1
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Silkenath B, Kläge D, Altwein H, Schmidhäuser N, Mayer G, Hartig JS, Wittmann V. Phosphonate and Thiasugar Analogues of Glucosamine-6-phosphate: Activation of the glmS Riboswitch and Antibiotic Activity. ACS Chem Biol 2023; 18:2324-2334. [PMID: 37793187 PMCID: PMC10594590 DOI: 10.1021/acschembio.3c00452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/19/2023] [Indexed: 10/06/2023]
Abstract
The glmS riboswitch is a motif found in 5'-untranslated regions of bacterial mRNA that controls the synthesis of glucosamine-6-phosphate (GlcN6P), an essential building block for the bacterial cell wall, by a feedback mechanism. Activation of the glmS riboswitch by GlcN6P mimics interferes with the ability of bacteria to synthesize its cell wall. Accordingly, GlcN6P mimics acting as glmS activators are promising candidates for future antibiotic drugs that may overcome emerging bacterial resistance against established antibiotics. We describe the synthesis of a series of phosphonate mimics of GlcN6P as well as the thiasugar analogue of GlcN6P. The phosphonate mimics differ in their pKa value to answer the question of whether derivatives with a pKa matching that of GlcN6P would be efficient glmS activators. We found that all derivatives activate the riboswitch, however, less efficiently than GlcN6P. This observation can be explained by the missing hydrogen bonds in the case of phosphonates and is valuable information for the design of future GlcN6P mimics. The thiasugar analogue of GlcN6P on the other hand turned out to be a glmS riboswitch activator with the same activity as the natural metabolite GlcN6P. The nonphosphorylated thiasugar displayed antimicrobial activity against certain bacilli. Therefore, the compound is a promising lead structure for the development of future antibiotics with a potentially novel mode of action.
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Affiliation(s)
- Bjarne Silkenath
- Department
of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Dennis Kläge
- Department
of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Hanna Altwein
- Department
of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Nina Schmidhäuser
- Department
of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Günter Mayer
- LIMES
Institute, Center for Aptamer Research & Development, University of Bonn, 53121 Bonn, Germany
| | - Jörg S. Hartig
- Department
of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Valentin Wittmann
- Department
of Chemistry, University of Konstanz, 78457 Konstanz, Germany
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2
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Stängle D, Silkenath B, Gehle P, Esser A, Mayer G, Wittmann V. Carba-Sugar Analogs of Glucosamine-6-Phosphate: New Activators for the glmS Riboswitch. Chemistry 2023; 29:e202202378. [PMID: 36326082 PMCID: PMC10099210 DOI: 10.1002/chem.202202378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Indexed: 11/06/2022]
Abstract
Riboswitches are 5'-untranslated mRNA regions mostly found in bacteria. They are promising drug targets to overcome emerging bacterial resistance against commonly used antibiotics. The glmS riboswitch is unique among the family of riboswitches as it is a ribozyme that undergoes self-cleavage upon binding to glucosamine-6-phosphate (GlcN6P). Previously, we showed that carba glucosamine-6-phosphate (carba-GlcN6P) induces self-cleavage of the riboswitch with a potency similar to that of GlcN6P. Here, we report a synthetic approach to a new class of carba-GlcN6P derivatives with an alkoxy substituent in the carba position. Key features of the synthesis are a ring closing metathesis followed by a hydroboration. The strategy gives access to libraries of carba-GlcN6P derivatives. Ribozyme cleavage assays unraveled new activators for the glmS riboswitch from Listeria monocytogenes and Clostridium difficile.
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Affiliation(s)
- David Stängle
- Department of ChemistryUniversity of KonstanzUniversitätsstraße 1078464KonstanzGermany
| | - Bjarne Silkenath
- Department of ChemistryUniversity of KonstanzUniversitätsstraße 1078464KonstanzGermany
| | - Paul Gehle
- LIMES InstituteCenter for Aptamer Research & DevelopmentUniversity of BonnGerhard-Domagk-Straße 153121BonnGermany
| | - Anna Esser
- LIMES InstituteCenter for Aptamer Research & DevelopmentUniversity of BonnGerhard-Domagk-Straße 153121BonnGermany
| | - Günter Mayer
- LIMES InstituteCenter for Aptamer Research & DevelopmentUniversity of BonnGerhard-Domagk-Straße 153121BonnGermany
| | - Valentin Wittmann
- Department of ChemistryUniversity of KonstanzUniversitätsstraße 1078464KonstanzGermany
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3
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Krochmal D, Shao Y, Li NS, DasGupta S, Shelke SA, Koirala D, Piccirilli JA. Structural basis for substrate binding and catalysis by a self-alkylating ribozyme. Nat Chem Biol 2022; 18:376-384. [PMID: 35058645 DOI: 10.1038/s41589-021-00950-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 11/23/2021] [Indexed: 12/26/2022]
Abstract
Ribozymes that react with small-molecule probes have important applications in transcriptomics and chemical biology, such as RNA labeling and imaging. Understanding the structural basis for these RNA-modifying reactions will enable the development of better tools for studying RNA. Nevertheless, high-resolution structures and underlying catalytic mechanisms for members of this ribozyme class remain elusive. Here, we focus on a self-alkylating ribozyme that catalyzes nitrogen-carbon bond formation between a specific guanine and a 2,3-disubstituted epoxide substrate and report the crystal structures of a self-alkylating ribozyme, including both alkylated and apo forms, at 1.71-Å and 2.49-Å resolution, respectively. The ribozyme assumes an elongated hairpin-like architecture preorganized to accommodate the epoxide substrate in a hook-shaped conformation. Observed reactivity of substrate analogs together with an inverse, log-linear pH dependence of the reaction rate suggests a requirement for epoxide protonation, possibly assisted by the ether oxygens within the substrate.
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Affiliation(s)
- Daniel Krochmal
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Yaming Shao
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Nan-Sheng Li
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Saurja DasGupta
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Sandip A Shelke
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Deepak Koirala
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD, USA.
| | - Joseph A Piccirilli
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
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4
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Panchapakesan SSS, Breaker RR. The case of the missing allosteric ribozymes. Nat Chem Biol 2021; 17:375-382. [PMID: 33495645 PMCID: PMC8880209 DOI: 10.1038/s41589-020-00713-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 11/13/2020] [Indexed: 01/28/2023]
Abstract
The RNA World theory encompasses the hypothesis that sophisticated ribozymes and riboswitches were the primary drivers of metabolic processes in ancient organisms. Several types of catalytic RNAs and many classes of ligand-sensing RNA switches still exist in modern cells. Curiously, allosteric ribozymes formed by the merger of RNA enzyme and RNA switch components are largely absent in today's biological systems. This is true despite the striking abundances of various classes of both self-cleaving ribozymes and riboswitch aptamers. Here we present the known types of ligand-controlled ribozymes and riboswitches and discuss the possible reasons why fused ribozyme-aptamer constructs have been disfavored through evolution.
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Affiliation(s)
- Shanker S. S. Panchapakesan
- Department of Molecular, Cellular and Developmental
Biology, Yale University, P.O. Box 208103, New Haven, CT 06520-8103, USA
| | - Ronald R. Breaker
- Department of Molecular, Cellular and Developmental
Biology, Yale University, P.O. Box 208103, New Haven, CT 06520-8103, USA.,Howard Hughes Medical Institute, Yale University, P.O. Box
208103, New Haven, CT 06520-8103, USA.,Department of Molecular Biophysics and Biochemistry, Yale
University, P.O. Box 208103, New Haven, CT 06520-8103, USA
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5
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Dönmüş B, Ünal S, Kirmizitaş FC, Türkoğlu Laçin N. Virus-associated ribozymes and nano carriers against COVID-19. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2021; 49:204-218. [PMID: 33645342 DOI: 10.1080/21691401.2021.1890103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a zoo tonic, highly pathogenic virus. The new type of coronavirus with contagious nature spread from Wuhan (China) to the whole world in a very short time and caused the new coronavirus disease (COVID-19). COVID-19 has turned into a global public health crisis due to spreading by close person-to-person contact with high transmission capacity. Thus, research about the treatment of the damages caused by the virus or prevention from infection increases everyday. Besides, there is still no approved and definitive, standardized treatment for COVID-19. However, this disaster experienced by human beings has made us realize the significance of having a system ready for use to prevent humanity from viral attacks without wasting time. As is known, nanocarriers can be targeted to the desired cells in vitro and in vivo. The nano-carrier system targeting a specific protein, containing the enzyme inhibiting the action of the virus can be developed. The system can be used by simple modifications when we encounter another virus epidemic in the future. In this review, we present a potential treatment method consisting of a nanoparticle-ribozyme conjugate, targeting ACE-2 receptors by reviewing the virus-associated ribozymes, their structures, types and working mechanisms.
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Affiliation(s)
- Beyza Dönmüş
- Molecular Biology and Genetics Department, Yıldız Technical University, Istanbul, Turkey
| | - Sinan Ünal
- Molecular Biology and Genetics Department, Yıldız Technical University, Istanbul, Turkey
| | - Fatma Ceren Kirmizitaş
- Molecular Biology and Genetics Department, Yıldız Technical University, Istanbul, Turkey
| | - Nelisa Türkoğlu Laçin
- Molecular Biology and Genetics Department, Yıldız Technical University, Istanbul, Turkey
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6
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Andreasson JOL, Savinov A, Block SM, Greenleaf WJ. Comprehensive sequence-to-function mapping of cofactor-dependent RNA catalysis in the glmS ribozyme. Nat Commun 2020; 11:1663. [PMID: 32245964 PMCID: PMC7125110 DOI: 10.1038/s41467-020-15540-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 03/05/2020] [Indexed: 11/24/2022] Open
Abstract
Massively parallel, quantitative measurements of biomolecular activity across sequence space can greatly expand our understanding of RNA sequence-function relationships. We report the development of an RNA-array assay to perform such measurements and its application to a model RNA: the core glmS ribozyme riboswitch, which performs a ligand-dependent self-cleavage reaction. We measure the cleavage rates for all possible single and double mutants of this ribozyme across a series of ligand concentrations, determining kcat and KM values for active variants. These systematic measurements suggest that evolutionary conservation in the consensus sequence is driven by maintenance of the cleavage rate. Analysis of double-mutant rates and associated mutational interactions produces a structural and functional mapping of the ribozyme sequence, revealing the catalytic consequences of specific tertiary interactions, and allowing us to infer structural rearrangements that permit certain sequence variants to maintain activity.
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Affiliation(s)
- Johan O L Andreasson
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA
| | - Andrew Savinov
- Biophysics Program, Stanford University, Stanford, CA, 94305, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Steven M Block
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
- Department of Applied Physics, Stanford University, Stanford, CA, 94305, USA.
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
- Department of Applied Physics, Stanford University, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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7
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Abstract
A growing collection of bacterial riboswitch classes is being discovered that sense central metabolites, coenzymes, and signaling molecules. Included among the various mechanisms of gene regulation exploited by these RNA regulatory elements are several that modulate messenger RNA (mRNA) translation. In this review, the mechanisms of riboswitch-mediated translation control are summarized to highlight both their diversity and potential ancient origins. These mechanisms include ligand-gated presentation or occlusion of ribosome-binding sites, control of alternative splicing of mRNAs, and the regulation of mRNA stability. Moreover, speculation on the potential for novel riboswitch discoveries is presented, including a discussion on the potential for the discovery of a greater diversity of mechanisms for translation control.
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Affiliation(s)
- Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103
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8
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Gu Y, Lv X, Liu Y, Li J, Du G, Chen J, Rodrigo LA, Liu L. Synthetic redesign of central carbon and redox metabolism for high yield production of N-acetylglucosamine in Bacillus subtilis. Metab Eng 2018; 51:59-69. [PMID: 30343048 DOI: 10.1016/j.ymben.2018.10.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 09/26/2018] [Accepted: 10/01/2018] [Indexed: 01/06/2023]
Abstract
One of the primary goals of microbial metabolic engineering is to achieve high titer, yield and productivity (TYP) of engineered strains. This TYP index requires optimized carbon flux toward desired molecule with minimal by-product formation. De novo redesign of central carbon and redox metabolism holds great promise to alleviate pathway bottleneck and improve carbon and energy utilization efficiency. The engineered strain, with the overexpression or deletion of multiple genes, typically can't meet the TYP index, due to overflow of central carbon and redox metabolism that compromise the final yield, despite a high titer or productivity might be achieved. To solve this challenge, we reprogramed the central carbon and redox metabolism of Bacillus subtilis and achieved high TYP production of N-acetylglucosamine. Specifically, a "push-pull-promote" approach efficiently reduced the overflown acetyl-CoA flux and eliminated byproduct formation. Four synthetic NAD(P)-independent metabolic routes were introduced to rewire the redox metabolism to minimize energy loss. Implementation of these genetic strategies led us to obtain a B. subtilis strain with superior TYP index. GlcNAc titer in shake flask was increased from 6.6 g L-1 to 24.5 g L-1, the yield was improved from 0.115 to 0.468 g GlcNAc g-1 glucose, and the productivity was increased from 0.274 to 0.437 g L-1 h-1. These titer and yield are the highest levels ever reported and, the yield reached 98% of the theoretical pathway yield (0.478 g g-1 glucose). The synthetic redesign of carbon metabolism and redox metabolism represent a novel and general metabolic engineering strategy to improve the performance of microbial cell factories.
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Affiliation(s)
- Yang Gu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jian Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | | | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China.
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9
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Seith DD, Bingaman JL, Veenis AJ, Button AC, Bevilacqua PC. Elucidation of Catalytic Strategies of Small Nucleolytic Ribozymes From Comparative Analysis of Active Sites. ACS Catal 2018; 8:314-327. [PMID: 32547833 PMCID: PMC7296830 DOI: 10.1021/acscatal.7b02976] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A number of small, self-cleaving ribozyme classes have been identified including the hammerhead, hairpin, hepatitis delta virus (HDV), Varkud satellite (VS), glmS, twister, hatchet, pistol, and twister sister ribozymes. Within the active sites of these ribozymes, myriad functional groups contribute to catalysis. There has been extensive structure-function analysis of individual ribozymes, but the extent to which catalytic devices are shared across different ribozyme classes is unclear. As such, emergent catalytic principles for ribozymes may await discovery. Identification of conserved catalytic devices can deepen our understanding of RNA catalysis specifically and of enzymic catalysis generally. To probe similarities and differences amongst ribozyme classes, active sites from more than 80 high-resolution crystal structures of self-cleaving ribozymes were compared computationally. We identify commonalities amongst ribozyme classes pertaining to four classic catalytic devices: deprotonation of the 2'OH nucleophile (γ), neutralization of the non-bridging oxygens of the scissile phosphate (β), neutralization of the O5' leaving group (δ), and in-line nucleophilic attack (α). In addition, we uncover conservation of two catalytic devices, each of which centers on the activation of the 2'OH nucleophile by a guanine: one to acidify the 2'OH by hydrogen bond donation to it (γ') and one to acidify the 2'OH by releasing it from non-productive interactions by competitive hydrogen bonding (γ''). Our findings reveal that the amidine functionalities of G, A, and C are especially important for these strategies, and help explain absence of U at ribozyme active sites. The identified γ' and γ'' catalytic strategies help unify the catalytic strategies shared amongst catalytic RNAs and may be important for large ribozymes, as well as protein enzymes that act on nucleic acids.
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Affiliation(s)
- Daniel D. Seith
- Department of Chemistry and Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
- These two authors contributed equally to this work
| | - Jamie L. Bingaman
- Department of Chemistry and Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
- These two authors contributed equally to this work
| | - Andrew J. Veenis
- Department of Chemistry and Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Aileen C. Button
- Department of Chemistry and Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
- Department of Biochemistry, The University of Vermont, Burlington, Vermont 05405
| | - Philip C. Bevilacqua
- Department of Chemistry and Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
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10
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Mlýnský V, Kührová P, Jurečka P, Šponer J, Otyepka M, Banáš P. Mapping the Chemical Space of the RNA Cleavage and Its Implications for Ribozyme Catalysis. J Phys Chem B 2017; 121:10828-10840. [DOI: 10.1021/acs.jpcb.7b09129] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vojtěch Mlýnský
- Regional Centre
of Advanced Technologies and Materials, Department of Physical Chemistry,
Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), via
Bonomea 265, 34136 Trieste, Italy
| | - Petra Kührová
- Regional Centre
of Advanced Technologies and Materials, Department of Physical Chemistry,
Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Petr Jurečka
- Regional Centre
of Advanced Technologies and Materials, Department of Physical Chemistry,
Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Jiří Šponer
- Regional Centre
of Advanced Technologies and Materials, Department of Physical Chemistry,
Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolská 135, 612 65 Brno, Czech Republic
| | - Michal Otyepka
- Regional Centre
of Advanced Technologies and Materials, Department of Physical Chemistry,
Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Pavel Banáš
- Regional Centre
of Advanced Technologies and Materials, Department of Physical Chemistry,
Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolská 135, 612 65 Brno, Czech Republic
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11
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Passalacqua LFM, Jimenez RM, Fong JY, Lupták A. Allosteric Modulation of the Faecalibacterium prausnitzii Hepatitis Delta Virus-like Ribozyme by Glucosamine 6-Phosphate: The Substrate of the Adjacent Gene Product. Biochemistry 2017; 56:6006-6014. [PMID: 29045794 DOI: 10.1021/acs.biochem.7b00879] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Self-cleaving ribozymes were discovered 30 years ago and have been found throughout nature, from bacteria to animals, but little is known about their biological functions and regulation, particularly how cofactors and metabolites alter their activity. A hepatitis delta virus-like self-cleaving ribozyme maps upstream of a phosphoglucosamine mutase (glmM) open reading frame in the genome of the human gut bacterium Faecalibacterium prausnitzii. The presence of a ribozyme in the untranslated region of glmM suggests a regulation mechanism of gene expression. In the bacterial hexosamine biosynthesis pathway, the enzyme glmM catalyzes the isomerization of glucosamine 6-phosphate into glucosamine 1-phosphate. In this study, we investigated the effect of these metabolites on the co-transcriptional self-cleavage rate of the ribozyme. Our results suggest that glucosamine 6-phosphate, but not glucosamine 1-phosphate, is an allosteric ligand that increases the self-cleavage rate of drz-Fpra-1, providing the first known example of allosteric modulation of a self-cleaving ribozyme by the substrate of the adjacent gene product. Given that the ribozyme is activated by the glmM substrate, but not the product, this allosteric modulation may represent a potential feed-forward mechanism of gene expression regulation in bacteria.
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Affiliation(s)
- Luiz F M Passalacqua
- Department of Pharmaceutical Sciences, University of California , Irvine, California 92697, United States
| | - Randi M Jimenez
- Department of Molecular Biology and Biochemistry, University of California , Irvine, California 92697, United States
| | - Jennifer Y Fong
- Department of Pharmaceutical Sciences, University of California , Irvine, California 92697, United States
| | - Andrej Lupták
- Department of Pharmaceutical Sciences, University of California , Irvine, California 92697, United States.,Department of Molecular Biology and Biochemistry, University of California , Irvine, California 92697, United States.,Department of Chemistry, University of California , Irvine, California 92697, United States
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12
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Matzner D, Schüller A, Seitz T, Wittmann V, Mayer G. Fluoro-Carba-Sugars are Glycomimetic Activators of the glmS Ribozyme. Chemistry 2017; 23:12604-12612. [PMID: 28661578 DOI: 10.1002/chem.201702371] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Indexed: 11/05/2022]
Abstract
The glmS ribozyme is a bacterial gene-regulating riboswitch that controls cell wall synthesis, depending on glucosamine-6-phosphate as a cofactor. Due to the presence of this ribozyme in several human pathogen bacteria (e.g., MRSA, VRSA), the glmS ribozyme represents an attractive target for the development of artificial cofactors. The substitution of the ring oxygen in carbohydrates by functionalized methylene groups leads to a new generation of glycomimetics that exploits distinct interaction possibilities with their target structure in biological systems. Herein, we describe the synthesis of mono-fluoro-modified carba variants of α-d-glucosamine and β-l-idosamine. (5aR)-Fluoro-carba-α-d-glucosamine-6-phosphate is a synthetic mimic of the natural ligand of the glmS ribozyme and is capable of effectively addressing its unique self-cleavage mechanism. However, in contrast to what was expected, the activity is significantly decreased compared to its non-fluorinated analog. By combining self-cleavage assays with the Bacillus subtilis and Staphylococcus aureus glmS ribozyme and molecular docking studies, we provide a structure-activity relationship for fluorinated carba-sugars.
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Affiliation(s)
- Daniel Matzner
- Life & Medical Sciences Institute, University of Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany
| | - Anna Schüller
- Life & Medical Sciences Institute, University of Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany
| | - Torben Seitz
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.,Current address: Cilag AG, Schaffhausen, Switzerland
| | - Valentin Wittmann
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Günter Mayer
- Life & Medical Sciences Institute, University of Bonn, Gerhard-Domagk-Str. 1, 53121, Bonn, Germany
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13
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Ignatov D, Johansson J. RNA-mediated signal perception in pathogenic bacteria. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [PMID: 28792118 DOI: 10.1002/wrna.1429] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 05/11/2017] [Accepted: 05/11/2017] [Indexed: 11/09/2022]
Abstract
Bacterial pathogens encounter several different environments during an infection, many of them possibly being detrimental. In order to sense its surroundings and adjust the gene expression accordingly, different regulatory schemes are undertaken. With these, the bacterium appropriately can differentiate between various environmental cues to express the correct virulence factor at the appropriate time and place. An attractive regulator device is RNA, which has an outstanding ability to alter its structure in response to external stimuli, such as metabolite concentration or alterations in temperature, to control its downstream gene expression. This review will describe the function of riboswitches and thermometers, with a particular emphasis on regulatory RNAs being important for bacterial pathogenicity. WIREs RNA 2017, 8:e1429. doi: 10.1002/wrna.1429 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Dmitriy Ignatov
- Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden.,Department of Molecular Biology, Umeå University, Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
| | - Jörgen Johansson
- Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden.,Department of Molecular Biology, Umeå University, Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden, Umeå University, Umeå, Sweden
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14
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Bingaman JL, Gonzalez IY, Wang B, Bevilacqua PC. Activation of the glmS Ribozyme Nucleophile via Overdetermined Hydrogen Bonding. Biochemistry 2017; 56:4313-4317. [DOI: 10.1021/acs.biochem.7b00662] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jamie L. Bingaman
- 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
| | - Inanllely Y. Gonzalez
- Department
of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Bo Wang
- Department
of Chemistry, 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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15
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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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16
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Lau MWL, Trachman RJ, Ferré-D'Amaré AR. A divalent cation-dependent variant of the glmS ribozyme with stringent Ca 2+ selectivity co-opts a preexisting nonspecific metal ion-binding site. RNA (NEW YORK, N.Y.) 2017; 23:355-364. [PMID: 27932587 PMCID: PMC5311495 DOI: 10.1261/rna.059824.116] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 11/28/2016] [Indexed: 05/29/2023]
Abstract
Ribozymes use divalent cations for structural stabilization, as catalytic cofactors, or both. Because of the prominent role of Ca2+ in intracellular signaling, engineered ribozymes with stringent Ca2+ selectivity would be important in biotechnology. The wild-type glmS ribozyme (glmSWT) requires glucosamine-6-phosphate (GlcN6P) as a catalytic cofactor. Previously, a glmS ribozyme variant with three adenosine mutations (glmSAAA) was identified, which dispenses with GlcN6P and instead uses, with little selectivity, divalent cations as cofactors for site-specific RNA cleavage. We now report a Ca2+-specific ribozyme (glmSCa) evolved from glmSAAA that is >10,000 times more active in Ca2+ than Mg2+, is inactive in even 100 mM Mg2+, and is not responsive to GlcN6P. This stringent selectivity, reminiscent of the protein nuclease from Staphylococcus, allows rapid and selective ribozyme inactivation using a Ca2+ chelator such as EGTA. Because glmSCa functions in physiologically relevant Ca2+ concentrations, it can form the basis for intracellular sensors that couple Ca2+ levels to RNA cleavage. Biochemical analysis of glmSCa reveals that it has co-opted for selective Ca2+ binding a nonspecific cation-binding site responsible for structural stabilization in glmSWT and glmSAAA Fine-tuning of the selectivity of the cation site allows repurposing of this preexisting molecular feature.
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Affiliation(s)
- Matthew W L Lau
- National Heart, Lung and Blood Institute, Bethesda, Maryland 20892-8012, USA
| | - Robert J Trachman
- National Heart, Lung and Blood Institute, Bethesda, Maryland 20892-8012, USA
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17
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Lau MWL, Ferré-D'Amaré AR. Many Activities, One Structure: Functional Plasticity of Ribozyme Folds. Molecules 2016; 21:molecules21111570. [PMID: 27869745 PMCID: PMC6273943 DOI: 10.3390/molecules21111570] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 11/12/2016] [Accepted: 11/14/2016] [Indexed: 01/01/2023] Open
Abstract
Catalytic RNAs, or ribozymes, are involved in a number of essential biological processes, such as replication of RNA genomes and mobile genetic elements, RNA splicing, translation, and RNA degradation. The function of ribozymes requires the formation of active sites decorated with RNA functional groups within defined three-dimensional (3D) structures. The genotype (sequence) of RNAs ultimately determines what 3D structures they adopt (as a function of their environmental conditions). These 3D structures, in turn, give rise to biochemical activity, which can further elaborate them by catalytic rearrangements or association with other molecules. The fitness landscape of a non-periodic linear polymer, such as RNA, relates its primary structure to a phenotype. Two major challenges in the analysis of ribozymes is to map all possible genotypes to their corresponding catalytic activity (that is, to determine their fitness landscape experimentally), and to understand whether their genotypes and three-dimensional structures can support multiple different catalytic functions. Recently, the combined results of experiments that employ in vitro evolution methods, high-throughput sequencing and crystallographic structure determination have hinted at answers to these two questions: while the fitness landscape of ribozymes is rugged, meaning that their catalytic activity cannot be optimized by a smooth trajectory in sequence space, once an RNA achieves a stable three-dimensional fold, it can be endowed with distinctly different biochemical activities through small changes in genotype. This functional plasticity of highly structured RNAs may be particularly advantageous for the adaptation of organisms to drastic changes in selective pressure, or for the development of new biotechnological tools.
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Affiliation(s)
- Matthew W L Lau
- National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892-8012, USA.
| | - Adrian R Ferré-D'Amaré
- National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892-8012, USA.
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18
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Zhang S, Stevens D, Goyal P, Bingaman JL, Bevilacqua PC, Hammes-Schiffer S. Assessing the Potential Effects of Active Site Mg 2+ Ions in the glmS Ribozyme-Cofactor Complex. J Phys Chem Lett 2016; 7:3984-3988. [PMID: 27677922 PMCID: PMC5117136 DOI: 10.1021/acs.jpclett.6b01854] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 09/14/2016] [Indexed: 06/06/2023]
Abstract
Ribozymes employ diverse catalytic strategies in their self-cleavage mechanisms, including the use of divalent metal ions. This work explores the effects of Mg2+ ions in the active site of the glmS ribozyme-GlcN6P cofactor complex using computational methods. Deleterious and potentially beneficial effects of an active site Mg2+ ion on the self-cleavage reaction were identified. The presence of a Mg2+ ion near the scissile phosphate oxygen atoms at the cleavage site was determined to be deleterious, and thereby anticatalytic, due to electrostatic repulsion of the cofactor, disruption of key hydrogen-bonding interactions, and obstruction of nucleophilic attack. On the other hand, the presence of a Mg2+ ion at another position in the active site, the Hoogsteen face of the putative base, was found to avoid these deleterious effects and to be potentially catalytically favorable owing to the stabilization of negative charge and pKa shifting of the guanine base.
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Affiliation(s)
- Sixue Zhang
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801-3364, United States
| | - David
R. Stevens
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801-3364, United States
| | - Puja Goyal
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801-3364, United States
| | - Jamie L. Bingaman
- Department of Chemistry and Center
for RNA Molecular Biology and Department of Biochemistry
and Molecular Biology, The Pennsylvania
State University, University Park, Pennsylvania 16802, United States
| | - Philip C. Bevilacqua
- Department of Chemistry and Center
for RNA Molecular Biology and Department of Biochemistry
and Molecular Biology, The Pennsylvania
State University, University Park, Pennsylvania 16802, United States
| | - Sharon Hammes-Schiffer
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801-3364, United States
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19
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Lau MWL, Ferré-D'Amaré AR. In vitro evolution of coenzyme-independent variants from the glmS ribozyme structural scaffold. Methods 2016; 106:76-81. [PMID: 27130889 PMCID: PMC4981508 DOI: 10.1016/j.ymeth.2016.04.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 04/18/2016] [Accepted: 04/25/2016] [Indexed: 12/26/2022] Open
Abstract
Uniquely among known natural ribozymes that cleave RNA sequence-specifically, the glmS ribozyme-riboswitch employs a small molecule, glucosamine-6-phosphate (GlcN6P) as a catalytic cofactor. In vitro selection was employed to search for coenzyme-independent variants of this ribozyme. In addition to shedding light on the catalytic mechanism of the ribozyme, such variants could resemble the evolutionary ancestors of the modern, GlcN6P-regulated ribozyme-riboswitch. A mutant pool was constructed such that the secondary structure elements, which define the triply-pseudoknotted global fold of the ribozyme, was preserved. A stringent selection scheme that relies on thiol-mercury affinity chromatography for separating active and inactive sequences ultimately yielded a triple mutant with a cleavage rate exceeding 3min(-1) that only requires divalent cations for activity. Mutational analysis demonstrated that a point reversion of the variant toward the wild-type sequence was sufficient to partially restore GlcN6P-dependence, suggesting that coenzyme dependence can be readily be acquired by RNAs that adopt the glmS ribozyme fold. The methods employed to perform this selection experiment are described in detail in this review.
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Affiliation(s)
- Matthew W L Lau
- National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892-8012, USA
| | - Adrian R Ferré-D'Amaré
- National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892-8012, USA.
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20
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Kuechler ER, Giese TJ, York DM. VR-SCOSMO: A smooth conductor-like screening model with charge-dependent radii for modeling chemical reactions. J Chem Phys 2016; 144:164115. [PMID: 27131539 PMCID: PMC4851621 DOI: 10.1063/1.4946779] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 04/01/2016] [Indexed: 12/23/2022] Open
Abstract
To better represent the solvation effects observed along reaction pathways, and of ionic species in general, a charge-dependent variable-radii smooth conductor-like screening model (VR-SCOSMO) is developed. This model is implemented and parameterized with a third order density-functional tight binding quantum model, DFTB3/3OB-OPhyd, a quantum method which was developed for organic and biological compounds, utilizing a specific parameterization for phosphate hydrolysis reactions. Unlike most other applications with the DFTB3/3OB model, an auxiliary set of atomic multipoles is constructed from the underlying DFTB3 density matrix which is used to interact the solute with the solvent response surface. The resulting method is variational, produces smooth energies, and has analytic gradients. As a baseline, a conventional SCOSMO model with fixed radii is also parameterized. The SCOSMO and VR-SCOSMO models shown have comparable accuracy in reproducing neutral-molecule absolute solvation free energies; however, the VR-SCOSMO model is shown to reduce the mean unsigned errors (MUEs) of ionic compounds by half (about 2-3 kcal/mol). The VR-SCOSMO model presents similar accuracy as a charge-dependent Poisson-Boltzmann model introduced by Hou et al. [J. Chem. Theory Comput. 6, 2303 (2010)]. VR-SCOSMO is then used to examine the hydrolysis of trimethylphosphate and seven other phosphoryl transesterification reactions with different leaving groups. Two-dimensional energy landscapes are constructed for these reactions and calculated barriers are compared to those obtained from ab initio polarizable continuum calculations and experiment. Results of the VR-SCOSMO model are in good agreement in both cases, capturing the rate-limiting reaction barrier and the nature of the transition state.
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Affiliation(s)
- Erich R Kuechler
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-8087, USA
| | - Timothy J Giese
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-8087, USA
| | - Darrin M York
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-8087, USA
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21
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Jimenez RM, Polanco JA, Lupták A. Chemistry and Biology of Self-Cleaving Ribozymes. Trends Biochem Sci 2015; 40:648-661. [PMID: 26481500 DOI: 10.1016/j.tibs.2015.09.001] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 08/28/2015] [Accepted: 09/01/2015] [Indexed: 11/26/2022]
Abstract
Self-cleaving ribozymes were discovered 30 years ago, but their biological distribution and catalytic mechanisms are only beginning to be defined. Each ribozyme family is defined by a distinct structure, with unique active sites accelerating the same transesterification reaction across the families. Biochemical studies show that general acid-base catalysis is the most common mechanism of self-cleavage, but metal ions and metabolites can be used as cofactors. Ribozymes have been discovered in highly diverse genomic contexts throughout nature, from viroids to vertebrates. Their biological roles include self-scission during rolling-circle replication of RNA genomes, co-transcriptional processing of retrotransposons, and metabolite-dependent gene expression regulation in bacteria. Other examples, including highly conserved mammalian ribozymes, suggest that many new biological roles are yet to be discovered.
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Affiliation(s)
- Randi M Jimenez
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - Julio A Polanco
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - Andrej Lupták
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA; Department of Pharmaceutical Sciences, University of California, Irvine, CA, USA; Department of Chemistry, University of California, Irvine, CA, USA.
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22
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Dubecký M, Walter NG, Šponer J, Otyepka M, Banáš P. Chemical feasibility of the general acid/base mechanism of glmS ribozyme self-cleavage. Biopolymers 2015; 103:550-62. [PMID: 25858644 PMCID: PMC4553064 DOI: 10.1002/bip.22657] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 03/17/2015] [Accepted: 04/02/2015] [Indexed: 01/28/2023]
Abstract
In numerous Gram-positive bacteria, the glmS ribozyme or catalytic riboswitch regulates the expression of glucosamine-6-phosphate (GlcN6P) synthase via site-specific cleavage of its sugar-phosphate backbone in response to GlcN6P ligand binding. Biochemical data have suggested a crucial catalytic role for an active site guanine (G40 in Thermoanaerobacter tengcongensis, G33 in Bacillus anthracis). We used hybrid quantum chemical/molecular mechanical (QM/MM) calculations to probe the mechanism where G40 is deprotonated and acts as a general base. The calculations suggest that the deprotonated guanine G40(-) is sufficiently reactive to overcome the thermodynamic penalty arising from its rare protonation state, and thus is able to activate the A-1(2'-OH) group toward nucleophilic attack on the adjacent backbone. Furthermore, deprotonation of A-1(2'-OH) and nucleophilic attack are predicted to occur as separate steps, where activation of A-1(2'-OH) precedes nucleophilic attack. Conversely, the transition state associated with the rate-determining step corresponds to concurrent nucleophilic attack and protonation of the G1(O5') leaving group by the ammonium moiety of the GlcN6P cofactor. Overall, our calculations help to explain the crucial roles of G40 (as a general base) and GlcN6P (as a general acid) during glmS ribozyme self-cleavage. In addition, we show that the QM/MM description of the glmS ribozyme self-cleavage reaction is significantly more sensitive to the size of the QM region and the quality of the QM-MM coupling than that of other small ribozymes.
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Affiliation(s)
- Matúš Dubecký
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46, Olomouc, Czech Republic
| | - Nils G. Walter
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
- CEITEC – Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46, Olomouc, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46, Olomouc, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
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23
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Dong X, Tian Z, Yang X, Xue Y. Theoretical study on the mechanism of self-cleavage reaction of the glmS ribozyme. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1667-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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24
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Zhang S, Ganguly A, Goyal P, Bingaman J, Bevilacqua PC, Hammes-Schiffer S. Role of the active site guanine in the glmS ribozyme self-cleavage mechanism: quantum mechanical/molecular mechanical free energy simulations. J Am Chem Soc 2015; 137:784-98. [PMID: 25526516 PMCID: PMC4308743 DOI: 10.1021/ja510387y] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Indexed: 11/30/2022]
Abstract
The glmS ribozyme catalyzes a self-cleavage reaction at the phosphodiester bond between residues A-1 and G1. This reaction is thought to occur by an acid-base mechanism involving the glucosamine-6-phosphate cofactor and G40 residue. Herein quantum mechanical/molecular mechanical free energy simulations and pKa calculations, as well as experimental measurements of the rate constant for self-cleavage, are utilized to elucidate the mechanism, particularly the role of G40. Our calculations suggest that an external base deprotonates either G40(N1) or possibly A-1(O2'), which would be followed by proton transfer from G40(N1) to A-1(O2'). After this initial deprotonation, A-1(O2') starts attacking the phosphate as a hydroxyl group, which is hydrogen-bonded to deprotonated G40, concurrent with G40(N1) moving closer to the hydroxyl group and directing the in-line attack. Proton transfer from A-1(O2') to G40 is concomitant with attack of the scissile phosphate, followed by the remainder of the cleavage reaction. A mechanism in which an external base does not participate, but rather the proton transfers from A-1(O2') to a nonbridging oxygen during nucleophilic attack, was also considered but deemed to be less likely due to its higher effective free energy barrier. The calculated rate constant for the favored mechanism is in agreement with the experimental rate constant measured at biological Mg(2+) ion concentration. According to these calculations, catalysis is optimal when G40 has an elevated pKa rather than a pKa shifted toward neutrality, although a balance among the pKa's of A-1, G40, and the nonbridging oxygen is essential. These results have general implications, as the hammerhead, hairpin, and twister ribozymes have guanines at a similar position as G40.
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Affiliation(s)
- Sixue Zhang
- Department
of Chemistry, University of Illinois at
Urbana—Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Abir Ganguly
- Department
of Chemistry, University of Illinois at
Urbana—Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Puja Goyal
- Department
of Chemistry, University of Illinois at
Urbana—Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Jamie
L. Bingaman
- Department
of Chemistry and Center for RNA Molecular Biology, Pennsylvania State University, 104 Chemistry Building, University Park, Pennsylvania 16802, United States
| | - Philip C. Bevilacqua
- Department
of Chemistry and Center for RNA Molecular Biology, Pennsylvania State University, 104 Chemistry Building, 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
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25
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Trausch JJ, Batey RT. Design of Modular “Plug-and-Play” Expression Platforms Derived from Natural Riboswitches for Engineering Novel Genetically Encodable RNA Regulatory Devices. Methods Enzymol 2015; 550:41-71. [DOI: 10.1016/bs.mie.2014.10.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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26
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Abstract
Heterocyclic nucleic acid bases and their analogs can adopt multiple tautomeric forms due to the presence of multiple solvent-exchangeable protons. In DNA, spontaneous formation of minor tautomers has been speculated to contribute to mutagenic mispairings during DNA replication, whereas in RNA, minor tautomeric forms have been proposed to enhance the structural and functional diversity of RNA enzymes and aptamers. This review summarizes the role of tautomerism in RNA biochemistry, specifically focusing on the role of tautomerism in catalysis of small self-cleaving ribozymes and recognition of ligand analogs by riboswitches. Considering that the presence of multiple tautomers of nucleic acid bases is a rare occurrence, and that tautomers typically interconvert on a fast time scale, methods for studying rapid tautomerism in the context of nucleic acids under biologically relevant aqueous conditions are also discussed.
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Affiliation(s)
- Vipender Singh
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Bogdan I Fedeles
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - John M Essigmann
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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27
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Joseph AA, Dhurandhare VM, Chang CW, Verma VP, Mishra GP, Ku CC, Lin CC, Wang CC. Chemoselective per-O-trimethylsilylation and homogeneous N-functionalisation of amino sugars. Chem Commun (Camb) 2015; 51:104-6. [DOI: 10.1039/c4cc06645f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
HomogeneousN-functionalisation of amino sugars can be achievedviaefficient CH3CN-promoted hexamethyldisilazane per-O-trimethylsilylation.
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Affiliation(s)
- A. Abragam Joseph
- Institute of Chemistry
- Academia Sinica
- Taipei 115
- Taiwan
- Department of Chemistry
| | - Vijay M. Dhurandhare
- Institute of Chemistry
- Academia Sinica
- Taipei 115
- Taiwan
- Chemical Biology and Molecular Biophysics Program
| | - Chun-Wei Chang
- Institute of Chemistry
- Academia Sinica
- Taipei 115
- Taiwan
- Chemical Biology and Molecular Biophysics Program
| | | | | | - Chiao-Chu Ku
- Institute of Chemistry
- Academia Sinica
- Taipei 115
- Taiwan
| | - Chun-Cheng Lin
- Department of Chemistry
- National Tsing Hua University
- Hsinchu 300
- Taiwan
| | - Cheng-Chung Wang
- Institute of Chemistry
- Academia Sinica
- Taipei 115
- Taiwan
- Chemical Biology and Molecular Biophysics Program
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28
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Fei X, Holmes T, Diddle J, Hintz L, Delaney D, Stock A, Renner D, McDevitt M, Berkowitz DB, Soukup JK. Phosphatase-inert glucosamine 6-phosphate mimics serve as actuators of the glmS riboswitch. ACS Chem Biol 2014; 9:2875-82. [PMID: 25254431 PMCID: PMC4273988 DOI: 10.1021/cb500458f] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
![]()
The glmS riboswitch is unique among gene-regulating
riboswitches and catalytic RNAs. This is because its own metabolite,
glucosamine-6-phosphate (GlcN6P), binds to the riboswitch and catalytically
participates in the RNA self-cleavage reaction, thereby providing
a novel negative feedback mechanism. Given that a number of pathogens
harbor the glmS riboswitch, artificial actuators
of this potential RNA target are of great interest. Structural/kinetic
studies point to the 2-amino and 6-phosphate ester functionalities
in GlcN6P as being crucial for this actuation. As a first step toward
developing artificial actuators, we have synthesized a series of nine
GlcN6P analogs bearing phosphatase-inert surrogates in place of the
natural phosphate ester. Self-cleavage assays with the Bacillus cereusglmS riboswitch
give a broad SAR. Two analogs display significant activity, namely,
the 6-deoxy-6-phosphonomethyl analog (5) and the 6-O-malonyl ether (13). Kinetic profiles show
a 22-fold and a 27-fold higher catalytic efficiency, respectively,
for these analogs vs glucosamine (GlcN). Given their nonhydrolyzable
phosphate surrogate functionalities, these analogs are arguably the
most robust artificial glmS riboswitch actuators
yet reported. Interestingly, the malonyl ether (13, extra
O atom) is much more effective than the simple malonate (17), and the “sterically true” phosphonate (5) is far superior to the chain-truncated (7) or chain-extended
(11) analogs, suggesting that positioning via Mg coordination
is important for activity. Docking results are consistent with this
view. Indeed, the viability of the phosphonate and 6-O-malonyl ether
mimics of GlcN6P points to a potential new strategy for artificial
actuation of the glmS riboswitch in a biological
setting, wherein phosphatase-resistance is paramount.
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Affiliation(s)
- Xiang Fei
- Department
of Chemistry, University of Nebraska, Lincoln, Nebraska 68588, United States
| | - Thomas Holmes
- Department
of Chemistry, Creighton University, Omaha, Nebraska 68178, United States
| | - Julianna Diddle
- Department
of Chemistry, Creighton University, Omaha, Nebraska 68178, United States
| | - Lauren Hintz
- Department
of Chemistry, Creighton University, Omaha, Nebraska 68178, United States
| | - Dan Delaney
- Department
of Chemistry, Creighton University, Omaha, Nebraska 68178, United States
| | - Alex Stock
- Department
of Chemistry, Creighton University, Omaha, Nebraska 68178, United States
| | - Danielle Renner
- Department
of Chemistry, Creighton University, Omaha, Nebraska 68178, United States
| | - Molly McDevitt
- Department
of Chemistry, Creighton University, Omaha, Nebraska 68178, United States
| | - David B. Berkowitz
- Department
of Chemistry, University of Nebraska, Lincoln, Nebraska 68588, United States
| | - Juliane K. Soukup
- Department
of Chemistry, Creighton University, Omaha, Nebraska 68178, United States
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29
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Zhao Y, Chen H, Du F, Yasmeen A, Dong J, Cui X, Tang Z. Signal amplification of glucosamine-6-phosphate based on ribozyme glmS. Biosens Bioelectron 2014; 62:337-42. [DOI: 10.1016/j.bios.2014.06.067] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 06/10/2014] [Accepted: 06/12/2014] [Indexed: 01/29/2023]
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30
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Ramesh A, Winkler WC. Metabolite-binding ribozymes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:989-994. [PMID: 24769284 DOI: 10.1016/j.bbagrm.2014.04.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 04/08/2014] [Accepted: 04/13/2014] [Indexed: 12/22/2022]
Abstract
Catalysis in the biological context was largely thought to be a protein-based phenomenon until the discovery of RNA catalysts called ribozymes. These discoveries demonstrated that many RNA molecules exhibit remarkable structural and functional versatility. By virtue of these features, naturally occurring ribozymes have been found to be involved in catalyzing reactions for fundamentally important cellular processes such as translation and RNA processing. Another class of RNAs called riboswitches directly binds ligands to control downstream gene expression. Most riboswitches regulate downstream gene expression by controlling premature transcription termination or by affecting the efficiency of translation initiation. However, one riboswitch class couples ligand-sensing to ribozyme activity. Specifically, the glmS riboswitch is a nucleolytic ribozyme, whose self-cleavage activity is triggered by the binding of GlcN6P. The products of this self-cleavage reaction are then targeted by cellular RNases for rapid degradation, thereby reducing glmS expression under conditions of sufficient GlcN6P. Since the discovery of the glmS ribozyme, other metabolite-binding ribozymes have been identified. Together, these discoveries have expanded the general understanding of noncoding RNAs and provided insights that will assist future development of synthetic riboswitch-ribozymes. A very broad overview of natural and synthetic ribozymes is presented herein with an emphasis on the structure and function of the glmS ribozyme as a paradigm for metabolite-binding ribozymes that control gene expression. This article is part of a Special Issue entitled: Riboswitches.
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Affiliation(s)
- Arati Ramesh
- The University of Texas Southwestern Medical Center, Department of Biophysics, 6001 Forest Park Rd, Dallas, USA.
| | - Wade C Winkler
- The University of Maryland, Department of Cell Biology and Molecular Genetics, 3112 Biosciences Research Building, College Park, MD, USA.
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31
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Lau MWL, Ferré-D'Amaré AR. An in vitro evolved glmS ribozyme has the wild-type fold but loses coenzyme dependence. Nat Chem Biol 2013; 9:805-10. [PMID: 24096303 DOI: 10.1038/nchembio.1360] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 09/05/2013] [Indexed: 12/26/2022]
Abstract
Uniquely among known ribozymes, the glmS ribozyme-riboswitch requires a small-molecule coenzyme, glucosamine-6-phosphate (GlcN6P). Although consistent with its gene-regulatory function, the use of GlcN6P is unexpected because all of the other characterized self-cleaving ribozymes use RNA functional groups or divalent cations for catalysis. To determine what active site features make this ribozyme reliant on GlcN6P and to evaluate whether it might have evolved from a coenzyme-independent ancestor, we isolated a GlcN6P-independent variant through in vitro selection. Three active site mutations suffice to generate a highly reactive RNA that adopts the wild-type fold but uses divalent cations for catalysis and is insensitive to GlcN6P. Biochemical and crystallographic comparisons of wild-type and mutant ribozymes show that a handful of functional groups fine-tune the RNA to be either coenzyme or cation dependent. These results indicate that a few mutations can confer new biochemical activities on structured RNAs. Thus, families of structurally related ribozymes with divergent function may exist.
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Affiliation(s)
- Matthew W L Lau
- National Heart, Lung and Blood Institute, Bethesda, Maryland, USA
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32
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Posakony JJ, Ferré-D'Amaré AR. Glucosamine and glucosamine-6-phosphate derivatives: catalytic cofactor analogues for the glmS ribozyme. J Org Chem 2013; 78:4730-43. [PMID: 23578404 DOI: 10.1021/jo400192e] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Two analogues of glucosamine-6-phosphate (GlcN6P, 1) and five of glucosamine (GlcN, 2) were prepared for evaluation as catalytic cofactors of the glmS ribozyme, a bacterial gene-regulatory RNA that controls cell wall biosynthesis. Glucosamine and allosamine with 3-azido substitutions were prepared by SN2 reactions of the respective 1,2,4,6-protected sugars; final acidic hydrolysis afforded the fully deprotected compounds as their TFA salts. A 6-phospho-2-aminoglucolactam (31) was prepared from glucosamine in a 13-step synthesis, which included a late-stage POCl3-phosphorylation. A simple and widely applicable 2-step procedure with the triethylsilyl (TES) protecting group was developed to selectively expose the 6-OH group in N-protected glucosamine analogues, which provided another route to chemical phosphorylation. Mitsunobu chemistry afforded 6-cyano (35) and 6-azido (36) analogues of GlcN-(Cbz), and the selectivity for the 6-position was confirmed by NMR (COSY, HMBC, HMQC) experiments. Compound 36 was converted to the fully deprotected 6-azido-GlcN (37) and 2,6-diaminoglucose (38) analogues. A 2-hydroxylamino glucose (42) analogue was prepared via an oxaziridine (41). Enzymatic phosphorylation of 42 and chemical phosphorylation of its 6-OH precursor (43) were possible, but 42 and the 6-phospho product (44) were unstable under neutral or basic conditions. Chemical phosphorylation of the previously described 2-guanidinyl-glucose (46) afforded its 6-phospho analogue (49) after final deprotection.
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Affiliation(s)
- Jeffrey J Posakony
- National Heart, Lung, and Blood Institute, 50 South Drive, MSC 8012, Bethesda, Maryland 20892-8012, USA.
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33
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Soukup JK. The structural and functional uniqueness of the glmS ribozyme. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 120:173-93. [PMID: 24156944 DOI: 10.1016/b978-0-12-381286-5.00005-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The glmS bacterial ribozyme/riboswitch is found in a number of Gram-positive bacteria, many of which are human pathogens. Investigation of the structure and function of the glmS catalyst will aid in the development of artificial agonists/antagonists that might function as novel antibiotics. The glmS ribozyme is mechanistically unique in that it is the first RNA catalyst identified to require a coenzyme, glucosamine-6-phosphate, for RNA self-cleavage. In addition, it is the first riboswitch identified to utilize self-cleavage as a mode of genetic regulation in metabolism. Significant biochemical and biophysical data exist for the glmS ribozyme and aid in mechanistically understanding the importance of RNA and coenzyme structure to function in acid-base catalysis.
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Affiliation(s)
- Juliane K Soukup
- Department of Chemistry, Creighton University, Omaha, Nebraska, USA
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