, Sweden
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110
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Koh CS, Sarin LP. Transfer RNA modification and infection – Implications for pathogenicity and host responses. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:419-432. [DOI: 10.1016/j.bbagrm.2018.01.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/04/2018] [Accepted: 01/19/2018] [Indexed: 12/19/2022]
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111
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Kremser J, Strebitzer E, Plangger R, Juen MA, Nußbaumer F, Glasner H, Breuker K, Kreutz C. Chemical synthesis and NMR spectroscopy of long stable isotope labelled RNA. Chem Commun (Camb) 2018; 53:12938-12941. [PMID: 29155431 DOI: 10.1039/c7cc06747j] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We showcase the high potential of the 2'-cyanoethoxymethyl (CEM) methodology to synthesize RNAs with naturally occurring modified residues carrying stable isotope (SI) labels for NMR spectroscopic applications. The method was applied to synthesize RNAs with sizes ranging between 60 to 80 nucleotides. The presented approach gives the possibility to selectively modify larger RNAs (>60 nucleotides) with atom-specifically 13C/15N-labelled building blocks. The method harbors the unique potential to address structural as well as dynamic features of these RNAs with NMR spectroscopy but also using other biophysical methods, such as mass spectrometry (MS), or small angle neutron/X-ray scattering (SANS, SAXS).
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Affiliation(s)
- J Kremser
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria.
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112
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Kumar VA. Evolution of specific 3'-5'-linkages in RNA in pre-biotic soup: a new hypothesis. Org Biomol Chem 2018; 14:10123-10133. [PMID: 27714238 DOI: 10.1039/c6ob01796g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
This article reviews the different possibilities towards progression of the formation of DNA/RNA in the chemical world, before life, in enzyme-free conditions. The advent of deoxyribo- and ribopentose-sugars, nucleosides, nucleotides and oligonucleotides in the prebiotic soup is briefly discussed. Further, the formation of early single stranded oligomers, base-pairing possibilities and information transfer based on the stability parameters of the derived duplexes is reviewed. Each theory has its own merits and demerits which we have elaborated upon. Lastly, using clues from this literature, a possible explanation for the specific 3'-5'-linkages in RNA is proposed.
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Affiliation(s)
- Vaijayanti A Kumar
- Organic Chemistry Division, CSIR-National Chemical Laboratory, Dr Homi Bhabha Road, Pune, 411008, India.
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113
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Evolution of Eukaryal and Archaeal Pseudouridine Synthase Pus10. J Mol Evol 2018; 86:77-89. [PMID: 29349599 DOI: 10.1007/s00239-018-9827-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 01/03/2018] [Indexed: 10/18/2022]
Abstract
In archaea, pseudouridine (Ψ) synthase Pus10 modifies uridine (U) to Ψ at positions 54 and 55 of tRNA. In contrast, Pus10 is not found in bacteria, where modifications at those two positions are carried out by TrmA (U54 to m5U54) and TruB (U55 to Ψ55). Many eukaryotes have an apparent redundancy; their genomes contain orthologs of archaeal Pus10 and bacterial TrmA and TruB. Although eukaryal Pus10 genes share a conserved catalytic domain with archaeal Pus10 genes, their biological roles are not clear for the two reasons. First, experimental evidence suggests that human Pus10 participates in apoptosis induced by the tumor necrosis factor-related apoptosis-inducing ligand. Whether the function of human Pus10 is in place or in addition to of Ψ synthesis in tRNA is unknown. Second, Pus10 is found in earlier evolutionary branches of fungi (such as chytrid Batrachochytrium) but is absent in all dikaryon fungi surveyed (Ascomycetes and Basidiomycetes). We did a comprehensive analysis of sequenced genomes and found that orthologs of Pus10, TrmA, and TruB were present in all the animals, plants, and protozoa surveyed. This indicates that the common eukaryotic ancestor possesses all the three genes. Next, we examined 116 archaeal and eukaryotic Pus10 protein sequences to find that Pus10 existed as a single copy gene in all the surveyed genomes despite ancestral whole genome duplications had occurred. This indicates a possible deleterious gene dosage effect. Our results suggest that functional redundancy result in gene loss or neofunctionalization in different evolutionary lineages.
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114
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115
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Becker S, Schneider C, Okamura H, Crisp A, Amatov T, Dejmek M, Carell T. Wet-dry cycles enable the parallel origin of canonical and non-canonical nucleosides by continuous synthesis. Nat Commun 2018; 9:163. [PMID: 29323115 PMCID: PMC5765019 DOI: 10.1038/s41467-017-02639-1] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 12/14/2017] [Indexed: 12/28/2022] Open
Abstract
The molecules of life were created by a continuous physicochemical process on an early Earth. In this hadean environment, chemical transformations were driven by fluctuations of the naturally given physical parameters established for example by wet-dry cycles. These conditions might have allowed for the formation of (self)-replicating RNA as the fundamental biopolymer during chemical evolution. The question of how a complex multistep chemical synthesis of RNA building blocks was possible in such an environment remains unanswered. Here we report that geothermal fields could provide the right setup for establishing wet-dry cycles that allow for the synthesis of RNA nucleosides by continuous synthesis. Our model provides both the canonical and many ubiquitous non-canonical purine nucleosides in parallel by simple changes of physical parameters such as temperature, pH and concentration. The data show that modified nucleosides were potentially formed as competitor molecules. They could in this sense be considered as molecular fossils.
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Affiliation(s)
- Sidney Becker
- Center for Integrated Protein Science Munich CiPSM at the Department of Chemistry, Ludwig-Maximilians-Universität München, 81377, Munich, Germany
| | - Christina Schneider
- Center for Integrated Protein Science Munich CiPSM at the Department of Chemistry, Ludwig-Maximilians-Universität München, 81377, Munich, Germany
| | - Hidenori Okamura
- Center for Integrated Protein Science Munich CiPSM at the Department of Chemistry, Ludwig-Maximilians-Universität München, 81377, Munich, Germany
| | - Antony Crisp
- Center for Integrated Protein Science Munich CiPSM at the Department of Chemistry, Ludwig-Maximilians-Universität München, 81377, Munich, Germany
| | - Tynchtyk Amatov
- Center for Integrated Protein Science Munich CiPSM at the Department of Chemistry, Ludwig-Maximilians-Universität München, 81377, Munich, Germany
| | - Milan Dejmek
- Institute of Organic Chemistry and Biochemistry ASCR, 16610, Prague 6, Czech Republic
| | - Thomas Carell
- Center for Integrated Protein Science Munich CiPSM at the Department of Chemistry, Ludwig-Maximilians-Universität München, 81377, Munich, Germany.
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116
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Filippova JA, Semenov DV, Juravlev ES, Komissarov AB, Richter VA, Stepanov GA. Modern Approaches for Identification of Modified Nucleotides in RNA. BIOCHEMISTRY (MOSCOW) 2018; 82:1217-1233. [PMID: 29223150 DOI: 10.1134/s0006297917110013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This review considers approaches for detection of modified monomers in the RNA structure of living organisms. Recently, some data on dynamic alterations in the pool of modifications of the key RNA species that depend on external factors affecting the cells and physiological conditions of the whole organism have been accumulated. The recent studies have presented experimental data on relationship between the mechanisms of formation of modified/minor nucleotides of RNA in mammalian cells and the development of various pathologies. The development of novel methods for detection of chemical modifications of RNA nucleotides in the cells of living organisms and accumulation of knowledge on the contribution of modified monomers to metabolism and functioning of individual RNA species establish the basis for creation of novel diagnostic and therapeutic approaches. This review includes a short description of routine methods for determination of modified nucleotides in RNA and considers in detail modern approaches that enable not only detection but also quantitative assessment of the modification level of various nucleotides in individual RNA species.
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Affiliation(s)
- J A Filippova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
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117
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Deryusheva S, Gall JG. Orchestrated positioning of post-transcriptional modifications at the branch point recognition region of U2 snRNA. RNA (NEW YORK, N.Y.) 2018; 24:30-42. [PMID: 28974555 PMCID: PMC5733568 DOI: 10.1261/rna.063842.117] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 09/25/2017] [Indexed: 05/21/2023]
Abstract
The branch point recognition region of spliceosomal snRNA U2 is heavily modified post-transcriptionally in most eukaryotic species. We focused on this region to learn how nearby positions may interfere with each other when targeted for modification. Using an in vivo yeast Saccharomyces cerevisiae cell system, we tested the modification activity of several guide RNAs from human, mouse, the frog Xenopus tropicalis, the fruit fly Drosophila melanogaster, and the worm Caenorhabditis elegans We experimentally verified predictions for vertebrate U2 modification guide RNAs SCARNA4 and SCARNA15, and identified a C. elegans ortholog of SCARNA15. We observed crosstalk between sites in the heavily modified regions, such that modification at one site may inhibit modification at nearby sites. This is true for the branch point recognition region of U2 snRNA, the 5' loop of U5 snRNA, and certain regions of rRNAs, when tested either in yeast or in HeLa cells. The position preceding a uridine targeted for isomerization by a box H/ACA guide RNA is the most sensitive for noncanonical base-pairing and modification (either pseudouridylation or 2'-O-methylation). Based on these findings, we propose that modification must occur stepwise starting with the most vulnerable positions and ending with the most inhibiting modifications. We discuss possible strategies that cells use to reach complete modification in heavily modified regions.
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Affiliation(s)
- Svetlana Deryusheva
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA
| | - Joseph G Gall
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA
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118
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McKenney KM, Rubio MAT, Alfonzo JD. Binding synergy as an essential step for tRNA editing and modification enzyme codependence in Trypanosoma brucei. RNA (NEW YORK, N.Y.) 2018; 24:56-66. [PMID: 29042505 PMCID: PMC5733570 DOI: 10.1261/rna.062893.117] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 10/02/2017] [Indexed: 05/10/2023]
Abstract
Transfer RNAs acquire a variety of naturally occurring chemical modifications during their maturation; these fine-tune their structure and decoding properties in a manner critical for protein synthesis. We recently reported that in the eukaryotic parasite, Trypanosoma brucei, a methylation and deamination event are unexpectedly interconnected, whereby the tRNA adenosine deaminase (TbADAT2/3) and the 3-methylcytosine methyltransferase (TbTrm140) strictly rely on each other for activity, leading to formation of m3C and m3U at position 32 in several tRNAs. Still however, it is not clear why these two enzymes, which work independently in other systems, are strictly codependent in T. brucei Here, we show that these enzymes exhibit binding synergism, or a mutual increase in binding affinity, that is more than the sum of the parts, when added together in a reaction. Although these enzymes interact directly with each other, tRNA binding assays using enzyme variants mutated in critical binding and catalytic sites indicate that the observed binding synergy stems from contributions from tRNA-binding domains distal to their active sites. These results provide a rationale for the known interactions of these proteins, while also speaking to the modulation of substrate specificity between seemingly unrelated enzymes. This information should be of value in furthering our understanding of how tRNA modification enzymes act together to regulate gene expression at the post-transcriptional level and provide a basis for the interdependence of such activities.
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Affiliation(s)
- Katherine M McKenney
- Department of Microbiology, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA
| | - Mary Anne T Rubio
- Department of Microbiology, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Juan D Alfonzo
- Department of Microbiology, Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA
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119
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Olvedy M, Scaravilli M, Hoogstrate Y, Visakorpi T, Jenster G, Martens-Uzunova ES. A comprehensive repertoire of tRNA-derived fragments in prostate cancer. Oncotarget 2017; 7:24766-77. [PMID: 27015120 PMCID: PMC5029740 DOI: 10.18632/oncotarget.8293] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 03/02/2016] [Indexed: 12/20/2022] Open
Abstract
Prostate cancer (PCa) is the most common cancer among men in developed countries. Although its genetic background is thoroughly investigated, rather little is known about the role of small non-coding RNAs (sncRNA) in this disease. tRNA-derived fragments (tRFs) represent a new class of sncRNAs, which are present in a broad range of species and have been reported to play a role in several cellular processes. Here, we analyzed the expression of tRFs in fresh frozen patient samples derived from normal adjacent prostate and different stages of PCa by RNA-sequencing. We identified 598 unique tRFs, many of which are deregulated in cancer samples when compared to normal adjacent tissue. Most of the identified tRFs are derived from the 5’- and 3’-ends of mature cytosolic tRNAs, but we also found tRFs produced from other parts of tRNAs, including pre-tRNA trailers and leaders, as well as tRFs from mitochondrial tRNAs. The 5’-derived tRFs comprise the most abundant class of tRFs in general and represent the major class among upregulated tRFs. The 3’-derived tRFs types are dominant among downregulated tRFs in PCa. We validated the expression of three tRFs using qPCR. The ratio of tRFs derived from tRNALysCTT and tRNAPheGAA emerged as a good indicator of progression-free survival and a candidate prognostic marker. This study provides a systematic catalogue of tRFs and their dysregulation in PCa and can serve as the basis for further research on the biomarker potential and functional roles of tRFs in this disease.
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Affiliation(s)
- Michael Olvedy
- Department of Urology, Erasmus MC, Rotterdam, The Netherlands.,Current address: VIB Center for the Biology of Disease, KU Leuven, Leuven, Belgium.,Current address: Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Mauro Scaravilli
- Institute of Biosciences and Medical Technology-BioMediTech, University of Tampere, Tampere, Finland.,Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | | | - Tapio Visakorpi
- Institute of Biosciences and Medical Technology-BioMediTech, University of Tampere, Tampere, Finland.,Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Guido Jenster
- Department of Urology, Erasmus MC, Rotterdam, The Netherlands
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120
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Ray AK, Naiyer S, Singh SS, Bhattacharya A, Bhattacharya S. Application of SHAPE reveals in vivo RNA folding under normal and growth-stressed conditions in the human parasite Entamoeba histolytica. Mol Biochem Parasitol 2017; 219:42-51. [PMID: 29175581 DOI: 10.1016/j.molbiopara.2017.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 11/30/2022]
Abstract
Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) is a versatile sequence independent method to probe RNA structure in vivo and in vitro. It has so far been tried mainly with model organisms. We show that cells of Entamoeba histolytica, a protozoan parasite of humans are hyper-sensitive to the in vivo SHAPE reagent, NAI, and show rapid loss of viability and RNA integrity. We optimized treatment conditions with 5.8S rRNA and Eh_U3 snoRNA to obtain NAI-modification while retaining RNA integrity. The modification patterns were highly reproducible. The in vivo folding was different from in vitro and correlated well with known interactions of 5.8S rRNA with proteins in vivo. The Eh_U3 snoRNA also showed many differences in its in vivo versus in vitro folding, which correlated with conserved interactions of this RNA with 18S rRNA and 5'-ETS. Further, Eh_U3 snoRNA obtained from serum-starved cells showed an open 3'-hinge structure, indicating disruption of 5'-ETS interaction. This could contribute to the observed slow processing of pre-rRNA in starved cells. Our work shows the applicability of SHAPE to study in vivo RNA folding in a parasite and will encourage the use of this reagent for RNA structure analysis in other such organisms.
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Affiliation(s)
- Ashwini Kumar Ray
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sarah Naiyer
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | | | - Alok Bhattacharya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Sudha Bhattacharya
- School of Environmental Sciences, Jawaharlal Nehru University, New Delhi, India.
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121
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Dewe JM, Fuller BL, Lentini JM, Kellner SM, Fu D. TRMT1-Catalyzed tRNA Modifications Are Required for Redox Homeostasis To Ensure Proper Cellular Proliferation and Oxidative Stress Survival. Mol Cell Biol 2017; 37:e00214-17. [PMID: 28784718 PMCID: PMC5640816 DOI: 10.1128/mcb.00214-17] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 05/17/2017] [Accepted: 07/29/2017] [Indexed: 02/07/2023] Open
Abstract
Mutations in the tRNA methyltransferase 1 (TRMT1) gene have been identified as the cause of certain forms of autosomal-recessive intellectual disability (ID). However, the molecular pathology underlying ID-associated TRMT1 mutations is unknown, since the biological role of the encoded TRMT1 protein remains to be determined. Here, we have elucidated the molecular targets and function of TRMT1 to uncover the cellular effects of ID-causing TRMT1 mutations. Using human cells that have been rendered deficient in TRMT1, we show that TRMT1 is responsible for catalyzing the dimethylguanosine (m2,2G) base modification in both nucleus- and mitochondrion-encoded tRNAs. TRMT1-deficient cells exhibit decreased proliferation rates, alterations in global protein synthesis, and perturbations in redox homeostasis, including increased endogenous ROS levels and hypersensitivity to oxidizing agents. Notably, ID-causing TRMT1 variants are unable to catalyze the formation of m2,2G due to defects in RNA binding and cannot rescue oxidative stress sensitivity. Our results uncover a biological role for TRMT1-catalyzed tRNA modification in redox metabolism and show that individuals with TRMT1-associated ID are likely to have major perturbations in cellular homeostasis due to the lack of m2,2G modifications.
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Affiliation(s)
- Joshua M Dewe
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York, USA
| | - Benjamin L Fuller
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York, USA
| | - Jenna M Lentini
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York, USA
| | | | - Dragony Fu
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, New York, USA
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122
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Michaelides IN, Tago N, Viverge B, Carell T. Synthesis of RNA Containing 5-Hydroxymethyl-, 5-Formyl-, and 5-Carboxycytidine. Chemistry 2017; 23:15894-15898. [PMID: 28906048 DOI: 10.1002/chem.201704216] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Indexed: 12/17/2022]
Abstract
5-Hydroxymethyl-, 5-formyl-, and 5-carboxy-2'-deoxycytidine are new epigenetic bases (hmdC, fdC, cadC) that were recently discovered in the DNA of higher eukaryotes. The same bases (5-hydroxymethyl-, 5-formyl-, and 5-carboxycytidine; hmC, fC, and caC) have now also been detected in mammalian RNA with a high abundance in mRNA. While DNA phosphoramidites (PAs) that allow the synthesis of xdC-containing oligonucleotides for deeper biological studies are available, the corresponding silyl-protected RNA PAs for fC and caC have not yet been disclosed. Here, we report novel RNA PAs for hmC, fC, and caC that can be used in routine RNA synthesis. The new building blocks are compatible with the canonical PAs and also with themselves, which enables even the synthesis of RNA strands containing all three of these bases. The study will pave the way for detailed physical, biochemical, and biological studies to unravel the function of these non-canonical modifications in RNA.
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Affiliation(s)
- Iacovos N Michaelides
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany.,Current address: AstraZeneca, 310 Cambridge Science Park, Milton Road, Cambridge, CB4 0FZ, UK
| | - Nobuhiro Tago
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Bastien Viverge
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Thomas Carell
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377, Munich, Germany
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123
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Stojković V, Fujimori DG. Mutations in RNA methylating enzymes in disease. Curr Opin Chem Biol 2017; 41:20-27. [PMID: 29059606 DOI: 10.1016/j.cbpa.2017.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Revised: 10/01/2017] [Accepted: 10/03/2017] [Indexed: 01/06/2023]
Abstract
RNA methylation is an abundant modification identified in various RNA species in both prokaryotic and eukaryotic organisms. However, the functional roles for the majority of these methylations remain largely unclear. In eukaryotes, many RNA methylations have been suggested to participate in fundamental cellular processes. Mutations in eukaryotic RNA methylating enzymes, and a consequent change in methylation, can lead to the development of diseases and disorders. In contrast, loss of RNA methylation in prokaryotes can be beneficial to microorganisms, especially under antibiotic pressure. Here we discuss several recent advances in understanding mutational landscape of both eukaryotic and prokaryotic RNA methylating enzymes and their relevance to disease and antibiotic resistance.
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Affiliation(s)
- Vanja Stojković
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, 600 16th St, MC2280, San Francisco, CA 94158, United States
| | - Danica Galonić Fujimori
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, 600 16th St, MC2280, San Francisco, CA 94158, United States; Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th St, MC2280, San Francisco, CA 94158, United States.
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124
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Tomkuvienė M, Ličytė J, Olendraitė I, Liutkevičiūtė Z, Clouet-d'Orval B, Klimašauskas S. Archaeal fibrillarin-Nop5 heterodimer 2'- O-methylates RNA independently of the C/D guide RNP particle. RNA (NEW YORK, N.Y.) 2017; 23:1329-1337. [PMID: 28576826 PMCID: PMC5558902 DOI: 10.1261/rna.059832.116] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 05/19/2017] [Indexed: 06/01/2023]
Abstract
Archaeal fibrillarin (aFib) is a well-characterized S-adenosyl methionine (SAM)-dependent RNA 2'-O-methyltransferase that is known to act in a large C/D ribonucleoprotein (RNP) complex together with Nop5 and L7Ae proteins and a box C/D guide RNA. In the reaction, the guide RNA serves to direct the methylation reaction to a specific site in tRNA or rRNA by sequence complementarity. Here we show that a Pyrococcus abyssi aFib-Nop5 heterodimer can alone perform SAM-dependent 2'-O-methylation of 16S and 23S ribosomal RNAs in vitro independently of L7Ae and C/D guide RNAs. Using tritium-labeling, mass spectrometry, and reverse transcription analysis, we identified three in vitro 2'-O-methylated positions in the 16S rRNA of P. abyssi, positions lying outside of previously reported pyrococcal C/D RNP methylation sites. This newly discovered stand-alone activity of aFib-Nop5 may provide an example of an ancestral activity retained in enzymes that were recruited to larger complexes during evolution.
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MESH Headings
- Archaea/genetics
- Archaea/metabolism
- Chromosomal Proteins, Non-Histone/chemistry
- Chromosomal Proteins, Non-Histone/metabolism
- Methylation
- Nucleic Acid Conformation
- Protein Binding
- Protein Multimerization
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/metabolism
- RNA, Ribosomal, 23S/chemistry
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 23S/metabolism
- Ribonucleoproteins/chemistry
- Ribonucleoproteins/metabolism
- Ribonucleoproteins, Small Nucleolar/chemistry
- Ribonucleoproteins, Small Nucleolar/metabolism
- Substrate Specificity
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Affiliation(s)
- Miglė Tomkuvienė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania
| | - Janina Ličytė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania
| | - Ingrida Olendraitė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Zita Liutkevičiūtė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania
| | - Béatrice Clouet-d'Orval
- Laboratoire de Microbiologie et Génétique Moléculaires UMR 5100, CNRS, Université de Toulouse, F-31062 Toulouse, France
| | - Saulius Klimašauskas
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Vilnius LT-10257, Lithuania
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125
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Phylogenetic and Functional Diversity of Total (DNA) and Expressed (RNA) Bacterial Communities in Urban Green Infrastructure Bioswale Soils. Appl Environ Microbiol 2017; 83:AEM.00287-17. [PMID: 28576763 DOI: 10.1128/aem.00287-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 05/26/2017] [Indexed: 01/08/2023] Open
Abstract
New York City (NYC) is pioneering green infrastructure with the use of bioswales and other engineered soil-based habitats to provide stormwater infiltration and other ecosystem functions. In addition to avoiding the environmental and financial costs of expanding traditional built infrastructure, green infrastructure is thought to generate cobenefits in the form of diverse ecological processes performed by its plant and microbial communities. Yet, although plant communities in these habitats are closely managed, we lack basic knowledge about how engineered ecosystems impact the distribution and functioning of soil bacteria. We sequenced amplicons of the 16S ribosomal subunit, as well as seven genes associated with functional pathways, generated from both total (DNA-based) and expressed (RNA) soil communities in the Bronx, NYC, NY, in order to test whether bioswale soils host characteristic bacterial communities with evidence for enriched microbial functioning, compared to nonengineered soils in park lawns and tree pits. Bioswales had distinct, phylogenetically diverse bacterial communities, including taxa associated with nutrient cycling and metabolism of hydrocarbons and other pollutants. Bioswale soils also had a significantly greater diversity of genes involved in several functional pathways, including carbon fixation (cbbL-R [cbbL gene, red-like subunit] and apsA), nitrogen cycling (noxZ and amoA), and contaminant degradation (bphA); conversely, no functional genes were significantly more abundant in nonengineered soils. These results provide preliminary evidence that urban land management can shape the diversity and activity of soil communities, with positive consequences for genetic resources underlying valuable ecological functions, including biogeochemical cycling and degradation of common urban pollutants.IMPORTANCE Management of urban soil biodiversity by favoring taxa associated with decontamination or other microbial metabolic processes is a powerful prospect, but it first requires an understanding of how engineered soil habitats shape patterns of microbial diversity. This research adds to our understanding of urban microbial biogeography by providing data on soil bacteria in bioswales, which had relatively diverse and compositionally distinct communities compared to park and tree pit soils. Bioswales also contained comparatively diverse pools of genes related to carbon sequestration, nitrogen cycling, and contaminant degradation, suggesting that engineered soils may serve as effective reservoirs of functional microbial biodiversity. We also examined both total (DNA-based) and expressed (RNA) communities, revealing that total bacterial communities (the exclusive targets in the vast majority of soil studies) were poor predictors of expressed community diversity, pointing to the value of quantifying RNA, especially when ecological functioning is considered.
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126
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Riml C, Lusser A, Ennifar E, Micura R. Synthesis, Thermodynamic Properties, and Crystal Structure of RNA Oligonucleotides Containing 5-Hydroxymethylcytosine. J Org Chem 2017; 82:7939-7945. [PMID: 28707898 DOI: 10.1021/acs.joc.7b01171] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
5-Hydroxymethylcytosine (hm5C) is an RNA modification that has attracted significant interest because of the finding that RNA hydroxymethylation can favor mRNA translation. For insight into the mechanistic details of hm5C function to be obtained, the availability of RNAs containing this modification at defined positions that can be used for in vitro studies is highly desirable. In this work, we present an eight-step route to 5-hydroxymethylcytidine (hm5rC) phosphoramidite for solid-phase synthesis of modified RNA oligonucleotides. Furthermore, we examined the effects of hm5rC on RNA duplex stability and its impact on structure formation using the sarcin-ricin loop (SRL) motif. Thermal denaturation experiments revealed that hm5rC increases RNA duplex stability. By contrast, when cytosine within an UNCG tetraloop motif was replaced by hm5rC, the thermodynamic stability of the corresponding hairpin fold was attenuated. Importantly, incorporation of hm5rC into the SRL motif resulted in an RNA crystal structure at 0.85 Å resolution. Besides changes in the hydration pattern at the site of modification, a slight opening of the hm5rC-G pair compared to the unmodified C-G in the native structure was revealed.
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Affiliation(s)
- Christian Riml
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck , 6020 Innsbruck, Austria
| | - Alexandra Lusser
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck , 6020 Innsbruck, Austria
| | - Eric Ennifar
- Université de Strasbourg, CNRS , Architecture et Réactivité des ARN, UPR 9002, 67000 Strasbourg, France
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck , 6020 Innsbruck, Austria
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127
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Nainar S, Marshall PR, Tyler CR, Spitale RC, Bredy TW. Evolving insights into RNA modifications and their functional diversity in the brain. Nat Neurosci 2017; 19:1292-8. [PMID: 27669990 DOI: 10.1038/nn.4378] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Accepted: 08/04/2016] [Indexed: 12/12/2022]
Abstract
In this Perspective, we expand the notion of temporal regulation of RNA in the brain and propose that the qualitative nature of RNA and its metabolism, together with RNA abundance, are essential for the molecular mechanisms underlying experience-dependent plasticity. We discuss emerging concepts in the newly burgeoning field of epitranscriptomics, which are predicted to be heavily involved in cognitive function. These include activity-induced RNA modifications, RNA editing, dynamic changes in the secondary structure of RNA, and RNA localization. Each is described with an emphasis on its role in regulating the function of both protein-coding genes, as well as various noncoding regulatory RNAs, and how each might influence learning and memory.
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Affiliation(s)
- Sarah Nainar
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, California, USA
| | - Paul R Marshall
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, California, USA.,Center for the Neurobiology of Learning and Memory, University of California Irvine, Irvine, California, USA
| | - Christina R Tyler
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, California, USA.,Center for the Neurobiology of Learning and Memory, University of California Irvine, Irvine, California, USA
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, California, USA
| | - Timothy W Bredy
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, California, USA.,Center for the Neurobiology of Learning and Memory, University of California Irvine, Irvine, California, USA.,Queensland Brain Institute, University of Queensland, Brisbane, Australia
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128
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Seelam PP, Sharma P, Mitra A. Structural landscape of base pairs containing post-transcriptional modifications in RNA. RNA (NEW YORK, N.Y.) 2017; 23:847-859. [PMID: 28341704 PMCID: PMC5435857 DOI: 10.1261/rna.060749.117] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 03/23/2017] [Indexed: 05/20/2023]
Abstract
Base pairs involving post-transcriptionally modified nucleobases are believed to play important roles in a wide variety of functional RNAs. Here we present our attempts toward understanding the structural and functional role of naturally occurring modified base pairs using a combination of X-ray crystal structure database analysis, sequence analysis, and advanced quantum chemical methods. Our bioinformatics analysis reveals that despite their presence in all major secondary structural elements, modified base pairs are most prevalent in tRNA crystal structures and most commonly involve guanine or uridine modifications. Further, analysis of tRNA sequences reveals additional examples of modified base pairs at structurally conserved tRNA regions and highlights the conservation patterns of these base pairs in three domains of life. Comparison of structures and binding energies of modified base pairs with their unmodified counterparts, using quantum chemical methods, allowed us to classify the base modifications in terms of the nature of their electronic structure effects on base-pairing. Analysis of specific structural contexts of modified base pairs in RNA crystal structures revealed several interesting scenarios, including those at the tRNA:rRNA interface, antibiotic-binding sites on the ribosome, and the three-way junctions within tRNA. These scenarios, when analyzed in the context of available experimental data, allowed us to correlate the occurrence and strength of modified base pairs with their specific functional roles. Overall, our study highlights the structural importance of modified base pairs in RNA and points toward the need for greater appreciation of the role of modified bases and their interactions, in the context of many biological processes involving RNA.
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Affiliation(s)
- Preethi P Seelam
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology Hyderabad (IIIT-H), Gachibowli, Hyderabad, Telangana 500032, India
| | - Purshotam Sharma
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
| | - Abhijit Mitra
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology Hyderabad (IIIT-H), Gachibowli, Hyderabad, Telangana 500032, India
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129
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Lin KY, Lin NS. Interfering Satellite RNAs of Bamboo mosaic virus. Front Microbiol 2017; 8:787. [PMID: 28522996 PMCID: PMC5415622 DOI: 10.3389/fmicb.2017.00787] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 04/18/2017] [Indexed: 11/13/2022] Open
Abstract
Satellite RNAs (satRNAs) are sub-viral agents that may interact with their cognate helper virus (HV) and host plant synergistically and/or antagonistically. SatRNAs totally depend on the HV for replication, so satRNAs and HV usually evolve similar secondary or tertiary RNA structures that are recognized by a replication complex, although satRNAs and HV do not share an appreciable sequence homology. The satRNAs of Bamboo mosaic virus (satBaMV), the only satRNAs of the genus Potexvirus, have become one of the models of how satRNAs can modulate HV replication and virus-induced symptoms. In this review, we summarize the molecular mechanisms underlying the interaction of interfering satBaMV and BaMV. Like other satRNAs, satBaMV mimics the secondary structures of 5'- and 3'-untranslated regions (UTRs) of BaMV as a molecular pretender. However, a conserved apical hairpin stem loop (AHSL) in the 5'-UTR of satBaMV was found as the key determinant for downregulating BaMV replication. In particular, two unique nucleotides (C60 and C83) in the AHSL of satBaMVs determine the satBaMV interference ability by competing for the replication machinery. Thus, transgenic plants expressing interfering satBaMV could confer resistance to BaMV, and interfering satBaMV could be used as biological-control agent. Unlike two major anti-viral mechanisms, RNA silencing and salicylic acid-mediated immunity, our findings in plants by in vivo competition assay and RNA deep sequencing suggested replication competition is involved in this transgenic satBaMV-mediated BaMV interference. We propose how a single nucleotide of satBaMV can make a great change in BaMV pathogenicity and the underlying mechanism.
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Affiliation(s)
- Kuan-Yu Lin
- Institute of Plant and Microbial Biology, Academia SinicaTaipei, Taiwan
| | - Na-Sheng Lin
- Institute of Plant and Microbial Biology, Academia SinicaTaipei, Taiwan
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130
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Yang X, Yang Y, Sun BF, Chen YS, Xu JW, Lai WY, Li A, Wang X, Bhattarai DP, Xiao W, Sun HY, Zhu Q, Ma HL, Adhikari S, Sun M, Hao YJ, Zhang B, Huang CM, Huang N, Jiang GB, Zhao YL, Wang HL, Sun YP, Yang YG. 5-methylcytosine promotes mRNA export - NSUN2 as the methyltransferase and ALYREF as an m 5C reader. Cell Res 2017; 27:606-625. [PMID: 28418038 PMCID: PMC5594206 DOI: 10.1038/cr.2017.55] [Citation(s) in RCA: 589] [Impact Index Per Article: 84.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 03/14/2017] [Accepted: 03/15/2017] [Indexed: 12/15/2022] Open
Abstract
5-methylcytosine (m5C) is a post-transcriptional RNA modification identified in both stable and highly abundant tRNAs and rRNAs, and in mRNAs. However, its regulatory role in mRNA metabolism is still largely unknown. Here, we reveal that m5C modification is enriched in CG-rich regions and in regions immediately downstream of translation initiation sites and has conserved, tissue-specific and dynamic features across mammalian transcriptomes. Moreover, m5C formation in mRNAs is mainly catalyzed by the RNA methyltransferase NSUN2, and m5C is specifically recognized by the mRNA export adaptor ALYREF as shown by in vitro and in vivo studies. NSUN2 modulates ALYREF's nuclear-cytoplasmic shuttling, RNA-binding affinity and associated mRNA export. Dysregulation of ALYREF-mediated mRNA export upon NSUN2 depletion could be restored by reconstitution of wild-type but not methyltransferase-defective NSUN2. Our study provides comprehensive m5C profiles of mammalian transcriptomes and suggests an essential role for m5C modification in mRNA export and post-transcriptional regulation.
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Affiliation(s)
- Xin Yang
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, China.,Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Yang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Bao-Fa Sun
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu-Sheng Chen
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jia-Wei Xu
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, China.,Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Wei-Yi Lai
- School of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China.,State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Ang Li
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xing Wang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Devi Prasad Bhattarai
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wen Xiao
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hui-Ying Sun
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Qin Zhu
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hai-Li Ma
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Samir Adhikari
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Min Sun
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ya-Juan Hao
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Bing Zhang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Chun-Min Huang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Niu Huang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Gui-Bin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yong-Liang Zhao
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Hai-Lin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Ying-Pu Sun
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, China
| | - Yun-Gui Yang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,School of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
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131
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Lorenz C, Lünse CE, Mörl M. tRNA Modifications: Impact on Structure and Thermal Adaptation. Biomolecules 2017; 7:E35. [PMID: 28375166 PMCID: PMC5485724 DOI: 10.3390/biom7020035] [Citation(s) in RCA: 216] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 03/27/2017] [Accepted: 03/28/2017] [Indexed: 12/27/2022] Open
Abstract
Transfer RNAs (tRNAs) are central players in translation, functioning as adapter molecules between the informational level of nucleic acids and the functional level of proteins. They show a highly conserved secondary and tertiary structure and the highest density of post-transcriptional modifications among all RNAs. These modifications concentrate in two hotspots-the anticodon loop and the tRNA core region, where the D- and T-loop interact with each other, stabilizing the overall structure of the molecule. These modifications can cause large rearrangements as well as local fine-tuning in the 3D structure of a tRNA. The highly conserved tRNA shape is crucial for the interaction with a variety of proteins and other RNA molecules, but also needs a certain flexibility for a correct interplay. In this context, it was shown that tRNA modifications are important for temperature adaptation in thermophilic as well as psychrophilic organisms, as they modulate rigidity and flexibility of the transcripts, respectively. Here, we give an overview on the impact of modifications on tRNA structure and their importance in thermal adaptation.
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Affiliation(s)
- Christian Lorenz
- Institute of Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany.
| | - Christina E Lünse
- Institute of Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany.
| | - Mario Mörl
- Institute of Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany.
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132
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Trm5 and TrmD: Two Enzymes from Distinct Origins Catalyze the Identical tRNA Modification, m¹G37. Biomolecules 2017; 7:biom7010032. [PMID: 28335556 PMCID: PMC5372744 DOI: 10.3390/biom7010032] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 03/07/2017] [Accepted: 03/16/2017] [Indexed: 11/17/2022] Open
Abstract
The N¹-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. The resultant modified nucleotide m¹G37 positively regulates the aminoacylation of the tRNA, and simultaneously functions to prevent the +1 frameshift on the ribosome. Interestingly, Trm5 and TrmD have completely distinct origins, and therefore bear different tertiary folds. In this review, we describe the different strategies utilized by Trm5 and TrmD to recognize their substrate tRNAs, mainly based on their crystal structures complexed with substrate tRNAs.
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133
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Rojas-Benítez D, Eggers C, Glavic A. Modulation of the Proteostasis Machinery to Overcome Stress Caused by Diminished Levels of t6A-Modified tRNAs in Drosophila. Biomolecules 2017; 7:biom7010025. [PMID: 28272317 PMCID: PMC5372737 DOI: 10.3390/biom7010025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 02/28/2017] [Indexed: 12/17/2022] Open
Abstract
Transfer RNAs (tRNAs) harbor a subset of post-transcriptional modifications required for structural stability or decoding function. N6-threonylcarbamoyladenosine (t6A) is a universally conserved modification found at position 37 in tRNA that pair A-starting codons (ANN) and is required for proper translation initiation and to prevent frame shift during elongation. In its absence, the synthesis of aberrant proteins is likely, evidenced by the formation of protein aggregates. In this work, our aim was to study the relationship between t6A-modified tRNAs and protein synthesis homeostasis machinery using Drosophila melanogaster. We used the Gal4/UAS system to knockdown genes required for t6A synthesis in a tissue and time specific manner and in vivo reporters of unfolded protein response (UPR) activation. Our results suggest that t6A-modified tRNAs, synthetized by the threonyl-carbamoyl transferase complex (TCTC), are required for organismal growth and imaginal cell survival, and is most likely to support proper protein synthesis.
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Affiliation(s)
- Diego Rojas-Benítez
- Centro de Regulación del Genoma, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800024, Chile..
| | - Cristián Eggers
- Centro de Regulación del Genoma, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800024, Chile..
| | - Alvaro Glavic
- Centro de Regulación del Genoma, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800024, Chile..
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134
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David R, Burgess A, Parker B, Li J, Pulsford K, Sibbritt T, Preiss T, Searle IR. Transcriptome-Wide Mapping of RNA 5-Methylcytosine in Arabidopsis mRNAs and Noncoding RNAs. THE PLANT CELL 2017; 29:445-460. [PMID: 28062751 PMCID: PMC5385953 DOI: 10.1105/tpc.16.00751] [Citation(s) in RCA: 160] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 12/08/2016] [Accepted: 01/02/2017] [Indexed: 05/20/2023]
Abstract
Posttranscriptional methylation of RNA cytosine residues to 5-methylcytosine (m5C) is an important modification with diverse roles, such as regulating stress responses, stem cell proliferation, and RNA metabolism. Here, we used RNA bisulfite sequencing for transcriptome-wide quantitative mapping of m5C in the model plant Arabidopsis thaliana We discovered more than a thousand m5C sites in Arabidopsis mRNAs, long noncoding RNAs, and other noncoding RNAs across three tissue types (siliques, seedling shoots, and roots) and validated a number of these sites. Quantitative differences in methylated sites between these three tissues suggest tissue-specific regulation of m5C. Perturbing the RNA m5C methyltransferase TRM4B resulted in the loss of m5C sites on mRNAs and noncoding RNAs and reduced the stability of tRNAAsp(GTC) We also demonstrate the importance of m5C in plant development, as trm4b mutants have shorter primary roots than the wild type due to reduced cell division in the root apical meristem. In addition, trm4b mutants show increased sensitivity to oxidative stress. Finally, we provide insights into the targeting mechanism of TRM4B by demonstrating that a 50-nucleotide sequence flanking m5C C3349 in MAIGO5 mRNA is sufficient to confer methylation of a transgene reporter in Nicotiana benthamiana.
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Affiliation(s)
- Rakesh David
- School of Biological Sciences, The University of Adelaide, The University of Adelaide and Shanghai Jiao Tong University Joint International Centre for Agriculture and Health, Adelaide, South Australia 5005, Australia
| | - Alice Burgess
- School of Biological Sciences, The University of Adelaide, The University of Adelaide and Shanghai Jiao Tong University Joint International Centre for Agriculture and Health, Adelaide, South Australia 5005, Australia
| | - Brian Parker
- Department of Biology, New York University, New York, New York 1003-6688
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Jun Li
- School of Biological Sciences, The University of Adelaide, The University of Adelaide and Shanghai Jiao Tong University Joint International Centre for Agriculture and Health, Adelaide, South Australia 5005, Australia
| | - Kalinya Pulsford
- School of Biological Sciences, The University of Adelaide, The University of Adelaide and Shanghai Jiao Tong University Joint International Centre for Agriculture and Health, Adelaide, South Australia 5005, Australia
| | - Tennille Sibbritt
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Thomas Preiss
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
- Victor Chang Cardiac Research Institute, Sydney, New South Wales 2010, Australia
| | - Iain Robert Searle
- School of Biological Sciences, The University of Adelaide, The University of Adelaide and Shanghai Jiao Tong University Joint International Centre for Agriculture and Health, Adelaide, South Australia 5005, Australia
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135
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David R, Burgess A, Parker B, Li J, Pulsford K, Sibbritt T, Preiss T, Searle IR. Transcriptome-Wide Mapping of RNA 5-Methylcytosine in Arabidopsis mRNAs and Noncoding RNAs. THE PLANT CELL 2017. [PMID: 28062751 DOI: 10.6084/m9.figshare.3408193.v2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Posttranscriptional methylation of RNA cytosine residues to 5-methylcytosine (m5C) is an important modification with diverse roles, such as regulating stress responses, stem cell proliferation, and RNA metabolism. Here, we used RNA bisulfite sequencing for transcriptome-wide quantitative mapping of m5C in the model plant Arabidopsis thaliana We discovered more than a thousand m5C sites in Arabidopsis mRNAs, long noncoding RNAs, and other noncoding RNAs across three tissue types (siliques, seedling shoots, and roots) and validated a number of these sites. Quantitative differences in methylated sites between these three tissues suggest tissue-specific regulation of m5C. Perturbing the RNA m5C methyltransferase TRM4B resulted in the loss of m5C sites on mRNAs and noncoding RNAs and reduced the stability of tRNAAsp(GTC) We also demonstrate the importance of m5C in plant development, as trm4b mutants have shorter primary roots than the wild type due to reduced cell division in the root apical meristem. In addition, trm4b mutants show increased sensitivity to oxidative stress. Finally, we provide insights into the targeting mechanism of TRM4B by demonstrating that a 50-nucleotide sequence flanking m5C C3349 in MAIGO5 mRNA is sufficient to confer methylation of a transgene reporter in Nicotiana benthamiana.
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Affiliation(s)
- Rakesh David
- School of Biological Sciences, The University of Adelaide, The University of Adelaide and Shanghai Jiao Tong University Joint International Centre for Agriculture and Health, Adelaide, South Australia 5005, Australia
| | - Alice Burgess
- School of Biological Sciences, The University of Adelaide, The University of Adelaide and Shanghai Jiao Tong University Joint International Centre for Agriculture and Health, Adelaide, South Australia 5005, Australia
| | - Brian Parker
- Department of Biology, New York University, New York, New York 1003-6688
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Jun Li
- School of Biological Sciences, The University of Adelaide, The University of Adelaide and Shanghai Jiao Tong University Joint International Centre for Agriculture and Health, Adelaide, South Australia 5005, Australia
| | - Kalinya Pulsford
- School of Biological Sciences, The University of Adelaide, The University of Adelaide and Shanghai Jiao Tong University Joint International Centre for Agriculture and Health, Adelaide, South Australia 5005, Australia
| | - Tennille Sibbritt
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Thomas Preiss
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory 2601, Australia
- Victor Chang Cardiac Research Institute, Sydney, New South Wales 2010, Australia
| | - Iain Robert Searle
- School of Biological Sciences, The University of Adelaide, The University of Adelaide and Shanghai Jiao Tong University Joint International Centre for Agriculture and Health, Adelaide, South Australia 5005, Australia
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136
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Abstract
The first chemical modification to RNA was discovered nearly 60 years ago; to date, more than 100 chemically distinct modifications have been identified in cellular RNA. With the recent development of novel chemical and/or biochemical methods, dynamic modifications to RNA have been identified in the transcriptome, including N6-methyladenosine (m6A), inosine (I), 5-methylcytosine (m5C), pseudouridine (Ψ), 5-hydroxymethylcytosine (hm5C), and N1-methyladenosine (m1A). Collectively, the multitude of RNA modifications are termed epitranscriptome, leading to the emerging field of epitranscriptomics. In this review, we primarily focus on recently reported chemical modifications to mRNA; we discuss their chemical properties, biological functions, and mechanisms with an emphasis on their high-throughput detection methods. We also envision that future tools, particularly novel chemical biology methods, could further facilitate and enable studies in the field of epitranscriptomics.
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Affiliation(s)
- Jinghui Song
- State
Key Laboratory of Protein and Plant Gene Research, School of Life
Sciences, and Peking-Tsinghua Center for Life Sciences and ‡Department of Chemical
Biology and Synthetic and Functional Biomolecules Center, College
of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Chengqi Yi
- State
Key Laboratory of Protein and Plant Gene Research, School of Life
Sciences, and Peking-Tsinghua Center for Life Sciences and ‡Department of Chemical
Biology and Synthetic and Functional Biomolecules Center, College
of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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137
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Abstract
RiboMeth-seq is a sequencing-based method for mapping and quantitation of one of the most abundant RNA modifications, ribose methylation. It is based on a simple chemical principle, namely the several orders of magnitude difference in nucleophilicity of a 2'-OH and a 2'-O-Me. Thus, the method combines alkaline fragmentation and a specialized library construction protocol based on 5'-OH and 2',3' cyclic phosphate ends to prepare RNA for sequencing. The read-ends of library fragments are used for mapping with nucleotide resolution and calculation of the fraction of molecules methylated at the 2'-O-Me sites.
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Affiliation(s)
- Nicolai Krogh
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, 3 Blegdamsvej, 18.2.22, DK-2200N, Copenhagen, Denmark
| | - Ulf Birkedal
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, 3 Blegdamsvej, 18.2.22, DK-2200N, Copenhagen, Denmark
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, 3 Blegdamsvej, 18.2.22, DK-2200N, Copenhagen, Denmark.
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138
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139
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S. P. P, Sharma P, Mitra A. Higher order structures involving post transcriptionally modified nucleobases in RNA. RSC Adv 2017. [DOI: 10.1039/c7ra05284g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Quantum chemical studies are carried out to understand the structures and stabilities of higher order structures involving post-transcriptionally modified nucleobases in RNA.
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Affiliation(s)
- Preethi S. P.
- Center for Computational Natural Sciences and Bioinformatics
- International Institute of Information Technology Hyderabad (IIIT-H)
- Hyderabad
- India
| | - Purshotam Sharma
- Computational Biochemistry Laboratory
- Department of Chemistry and Centre for Advanced Studies in Chemistry
- Panjab University
- Chandigarh
- India
| | - Abhijit Mitra
- Center for Computational Natural Sciences and Bioinformatics
- International Institute of Information Technology Hyderabad (IIIT-H)
- Hyderabad
- India
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140
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Incarnato D, Oliviero S. The RNA Epistructurome: Uncovering RNA Function by Studying Structure and Post-Transcriptional Modifications. Trends Biotechnol 2016; 35:318-333. [PMID: 27988057 DOI: 10.1016/j.tibtech.2016.11.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/11/2016] [Accepted: 11/21/2016] [Indexed: 01/15/2023]
Abstract
A large fraction of higher metazoan genomes transcribe RNA molecules whose functions extend far beyond carrying instructions for protein synthesis. Although RNA is apparently a simple molecule, the ways in which it performs many of its functions have remained highly elusive for decades. As learned from studying ribosomal and transfer RNAs, two of the key features influencing the function of RNA are its structure and post-transcriptional modifications. A deep understanding of RNA function therefore requires rapid and straightforward approaches to study the complex and intricate landscape of RNA structures and modifications. In this review we summarize and discuss the most recent methods and findings in the field of RNA biology, with an eye toward new frontiers and open questions.
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Affiliation(s)
- Danny Incarnato
- Human Genetics Foundation (HuGeF), Via Nizza 52, 10126 Torino, Italy; Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, Torino, Italy.
| | - Salvatore Oliviero
- Human Genetics Foundation (HuGeF), Via Nizza 52, 10126 Torino, Italy; Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, Torino, Italy.
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141
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Mwangi JN, Chiu NHL. High Percentage of Isomeric Human MicroRNA and Their Analytical Challenges. Noncoding RNA 2016; 2:ncrna2040013. [PMID: 29657271 PMCID: PMC5831925 DOI: 10.3390/ncrna2040013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 10/25/2016] [Accepted: 11/23/2016] [Indexed: 12/12/2022] Open
Abstract
MicroRNA (miR) are short non-coding RNAs known to post-transcriptionally regulate gene expression, and have been reported as biomarkers for various diseases. miR have also been served as potential drug targets. The identity, functions and detection of a specific miR are determined by its RNA sequence, whose composition is made up of only 4 canonical ribonucleotides. Hence, among over two thousand human miR, their nucleotide compositions are expected to be similar but the extent of similarity has not been reported. In this study, the sequences of mature human miR were downloaded from miRBase, and collated using different tools to determine and compare their nucleotide compositions and sequences. 55% of all human miR were found to be structural isomers. The structural isomers of miR (SimiR) are defined as having the same size and identical nucleotide composition. A number of SimiR were also found to have high sequence similarities. To investigate the extent of SimiR in biological samples, three disease models were chosen, and disease-associated miR were identified from miR2Disease. Among the disease models, as high as 73% of miR were found to be SimiR. This report provides the missing information about human miR and highlights the challenges on the detection of SimiR.
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Affiliation(s)
- Joseph N Mwangi
- Department of Chemistry and Biochemistry, Joint School of Nanoscience and Nanoengineering, University of North Carolina at Greensboro, Greensboro, NC 27412, USA.
| | - Norman H L Chiu
- Department of Chemistry and Biochemistry, Joint School of Nanoscience and Nanoengineering, University of North Carolina at Greensboro, Greensboro, NC 27412, USA.
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142
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Sloan KE, Warda AS, Sharma S, Entian KD, Lafontaine DLJ, Bohnsack MT. Tuning the ribosome: The influence of rRNA modification on eukaryotic ribosome biogenesis and function. RNA Biol 2016; 14:1138-1152. [PMID: 27911188 PMCID: PMC5699541 DOI: 10.1080/15476286.2016.1259781] [Citation(s) in RCA: 413] [Impact Index Per Article: 51.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
rRNAs are extensively modified during their transcription and subsequent maturation in the nucleolus, nucleus and cytoplasm. RNA modifications, which are installed either by snoRNA-guided or by stand-alone enzymes, generally stabilize the structure of the ribosome. However, they also cluster at functionally important sites of the ribosome, such as the peptidyltransferase center and the decoding site, where they facilitate efficient and accurate protein synthesis. The recent identification of sites of substoichiometric 2'-O-methylation and pseudouridylation has overturned the notion that all rRNA modifications are constitutively present on ribosomes, highlighting nucleotide modifications as an important source of ribosomal heterogeneity. While the mechanisms regulating partial modification and the functions of specialized ribosomes are largely unknown, changes in the rRNA modification pattern have been observed in response to environmental changes, during development, and in disease. This suggests that rRNA modifications may contribute to the translational control of gene expression.
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Affiliation(s)
- Katherine E Sloan
- a Institute for Molecular Biology, University Medical Center Göttingen, Georg-August-University , Göttingen , Germany
| | - Ahmed S Warda
- a Institute for Molecular Biology, University Medical Center Göttingen, Georg-August-University , Göttingen , Germany
| | - Sunny Sharma
- b RNA Molecular Biology and Center for Microscopy and Molecular Imaging, F.R.S./FNRS, Université Libre de Bruxelles , Charleroi-Gosselies , Belgium
| | - Karl-Dieter Entian
- c Institute for Molecular Biosciences, Goethe University , Frankfurt am Main , Germany
| | - Denis L J Lafontaine
- b RNA Molecular Biology and Center for Microscopy and Molecular Imaging, F.R.S./FNRS, Université Libre de Bruxelles , Charleroi-Gosselies , Belgium
| | - Markus T Bohnsack
- a Institute for Molecular Biology, University Medical Center Göttingen, Georg-August-University , Göttingen , Germany.,d Göttingen Centre for Molecular Biosciences, Georg-August-University , Göttingen , Germany
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143
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Chen K, Zhao BS, He C. Nucleic Acid Modifications in Regulation of Gene Expression. Cell Chem Biol 2016; 23:74-85. [PMID: 26933737 DOI: 10.1016/j.chembiol.2015.11.007] [Citation(s) in RCA: 188] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 11/13/2015] [Accepted: 11/13/2015] [Indexed: 10/22/2022]
Abstract
Nucleic acids carry a wide range of different chemical modifications. In contrast to previous views that these modifications are static and only play fine-tuning functions, recent research advances paint a much more dynamic picture. Nucleic acids carry diverse modifications and employ these chemical marks to exert essential or critical influences in a variety of cellular processes in eukaryotic organisms. This review covers several nucleic acid modifications that play important regulatory roles in biological systems, especially in regulation of gene expression: 5-methylcytosine (5mC) and its oxidative derivatives, and N(6)-methyladenine (6mA) in DNA; N(6)-methyladenosine (m(6)A), pseudouridine (Ψ), and 5-methylcytidine (m(5)C) in mRNA and long non-coding RNA. Modifications in other non-coding RNAs, such as tRNA, miRNA, and snRNA, are also briefly summarized. We provide brief historical perspective of the field, and highlight recent progress in identifying diverse nucleic acid modifications and exploring their functions in different organisms. Overall, we believe that work in this field will yield additional layers of both chemical and biological complexity as we continue to uncover functional consequences of known nucleic acid modifications and discover new ones.
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Affiliation(s)
- Kai Chen
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Boxuan Simen Zhao
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Chuan He
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA; Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.
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144
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Tripp V, Martin R, Orell A, Alkhnbashi OS, Backofen R, Randau L. Plasticity of archaeal C/D box sRNA biogenesis. Mol Microbiol 2016; 103:151-164. [PMID: 27743417 DOI: 10.1111/mmi.13549] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2016] [Indexed: 01/11/2023]
Abstract
Archaeal and eukaryotic organisms contain sets of C/D box s(no)RNAs with guide sequences that determine ribose 2'-O-methylation sites of target RNAs. The composition of these C/D box sRNA sets is highly variable between organisms and results in varying RNA modification patterns which are important for ribosomal RNA folding and stability. Little is known about the genomic organization of C/D box sRNA genes in archaea. Here, we aimed to obtain first insights into the biogenesis of these archaeal C/D box sRNAs and analyzed the genetic context of more than 300 archaeal sRNA genes. We found that the majority of these genes do not possess independent promoters but are rather located at positions that allow for co-transcription with neighboring genes and their start or stop codons were frequently incorporated into the conserved boxC and D motifs. The biogenesis of plasmid-encoded C/D box sRNA variants was analyzed in vivo in Sulfolobus acidocaldarius. It was found that C/D box sRNA maturation occurs independent of their genetic context and relies solely on the presence of intact RNA kink-turn structures. The observed plasticity of C/D box sRNA biogenesis is suggested to enable their accelerated evolution and, consequently, allow for adjustments of the RNA modification landscape.
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Affiliation(s)
- Vanessa Tripp
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, Marburg, 35043, Germany.,LOEWE Center for Synthetic Microbiology, SYNMIKRO, Karl-von-Frisch-Strasse 16, Marburg, 35043, Germany
| | - Roman Martin
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, Marburg, 35043, Germany
| | - Alvaro Orell
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, Marburg, 35043, Germany
| | - Omer S Alkhnbashi
- Bioinformatics group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, Freiburg, 79110, Germany
| | - Rolf Backofen
- Bioinformatics group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, Freiburg, 79110, Germany.,BIOSS Centre for Biological Signalling Studies, Cluster of Excellence, University of Freiburg, Germany
| | - Lennart Randau
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Strasse 10, Marburg, 35043, Germany.,LOEWE Center for Synthetic Microbiology, SYNMIKRO, Karl-von-Frisch-Strasse 16, Marburg, 35043, Germany
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145
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Abstract
Aside from nucleoli, Cajal bodies (CBs) are the best-characterized organelles of mammalian cell nuclei. Like nucleoli, CBs concentrate ribonucleoproteins (RNPs), in particular, spliceosomal small nuclear RNPs (snRNPs) and small nucleolar RNPs (snoRNPs). In one of the best-defined functions of CBs, most of the snoRNPs are involved in site-specific modification of snRNAs. The two major modifications are pseudouridylation and 2'-O-methylation that are guided by the box H/ACA and C/D snoRNPs, respectively. This review details the modifications, their function, the mechanism of modification, and the machineries involved. We dissect the different classes of noncoding RNAs that meet in CBs, guides and substrates. Open questions and conundrums, often raised and appearing due to experimental limitations, are pointed out and discussed. The emphasis of the review is on mammalian CBs and their function in modification of noncoding RNAs.
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Affiliation(s)
- U Thomas Meier
- a Albert Einstein College of Medicine , Department of Anatomy and Structural Biology , Bronx , NY , USA
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146
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Dowling DP, Miles ZD, Köhrer C, Maiocco SJ, Elliott SJ, Bandarian V, Drennan CL. Molecular basis of cobalamin-dependent RNA modification. Nucleic Acids Res 2016; 44:9965-9976. [PMID: 27638883 PMCID: PMC5175355 DOI: 10.1093/nar/gkw806] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 08/30/2016] [Accepted: 09/03/2016] [Indexed: 12/22/2022] Open
Abstract
Queuosine (Q) was discovered in the wobble position of a transfer RNA (tRNA) 47 years ago, yet the final biosynthetic enzyme responsible for Q-maturation, epoxyqueuosine (oQ) reductase (QueG), was only recently identified. QueG is a cobalamin (Cbl)-dependent, [4Fe-4S] cluster-containing protein that produces the hypermodified nucleoside Q in situ on four tRNAs. To understand how QueG is able to perform epoxide reduction, an unprecedented reaction for a Cbl-dependent enzyme, we have determined a series of high resolution structures of QueG from Bacillus subtilis. Our structure of QueG bound to a tRNATyr anticodon stem loop shows how this enzyme uses a HEAT-like domain to recognize the appropriate anticodons and position the hypermodified nucleoside into the enzyme active site. We find Q bound directly above the Cbl, consistent with a reaction mechanism that involves the formation of a covalent Cbl-tRNA intermediate. Using protein film electrochemistry, we show that two [4Fe-4S] clusters adjacent to the Cbl have redox potentials in the range expected for Cbl reduction, suggesting how Cbl can be activated for nucleophilic attack on oQ. Together, these structural and electrochemical data inform our understanding of Cbl dependent nucleic acid modification.
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Affiliation(s)
- Daniel P Dowling
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Zachary D Miles
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Caroline Köhrer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | - Sean J Elliott
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - Vahe Bandarian
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Catherine L Drennan
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA .,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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147
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Wang M, Zhu Y, Wang C, Fan X, Jiang X, Ebrahimi M, Qiao Z, Niu L, Teng M, Li X. Crystal structure of the two-subunit tRNA m(1)A58 methyltransferase TRM6-TRM61 from Saccharomyces cerevisiae. Sci Rep 2016; 6:32562. [PMID: 27582183 PMCID: PMC5007650 DOI: 10.1038/srep32562] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 08/09/2016] [Indexed: 01/19/2023] Open
Abstract
The N(1) methylation of adenine at position 58 (m(1)A58) of tRNA is an important post-transcriptional modification, which is vital for maintaining the stability of the initiator methionine tRNAi(Met). In eukaryotes, this modification is performed by the TRM6-TRM61 holoenzyme. To understand the molecular mechanism that underlies the cooperation of TRM6 and TRM61 in the methyl transfer reaction, we determined the crystal structure of TRM6-TRM61 holoenzyme from Saccharomyces cerevisiae in the presence and absence of its methyl donor S-Adenosyl-L-methionine (SAM). In the structures, two TRM6-TRM61 heterodimers assemble as a heterotetramer. Both TRM6 and TRM61 subunits comprise an N-terminal β-barrel domain linked to a C-terminal Rossmann-fold domain. TRM61 functions as the catalytic subunit, containing a methyl donor (SAM) binding pocket. TRM6 diverges from TRM61, lacking the conserved motifs used for binding SAM. However, TRM6 cooperates with TRM61 forming an L-shaped tRNA binding regions. Collectively, our results provide a structural basis for better understanding the m(1)A58 modification of tRNA occurred in Saccharomyces cerevisiae.
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Affiliation(s)
- Mingxing Wang
- Hefei National Laboratory for Physical Sciences at Microscale, Innovation Center for Cell Signalling Network, School of Life Science, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China.,Key Laboratory of Structural Biology, Hefei Science Center of CAS, Chinese Academy of Science, Hefei, Anhui, 230026, People's Republic of China
| | - Yuwei Zhu
- Hefei National Laboratory for Physical Sciences at Microscale, Innovation Center for Cell Signalling Network, School of Life Science, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China.,Key Laboratory of Structural Biology, Hefei Science Center of CAS, Chinese Academy of Science, Hefei, Anhui, 230026, People's Republic of China
| | - Chongyuan Wang
- Hefei National Laboratory for Physical Sciences at Microscale, Innovation Center for Cell Signalling Network, School of Life Science, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China.,Key Laboratory of Structural Biology, Hefei Science Center of CAS, Chinese Academy of Science, Hefei, Anhui, 230026, People's Republic of China
| | - Xiaojiao Fan
- Hefei National Laboratory for Physical Sciences at Microscale, Innovation Center for Cell Signalling Network, School of Life Science, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China.,Key Laboratory of Structural Biology, Hefei Science Center of CAS, Chinese Academy of Science, Hefei, Anhui, 230026, People's Republic of China
| | - Xuguang Jiang
- Hefei National Laboratory for Physical Sciences at Microscale, Innovation Center for Cell Signalling Network, School of Life Science, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China.,Key Laboratory of Structural Biology, Hefei Science Center of CAS, Chinese Academy of Science, Hefei, Anhui, 230026, People's Republic of China
| | - Mohammad Ebrahimi
- Hefei National Laboratory for Physical Sciences at Microscale, Innovation Center for Cell Signalling Network, School of Life Science, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China.,Key Laboratory of Structural Biology, Hefei Science Center of CAS, Chinese Academy of Science, Hefei, Anhui, 230026, People's Republic of China
| | - Zhi Qiao
- Hefei National Laboratory for Physical Sciences at Microscale, Innovation Center for Cell Signalling Network, School of Life Science, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China.,Key Laboratory of Structural Biology, Hefei Science Center of CAS, Chinese Academy of Science, Hefei, Anhui, 230026, People's Republic of China
| | - Liwen Niu
- Hefei National Laboratory for Physical Sciences at Microscale, Innovation Center for Cell Signalling Network, School of Life Science, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China.,Key Laboratory of Structural Biology, Hefei Science Center of CAS, Chinese Academy of Science, Hefei, Anhui, 230026, People's Republic of China
| | - Maikun Teng
- Hefei National Laboratory for Physical Sciences at Microscale, Innovation Center for Cell Signalling Network, School of Life Science, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China.,Key Laboratory of Structural Biology, Hefei Science Center of CAS, Chinese Academy of Science, Hefei, Anhui, 230026, People's Republic of China
| | - Xu Li
- Hefei National Laboratory for Physical Sciences at Microscale, Innovation Center for Cell Signalling Network, School of Life Science, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China.,Key Laboratory of Structural Biology, Hefei Science Center of CAS, Chinese Academy of Science, Hefei, Anhui, 230026, People's Republic of China
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148
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The physiology and habitat of the last universal common ancestor. Nat Microbiol 2016; 1:16116. [DOI: 10.1038/nmicrobiol.2016.116] [Citation(s) in RCA: 545] [Impact Index Per Article: 68.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 06/21/2016] [Indexed: 02/03/2023]
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149
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Marshall P, Bredy TW. Cognitive neuroepigenetics: the next evolution in our understanding of the molecular mechanisms underlying learning and memory? NPJ SCIENCE OF LEARNING 2016; 1:16014. [PMID: 27512601 PMCID: PMC4977095 DOI: 10.1038/npjscilearn.2016.14] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 06/02/2016] [Accepted: 06/21/2016] [Indexed: 05/02/2023]
Abstract
A complete understanding of the fundamental mechanisms of learning and memory continues to elude neuroscientists. Although many important discoveries have been made, the question of how memories are encoded and maintained at the molecular level remains. To date, this issue has been framed within the context of one of the most dominant concepts in molecular biology, the central dogma, and the result has been a protein-centric view of memory. Here we discuss the evidence supporting a role for neuroepigenetic mechanisms, which constitute dynamic and reversible, state-dependent modifications at all levels of control over cellular function, and their role in learning and memory. This neuroepigenetic view suggests that DNA, RNA and protein each influence one another to produce a holistic cellular state that contributes to the formation and maintenance of memory, and predicts a parallel and distributed system for the consolidation, storage and retrieval of the engram.
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Affiliation(s)
- Paul Marshall
- Department of Neurobiology and Behavior and Center for the Neurobiology of Learning and Memory, University of California Irvine, Irvine, CA, USA
| | - Timothy W Bredy
- Department of Neurobiology and Behavior and Center for the Neurobiology of Learning and Memory, University of California Irvine, Irvine, CA, USA
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
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150
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Dendrimer-RNA nanoparticles generate protective immunity against lethal Ebola, H1N1 influenza, and Toxoplasma gondii challenges with a single dose. Proc Natl Acad Sci U S A 2016; 113:E4133-42. [PMID: 27382155 DOI: 10.1073/pnas.1600299113] [Citation(s) in RCA: 271] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Vaccines have had broad medical impact, but existing vaccine technologies and production methods are limited in their ability to respond rapidly to evolving and emerging pathogens, or sudden outbreaks. Here, we develop a rapid-response, fully synthetic, single-dose, adjuvant-free dendrimer nanoparticle vaccine platform wherein antigens are encoded by encapsulated mRNA replicons. To our knowledge, this system is the first capable of generating protective immunity against a broad spectrum of lethal pathogen challenges, including H1N1 influenza, Toxoplasma gondii, and Ebola virus. The vaccine can be formed with multiple antigen-expressing replicons, and is capable of eliciting both CD8(+) T-cell and antibody responses. The ability to generate viable, contaminant-free vaccines within days, to single or multiple antigens, may have broad utility for a range of diseases.
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