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Structure and mechanism of the methyltransferase ribozyme MTR1. Nat Chem Biol 2022; 18:547-555. [PMID: 35301481 PMCID: PMC7612680 DOI: 10.1038/s41589-022-00976-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/13/2022] [Indexed: 11/20/2022]
Abstract
RNA-catalysed RNA methylation was recently shown to be part of the catalytic repertoire of ribozymes. The methyltransferase ribozyme MTR1 catalyses the site-specific synthesis of 1-methyladenosine (m1A) in RNA, using O6-methylguanine (m6G) as methyl group donor. Here we report the crystal structure of MTR1 at a resolution of 2.8 Å, which reveals a guanine binding site reminiscent of natural guanine riboswitches. The structure represents the postcatalytic state of a split ribozyme in complex with the m1A-containing RNA product and the demethylated cofactor guanine. The structural data suggest the mechanistic involvement of a protonated cytidine in the methyl transfer reaction. A synergistic effect of two 2'-O-methylated ribose residues in the active site results in accelerated methyl group transfer. Supported by these results, it seems plausible that modified nucleotides may have enhanced early RNA catalysis and that metabolite-binding riboswitches may resemble inactivated ribozymes that have lost their catalytic activity during evolution.
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2
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Möhler M, Höfer K, Jäschke A. Synthesis of 5'-Thiamine-Capped RNA. Molecules 2020; 25:E5492. [PMID: 33255222 PMCID: PMC7727699 DOI: 10.3390/molecules25235492] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 11/20/2020] [Accepted: 11/21/2020] [Indexed: 01/05/2023] Open
Abstract
RNA 5'-modifications are known to extend the functional spectrum of ribonucleotides. In recent years, numerous non-canonical 5'-modifications, including adenosine-containing cofactors from the group of B vitamins, have been confirmed in all kingdoms of life. The structural component of thiamine adenosine triphosphate (thiamine-ATP), a vitamin B1 derivative found to accumulate in Escherichia coli and other organisms in response to metabolic stress conditions, suggests an analogous function as a 5'-modification of RNA. Here, we report the synthesis of thiamine adenosine dinucleotides and the preparation of pure 5'-thiamine-capped RNAs based on phosphorimidazolide chemistry. Furthermore, we present the incorporation of thiamine-ATP and thiamine adenosine diphosphate (thiamine-ADP) as 5'-caps of RNA by T7 RNA polymerase. Transcripts containing the thiamine modification were modified specifically with biotin via a combination of thiazole ring opening, nucleophilic substitution and copper-catalyzed azide-alkyne cycloaddition. The highlighted methods provide easy access to 5'-thiamine RNA, which may be applied in the development of thiamine-specific RNA capture protocols as well as the discovery and confirmation of 5'-thiamine-capped RNAs in various organisms.
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Affiliation(s)
| | | | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany; (M.M.); (K.H.)
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Micura R, Höbartner C. Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes. Chem Soc Rev 2020; 49:7331-7353. [PMID: 32944725 DOI: 10.1039/d0cs00617c] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This review aims at juxtaposing common versus distinct structural and functional strategies that are applied by aptamers, riboswitches, and ribozymes/DNAzymes. Focusing on recently discovered systems, we begin our analysis with small-molecule binding aptamers, with emphasis on in vitro-selected fluorogenic RNA aptamers and their different modes of ligand binding and fluorescence activation. Fundamental insights are much needed to advance RNA imaging probes for detection of exo- and endogenous RNA and for RNA process tracking. Secondly, we discuss the latest gene expression-regulating mRNA riboswitches that respond to the alarmone ppGpp, to PRPP, to NAD+, to adenosine and cytidine diphosphates, and to precursors of thiamine biosynthesis (HMP-PP), and we outline new subclasses of SAM and tetrahydrofolate-binding RNA regulators. Many riboswitches bind protein enzyme cofactors that, in principle, can catalyse a chemical reaction. For RNA, however, only one system (glmS ribozyme) has been identified in Nature thus far that utilizes a small molecule - glucosamine-6-phosphate - to participate directly in reaction catalysis (phosphodiester cleavage). We wonder why that is the case and what is to be done to reveal such likely existing cellular activities that could be more diverse than currently imagined. Thirdly, this brings us to the four latest small nucleolytic ribozymes termed twister, twister-sister, pistol, and hatchet as well as to in vitro selected DNA and RNA enzymes that promote new chemistry, mainly by exploiting their ability for RNA labelling and nucleoside modification recognition. Enormous progress in understanding the strategies of nucleic acids catalysts has been made by providing thorough structural fundaments (e.g. first structure of a DNAzyme, structures of ribozyme transition state mimics) in combination with functional assays and atomic mutagenesis.
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Affiliation(s)
- Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck CMBI, Leopold-Franzens University Innsbruck, Innsbruck, Austria.
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Liu K, Lat PK, Yu HZ, Sen D. CLICK-17, a DNA enzyme that harnesses ultra-low concentrations of either Cu+ or Cu2+ to catalyze the azide-alkyne 'click' reaction in water. Nucleic Acids Res 2020; 48:7356-7370. [PMID: 32520335 PMCID: PMC7367168 DOI: 10.1093/nar/gkaa502] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/28/2020] [Accepted: 06/02/2020] [Indexed: 12/22/2022] Open
Abstract
To enable the optimal, biocompatible and non-destructive application of the highly useful copper (Cu+)-mediated alkyne-azide 'click' cycloaddition in water, we have isolated and characterized a 79-nucleotide DNA enzyme or DNAzyme, 'CLICK-17', that harnesses as low as sub-micromolar Cu+; or, surprisingly, Cu2+ (without added reductants such as ascorbate) to catalyze conjugation between a variety of alkyne and azide substrates, including small molecules, proteins and nucleic acids. CLICK-17's Cu+ catalysis is orders of magnitude faster than that of either Cu+ alone or of Cu+ complexed to PERMUT-17, a sequence-permuted DNA isomer of CLICK-17. With the less toxic Cu2+, CLICK-17 attains rates comparable to Cu+, under conditions where both Cu2+ alone and Cu2+ complexed with a classic accelerating ligand, THPTA, are wholly inactive. Cyclic voltammetry shows that CLICK-17, unlike PERMUT-17, powerfully perturbs the Cu(II)/Cu(I) redox potential. CLICK-17 thus provides a unique, DNA-derived ligand environment for catalytic copper within its active site. As a bona fide Cu2+-driven enzyme, with potential for being evolved to accept only designated substrates, CLICK-17 and future variants promise the fast, safe, and substrate-specific catalysis of 'click' bioconjugations, potentially on the surfaces of living cells.
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Affiliation(s)
- Kun Liu
- Dept. of Chemistry, Simon Fraser University, Burnaby BC V5A 1S6, Canada
| | - Prince Kumar Lat
- Dept. of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby BC V5A 1S6, Canada
| | - Hua-Zhong Yu
- Dept. of Chemistry, Simon Fraser University, Burnaby BC V5A 1S6, Canada.,Dept. of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby BC V5A 1S6, Canada
| | - Dipankar Sen
- Dept. of Chemistry, Simon Fraser University, Burnaby BC V5A 1S6, Canada.,Dept. of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby BC V5A 1S6, Canada
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Papastavrou N, Bande O, Marlière P, Groaz E, Herdewijn P. Vitamin-guanosine monophosphate conjugates for in vitro transcription priming. Chem Commun (Camb) 2020; 56:2787-2790. [PMID: 32025667 DOI: 10.1039/c9cc09427j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Expanding the catalytic repertoire of ribozymes to include vitamin synthesis requires efficient labelling of RNA with the substrate of interest, prior to in vitro selection. For this purpose, we rationally designed and synthesized six GMP-conjugates carrying a synthetic pre-thiamine or biotin precursor and investigated their transcription incorporation properties by T7 RNA polymerase.
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Affiliation(s)
- Nikolaos Papastavrou
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49-Box 1041, 3000 Leuven, Belgium.
| | - Omprakash Bande
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49-Box 1041, 3000 Leuven, Belgium.
| | - Philippe Marlière
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057 Evry, France.
| | - Elisabetta Groaz
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49-Box 1041, 3000 Leuven, Belgium.
| | - Piet Herdewijn
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49-Box 1041, 3000 Leuven, Belgium.
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Abstract
The emergence of functional cooperation between the three main classes of biomolecules - nucleic acids, peptides and lipids - defines life at the molecular level. However, how such mutually interdependent molecular systems emerged from prebiotic chemistry remains a mystery. A key hypothesis, formulated by Crick, Orgel and Woese over 40 year ago, posits that early life must have been simpler. Specifically, it proposed that an early primordial biology lacked proteins and DNA but instead relied on RNA as the key biopolymer responsible not just for genetic information storage and propagation, but also for catalysis, i.e. metabolism. Indeed, there is compelling evidence for such an 'RNA world', notably in the structure of the ribosome as a likely molecular fossil from that time. Nevertheless, one might justifiably ask whether RNA alone would be up to the task. From a purely chemical perspective, RNA is a molecule of rather uniform composition with all four bases comprising organic heterocycles of similar size and comparable polarity and pK a values. Thus, RNA molecules cover a much narrower range of steric, electronic and physicochemical properties than, e.g. the 20 amino acid side-chains of proteins. Herein we will examine the functional potential of RNA (and other nucleic acids) with respect to self-replication, catalysis and assembly into simple protocellular entities.
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Ruscito A, McConnell EM, Koudrina A, Velu R, Mattice C, Hunt V, McKeague M, DeRosa MC. In Vitro Selection and Characterization of DNA Aptamers to a Small Molecule Target. ACTA ACUST UNITED AC 2017; 9:233-268. [PMID: 29241295 DOI: 10.1002/cpch.28] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Aptamers, synthetic oligonucleotide-based molecular recognition probes, have found use in a wide array of biosensing technologies based on their tight and highly selective binding to a variety of molecular targets. However, the inherent challenges associated with the selection and characterization of aptamers for small molecule targets have resulted in their underrepresentation, despite the need for small molecule detection in fields such as medicine, the environment, and agriculture. This protocol describes the steps in the selection, sequencing, affinity characterization, and truncation of DNA aptamers that are specific for small molecule targets. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
| | - Erin M McConnell
- Chemistry Department, Carleton University, Ottawa, Ontario, Canada
| | - Anna Koudrina
- Chemistry Department, Carleton University, Ottawa, Ontario, Canada
| | - Ranganathan Velu
- Chemistry Department, Carleton University, Ottawa, Ontario, Canada
| | | | - Vernon Hunt
- Chemistry Department, Carleton University, Ottawa, Ontario, Canada
| | - Maureen McKeague
- Department of Health Sciences and Technology, ETH Zürich, Zurich, Switzerland
| | - Maria C DeRosa
- Chemistry Department, Carleton University, Ottawa, Ontario, Canada
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Bingaman JL, Zhang S, Stevens DR, Yennawar NH, Hammes-Schiffer S, Bevilacqua PC. The GlcN6P cofactor plays multiple catalytic roles in the glmS ribozyme. Nat Chem Biol 2017; 13:439-445. [PMID: 28192411 PMCID: PMC5362308 DOI: 10.1038/nchembio.2300] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 12/09/2016] [Indexed: 01/06/2023]
Abstract
RNA enzymes (ribozymes) have remarkably diverse biological roles despite having limited chemical diversity. Protein enzymes enhance their reactivity through recruitment of cofactors; likewise, the naturally occurring glmS ribozyme uses the glucosamine-6-phosphate (GlcN6P) organic cofactor for phosphodiester bond cleavage. Prior structural and biochemical studies have implicated GlcN6P as the general acid. Here we describe new catalytic roles of GlcN6P through experiments and calculations. Large stereospecific normal thio effects and a lack of metal-ion rescue in the holoribozyme indicate that nucleobases and the cofactor play direct chemical roles and align the active site for self-cleavage. Large stereospecific inverse thio effects in the aporibozyme suggest that the GlcN6P cofactor disrupts an inhibitory interaction of the nucleophile. Strong metal-ion rescue in the aporibozyme reveals that this cofactor also provides electrostatic stabilization. Ribozyme organic cofactors thus perform myriad catalytic roles, thereby allowing RNA to compensate for its limited functional diversity.
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Affiliation(s)
- Jamie L. Bingaman
- Department of Chemistry and Center for RNA Molecular
Biology, The Pennsylvania State University, University Park, Pennsylvania 16802,
United States
| | - Sixue Zhang
- Department of Chemistry, University of Illinois at
Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - David R. Stevens
- Department of Chemistry, University of Illinois at
Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Neela H. Yennawar
- X-ray Crystallography Facility, Huck Institutes of the Life
Sciences, The Pennsylvania State University, 8 Althouse Laboratory, University Park,
Pennsylvania 16802, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, University of Illinois at
Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Philip C. Bevilacqua
- Department of Chemistry and Center for RNA Molecular
Biology, The Pennsylvania State University, University Park, Pennsylvania 16802,
United States
- Department of Biochemistry and Molecular Biology, The
Pennsylvania State University, University Park, Pennsylvania 16802, United
States
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Monteverde DR, Gómez-Consarnau L, Suffridge C, Sañudo-Wilhelmy SA. Life's utilization of B vitamins on early Earth. GEOBIOLOGY 2017; 15:3-18. [PMID: 27477998 DOI: 10.1111/gbi.12202] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 06/10/2016] [Indexed: 06/06/2023]
Abstract
Coenzymes are essential across all domains of life. B vitamins (B1 -thiamin, B2 -riboflavin, B3 -niacin, B5 -pantothenate, B6 -pyridoxine, B7 -biotin, and B12 -cobalamin) represent the largest class of coenzymes, which participate in a diverse set of reactions including C1 -rearrangements, DNA repair, electron transfer, and fatty acid synthesis. B vitamin structures range from simple to complex heterocycles, yet, despite this complexity, multiple lines of evidence exist for their ancient origins including abiotic synthesis under putative early Earth conditions and/or meteorite transport. Thus, some of these critical coenzymes likely preceded life on Earth. Some modern organisms can synthesize their own B vitamins de novo while others must either scavenge them from the environment or establish a symbiotic relationship with a B vitamin producer. B vitamin requirements are widespread in some of the most ancient metabolisms including all six carbon fixation pathways, sulfate reduction, sulfur disproportionation, methanogenesis, acetogenesis, and photosynthesis. Understanding modern metabolic B vitamin requirements is critical for understanding the evolutionary conditions of ancient metabolisms as well as the biogeochemical cycling of critical elements such as S, C, and O.
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Affiliation(s)
- D R Monteverde
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
| | - L Gómez-Consarnau
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - C Suffridge
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - S A Sañudo-Wilhelmy
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
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Martin LL, Unrau PJ, Müller UF. RNA synthesis by in vitro selected ribozymes for recreating an RNA world. Life (Basel) 2015; 5:247-68. [PMID: 25610978 PMCID: PMC4390851 DOI: 10.3390/life5010247] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 12/22/2014] [Accepted: 01/13/2015] [Indexed: 01/20/2023] Open
Abstract
The RNA world hypothesis states that during an early stage of life, RNA molecules functioned as genome and as the only genome-encoded catalyst. This hypothesis is supported by several lines of evidence, one of which is the in vitro selection of catalytic RNAs (ribozymes) in the laboratory for a wide range of reactions that might have been used by RNA world organisms. This review focuses on three types of ribozymes that could have been involved in the synthesis of RNA, the core activity in the self-replication of RNA world organisms. These ribozyme classes catalyze nucleoside synthesis, triphosphorylation, and the polymerization of nucleoside triphosphates. The strengths and weaknesses regarding each ribozyme’s possible function in a self-replicating RNA network are described, together with the obstacles that need to be overcome before an RNA world organism can be generated in the laboratory.
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Affiliation(s)
- Lyssa L Martin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
| | - Peter J Unrau
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
| | - Ulrich F Müller
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0356, USA.
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From the RNA world to the RNA/protein world: contribution of some riboswitch-binding species? J Theor Biol 2015; 370:197-201. [PMID: 25571850 DOI: 10.1016/j.jtbi.2014.12.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 12/19/2014] [Accepted: 12/22/2014] [Indexed: 12/16/2022]
Abstract
Some amino acids and their formal derivatives, currently riboswitch-binding species, could have interacted with polyribonucletides in prebiotic environments, leading to the peptide formation. If the resulting compounds had led to a sustainable polymerization of amino acids and the new structures had catalytic activity, such would have been an important contribution to the transition from the RNA world to the RNA/Protein world.
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