1
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Kersten C, Archambault P, Köhler LP. Assessment of Nucleobase Protomeric and Tautomeric States in Nucleic Acid Structures for Interaction Analysis and Structure-Based Ligand Design. J Chem Inf Model 2024; 64:4485-4499. [PMID: 38766733 DOI: 10.1021/acs.jcim.4c00520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
With increasing interest in RNA as a therapeutic and a potential target, the role of RNA structures has become more important. Even slight changes in nucleobases, such as modifications or protomeric and tautomeric states, can have a large impact on RNA structure and function, while local environments in turn affect protonation and tautomerization. In this work, the application of empirical tools for pKa and tautomer prediction for RNA modifications was elucidated and compared with ab initio quantum mechanics (QM) methods and expanded toward macromolecular RNA structures, where QM is no longer feasible. In this regard, the Protonate3D functionality within the molecular operating environment (MOE) was expanded for nucleobase protomer and tautomer predictions and applied to reported examples of altered protonation states depending on the local environment. Overall, observations of nonstandard protomers and tautomers were well reproduced, including structural C+G:C(A) and A+GG motifs, several mismatches, and protonation of adenosine or cytidine as the general acid in nucleolytic ribozymes. Special cases, such as cobalt hexamine-soaked complexes or the deprotonation of guanosine as the general base in nucleolytic ribozymes, proved to be challenging. The collected set of examples shall serve as a starting point for the development of further RNA protonation prediction tools, while the presented Protonate3D implementation already delivers reasonable protonation predictions for RNA and DNA macromolecules. For cases where higher accuracy is needed, like following catalytic pathways of ribozymes, incorporation of QM-based methods can build upon the Protonate3D-generated starting structures. Likewise, this protonation prediction can be used for structure-based RNA-ligand design approaches.
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Affiliation(s)
- Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany
- Institute for Quantitative and Computational Biosciences, Johannes Gutenberg-University, BioZentrum I, Hanns-Dieter-Hüsch.Weg 15, 55128 Mainz, Germany
| | - Philippe Archambault
- Chemical Computing Group, 910-1010 Sherbrooke W., Montreal, Quebec, Canada H3A 2R7
| | - Luca P Köhler
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University, Staudingerweg 5, 55128 Mainz, Germany
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2
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Schwartz EA, Bravo JPK, Ahsan M, Macias LA, McCafferty CL, Dangerfield TL, Walker JN, Brodbelt JS, Palermo G, Fineran PC, Fagerlund RD, Taylor DW. RNA targeting and cleavage by the type III-Dv CRISPR effector complex. Nat Commun 2024; 15:3324. [PMID: 38637512 PMCID: PMC11026444 DOI: 10.1038/s41467-024-47506-y] [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: 08/21/2023] [Accepted: 04/02/2024] [Indexed: 04/20/2024] Open
Abstract
CRISPR-Cas are adaptive immune systems in bacteria and archaea that utilize CRISPR RNA-guided surveillance complexes to target complementary RNA or DNA for destruction1-5. Target RNA cleavage at regular intervals is characteristic of type III effector complexes6-8. Here, we determine the structures of the Synechocystis type III-Dv complex, an apparent evolutionary intermediate from multi-protein to single-protein type III effectors9,10, in pre- and post-cleavage states. The structures show how multi-subunit fusion proteins in the effector are tethered together in an unusual arrangement to assemble into an active and programmable RNA endonuclease and how the effector utilizes a distinct mechanism for target RNA seeding from other type III effectors. Using structural, biochemical, and quantum/classical molecular dynamics simulation, we study the structure and dynamics of the three catalytic sites, where a 2'-OH of the ribose on the target RNA acts as a nucleophile for in line self-cleavage of the upstream scissile phosphate. Strikingly, the arrangement at the catalytic residues of most type III complexes resembles the active site of ribozymes, including the hammerhead, pistol, and Varkud satellite ribozymes. Our work provides detailed molecular insight into the mechanisms of RNA targeting and cleavage by an important intermediate in the evolution of type III effector complexes.
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Affiliation(s)
- Evan A Schwartz
- Interdisciplinary Life Sciences Graduate Programs, University of Texas at Austin, Austin, TX, USA
| | - Jack P K Bravo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Mohd Ahsan
- Department of Bioengineering and Department of Chemistry, University of California, Riverside, CA, USA
| | - Luis A Macias
- Department of Chemistry, University of Texas at Austin, Austin, TX, USA
| | - Caitlyn L McCafferty
- Interdisciplinary Life Sciences Graduate Programs, University of Texas at Austin, Austin, TX, USA
| | - Tyler L Dangerfield
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Jada N Walker
- Department of Chemistry, University of Texas at Austin, Austin, TX, USA
| | | | - Giulia Palermo
- Department of Bioengineering and Department of Chemistry, University of California, Riverside, CA, USA.
| | - Peter C Fineran
- Microbiology and Immunology, University of Otago, PO Box 56, Dunedin, New Zealand
- Bioprotection Aotearoa, University of Otago, PO Box 56, Dunedin, New Zealand
- Genetics Otago, University of Otago, PO Box 56, Dunedin, New Zealand
| | - Robert D Fagerlund
- Microbiology and Immunology, University of Otago, PO Box 56, Dunedin, New Zealand.
- Bioprotection Aotearoa, University of Otago, PO Box 56, Dunedin, New Zealand.
- Genetics Otago, University of Otago, PO Box 56, Dunedin, New Zealand.
| | - David W Taylor
- Interdisciplinary Life Sciences Graduate Programs, University of Texas at Austin, Austin, TX, USA.
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA.
- LIVESTRONG Cancer Institutes, Dell Medical School, University of Texas at Austin, Austin, TX, USA.
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3
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Sabalette KB, Makarova L, Marcia M. G·U base pairing motifs in long non-coding RNAs. Biochimie 2023; 214:123-140. [PMID: 37353139 DOI: 10.1016/j.biochi.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 06/25/2023]
Abstract
Long non-coding RNAs (lncRNAs) are recently-discovered transcripts involved in gene expression regulation and associated with diseases. Despite the unprecedented molecular complexity of these transcripts, recent studies of the secondary and tertiary structure of lncRNAs are starting to reveal the principles of lncRNA structural organization, with important functional implications. It therefore starts to be possible to analyze lncRNA structures systematically. Here, using a set of prototypical and medically-relevant lncRNAs of known secondary structure, we specifically catalogue the distribution and structural environment of one of the first-identified and most frequently occurring non-canonical Watson-Crick interactions, the G·U base pair. We compare the properties of G·U base pairs in our set of lncRNAs to those of the G·U base pairs in other well-characterized transcripts, like rRNAs, tRNAs, ribozymes, and riboswitches. Furthermore, we discuss how G·U base pairs in these targets participate in establishing interactions with proteins or miRNAs, and how they enable lncRNA tertiary folding by forming intramolecular or metal-ion interactions. Finally, by identifying highly-G·U-enriched regions of yet unknown function in our target lncRNAs, we provide a new rationale for future experimental investigation of these motifs, which will help obtain a more comprehensive understanding of lncRNA functions and molecular mechanisms in the future.
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Affiliation(s)
- Karina Belen Sabalette
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs, Grenoble, 38042, France
| | - Liubov Makarova
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs, Grenoble, 38042, France
| | - Marco Marcia
- European Molecular Biology Laboratory (EMBL) Grenoble, 71 Avenue des Martyrs, Grenoble, 38042, France.
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4
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Deng J, Fang X, Huang L, Li S, Xu L, Ye K, Zhang J, Zhang K, Zhang QC. RNA structure determination: From 2D to 3D. FUNDAMENTAL RESEARCH 2023; 3:727-737. [PMID: 38933295 PMCID: PMC11197651 DOI: 10.1016/j.fmre.2023.06.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 06/04/2023] [Accepted: 06/05/2023] [Indexed: 06/28/2024] Open
Abstract
RNA molecules serve a wide range of functions that are closely linked to their structures. The basic structural units of RNA consist of single- and double-stranded regions. In order to carry out advanced functions such as catalysis and ligand binding, certain types of RNAs can adopt higher-order structures. The analysis of RNA structures has progressed alongside advancements in structural biology techniques, but it comes with its own set of challenges and corresponding solutions. In this review, we will discuss recent advances in RNA structure analysis techniques, including structural probing methods, X-ray crystallography, nuclear magnetic resonance, cryo-electron microscopy, and small-angle X-ray scattering. Often, a combination of multiple techniques is employed for the integrated analysis of RNA structures. We also survey important RNA structures that have been recently determined using various techniques.
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Affiliation(s)
- Jie Deng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Xianyang Fang
- Beijing Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Lin Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Shanshan Li
- MOE Key Laboratory for Cellular Dynamics and Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Lilei Xu
- Beijing Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinsong Zhang
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Kaiming Zhang
- MOE Key Laboratory for Cellular Dynamics and Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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5
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Sapkota KP, Li S, Zhang J. Cotranscriptional Assembly and Native Purification of Large RNA-RNA Complexes for Structural Analyses. Methods Mol Biol 2023; 2568:1-12. [PMID: 36227558 DOI: 10.1007/978-1-0716-2687-0_1] [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] [Indexed: 06/16/2023]
Abstract
Recent technological developments such as cryogenic electron microscopy (Cryo-EM) and X-ray free electron lasers (XFEL) have significantly expanded the available toolkit to visualize large, complex noncoding RNAs and their complexes. Consequently, the quality of the RNA sample, as measured by its chemical monodispersity and conformational homogeneity, has become the bottleneck that frequently precludes effective structural analyses. Here we describe a general RNA sample preparation protocol that combines cotranscriptional RNA folding and RNA-RNA complex assembly, followed by native purification of stoichiometric complexes. We illustrate and discuss the utility of this versatile method in overcoming RNA misfolding and enabling the structural and mechanistic elucidations of the T-box riboswitch-tRNA complexes.
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Affiliation(s)
- Krishna P Sapkota
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Shuang Li
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
- Structural Biochemistry Unit, National Institute of Dental and Craniofacial Research, Bethesda, MD, USA
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA.
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6
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Lennon SR, Batey RT. Regulation of Gene Expression Through Effector-dependent Conformational Switching by Cobalamin Riboswitches. J Mol Biol 2022; 434:167585. [PMID: 35427633 PMCID: PMC9474592 DOI: 10.1016/j.jmb.2022.167585] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 04/04/2022] [Accepted: 04/06/2022] [Indexed: 11/16/2022]
Abstract
Riboswitches are an outstanding example of genetic regulation mediated by RNA conformational switching. In these non-coding RNA elements, the occupancy status of a ligand-binding domain governs the mRNA's decision to form one of two mutually exclusive structures in the downstream expression platform. Temporal constraints upon the function of many riboswitches, requiring folding of complex architectures and conformational switching in a limited co-transcriptional timeframe, make them ideal model systems for studying these processes. In this review, we focus on the mechanism of ligand-directed conformational changes in one of the most widely distributed riboswitches in bacteria: the cobalamin family. We describe the architectural features of cobalamin riboswitches whose structures have been determined by x-ray crystallography, which suggest a direct physical role of cobalamin in effecting the regulatory switch. Next, we discuss a series of experimental approaches applied to several model cobalamin riboswitches that interrogate these structural models. As folding is central to riboswitch function, we consider the differences in folding landscapes experienced by RNAs that are produced in vitro and those that are allowed to fold co-transcriptionally. Finally, we highlight a set of studies that reveal the difficulties of studying cobalamin riboswitches outside the context of transcription and that co-transcriptional approaches are essential for developing a more accurate picture of their structure-function relationships in these switches. This understanding will be essential for future advancements in the use of small-molecule guided RNA switches in a range of applications such as biosensors, RNA imaging tools, and nucleic acid-based therapies.
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Affiliation(s)
- Shelby R Lennon
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA
| | - Robert T Batey
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA.
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7
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Ekesan Ş, McCarthy E, Case DA, York DM. RNA Electrostatics: How Ribozymes Engineer Active Sites to Enable Catalysis. J Phys Chem B 2022; 126:5982-5990. [PMID: 35862934 PMCID: PMC9496635 DOI: 10.1021/acs.jpcb.2c03727] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Electrostatic interactions are fundamental to RNA structure and function, and intimately influenced by solvation and the ion atmosphere. RNA enzymes, or ribozymes, are catalytic RNAs that are able to enhance reaction rates over a million-fold, despite having only a limited repertoire of building blocks and available set of chemical functional groups. Ribozyme active sites usually occur at junctions where negatively charged helices come together, and in many cases leverage this strained electrostatic environment to recruit metal ions in solution that can assist in catalysis. Similar strategies have been implicated in related artificially engineered DNA enzymes. Herein, we apply Poisson-Boltzmann, 3D-RISM, and molecular simulations to study a set of metal-dependent small self-cleaving ribozymes (hammerhead, pistol, and Varkud satellite) as well as an artificially engineered DNAzyme (8-17) to examine electrostatic features and their relation to the recruitment of monovalent and divalent metal ions important for activity. We examine several fundamental roles for these ions that include: (1) structural integrity of the catalytically active state, (2) pKa tuning of residues involved in acid-base catalysis, and (3) direct electrostatic stabilization of the transition state via Lewis acid catalysis. Taken together, these examples demonstrate how RNA electrostatics orchestrates the site-specific and territorial binding of metal ions to play important roles in catalysis.
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Affiliation(s)
- Şölen Ekesan
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Erika McCarthy
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - David A. Case
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Darrin M. York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
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8
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Ekesan Ş, York DM. Who stole the proton? Suspect general base guanine found with a smoking gun in the pistol ribozyme. Org Biomol Chem 2022; 20:6219-6230. [PMID: 35452066 PMCID: PMC9378597 DOI: 10.1039/d2ob00234e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The pistol ribozyme (Psr) is one among the most recently discovered classes of small nucleolytic ribozymes that catalyze site-specific RNA self-cleavage through 2'-O-transphosphorylation. The Psr contains a conserved guanine (G40) that in crystal structures is in a position suggesting it plays the role of the general base to abstract a proton from the nucleophile to activate the reaction. Although some functional data is consistent with this mechanistic role, a notable exception is 2-aminopurine (2AP) substitution which has no effect on the rate, unlike similar substitutions across other so-called "G + M" and "G + A" ribozyme classes. Herein we postulate that an alternate conserved guanine, G42, is the primary general base, and provide evidence from molecular simulations that the active site of Psr can undergo local refolding into a structure that is consistent with the common "L-platform/L-scaffold" architecture identified in G + M and G + A ribozyme classes with Psr currently the notable exception. We summarize the key currently available experimental data and present new classical and combined quantum mechanical/molecular mechanical simulation results that collectively suggest a new hypothesis. We hypothesize that there are two available catalytic pathways supported by different conformational states connected by a local refolding of the active site: (1) a primary pathway with an active site architecture aligned with the L-platform/L-scaffold framework where G42 acts as a general base, and (2) a secondary pathway with the crystallographic active site architecture where G40 acts as a general base. We go on to make several experimentally testable predictions, and suggest specific experiments that would ultimately bring closure to the mystery as to "who stole the proton in the pistol ribozyme?".
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Affiliation(s)
- Şölen Ekesan
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.
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9
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Box-shaped ribozyme octamer formed by face-to-face dimerization of a pair of square-shaped ribozyme tetramers. J Biosci Bioeng 2022; 134:195-202. [PMID: 35810135 DOI: 10.1016/j.jbiosc.2022.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/14/2022] [Accepted: 06/14/2022] [Indexed: 11/21/2022]
Abstract
Naturally occurring ribozymes with defined three-dimensional (3D) structures serve as promising platforms for the design and construction of artificial RNA nanostructures. We constructed a hexameric ribozyme nanostructure by face-to-face dimerization of a pair of triangular ribozyme trimers, unit RNAs of which were derived from the Tetrahymena group I ribozyme. In this study, we have expanded the dimerization strategy to a square-shaped ribozyme tetramer by introducing four pillar units. The resulting box-shaped nanostructures, which contained eight ribozyme units, can be assembled from either four or two components of their unit RNAs.
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10
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Singh J, Paliwal K, Litfin T, Singh J, Zhou Y. Predicting RNA distance-based contact maps by integrated deep learning on physics-inferred secondary structure and evolutionary-derived mutational coupling. Bioinformatics 2022; 38:3900-3910. [PMID: 35751593 PMCID: PMC9364379 DOI: 10.1093/bioinformatics/btac421] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 04/30/2022] [Accepted: 06/28/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Recently, AlphaFold2 achieved high experimental accuracy for the majority of proteins in Critical Assessment of Structure Prediction (CASP 14). This raises the hope that one day, we may achieve the same feat for RNA structure prediction for those structured RNAs, which is as fundamentally and practically important similar to protein structure prediction. One major factor in the recent advancement of protein structure prediction is the highly accurate prediction of distance-based contact maps of proteins. RESULTS Here, we showed that by integrated deep learning with physics-inferred secondary structures, co-evolutionary information and multiple sequence-alignment sampling, we can achieve RNA contact-map prediction at a level of accuracy similar to that in protein contact-map prediction. More importantly, highly accurate prediction for top L long-range contacts can be assured for those RNAs with a high effective number of homologous sequences (Neff > 50). The initial use of the predicted contact map as distance-based restraints confirmed its usefulness in 3D structure prediction. AVAILABILITY AND IMPLEMENTATION SPOT-RNA-2D is available as a web server at https://sparks-lab.org/server/spot-rna-2d/ and as a standalone program at https://github.com/jaswindersingh2/SPOT-RNA-2D. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | - Thomas Litfin
- Institute for Glycomics, Griffith University, Parklands Dr. Southport, QLD 4222, Australia
| | - Jaspreet Singh
- Signal Processing Laboratory, School of Engineering and Built Environment, Griffith University, Brisbane, QLD 4111, Australia
| | - Yaoqi Zhou
- To whom correspondence should be addressed. or or
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11
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Bou-Nader C, Zhang J. Rational engineering enables co-crystallization and structural determination of the HIV-1 matrix-tRNA complex. STAR Protoc 2022; 3:101056. [PMID: 35005638 PMCID: PMC8715211 DOI: 10.1016/j.xpro.2021.101056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Host tRNAs specifically interact with the matrix domain (MA) of HIV-1 major structural polyprotein, Gag, to control its membrane localization and virion assembly. In this protocol, we describe the purification and engineering of HIV-1 MA and tRNA, and the co-crystallization and structure determination of the complex using X-ray crystallography. Rational engineering of the tRNA surface created tRNA-tRNA packing contacts that drove the formation of diffraction-quality co-crystals. This protocol can be adapted to solve other ribonucleoprotein complex structures containing structured RNAs. For complete details on the use and execution of this protocol, please refer to Bou-Nader et al. (2021).
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Affiliation(s)
- Charles Bou-Nader
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
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12
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Abstract
In recent years, it has become clear that RNA molecules are involved in almost all vital cellular processes and pathogenesis of human disorders. The functional diversity of RNA comes from its structural richness. Although composed of only four nucleotides, RNA molecules present a plethora of secondary and tertiary structures critical for intra and intermolecular contacts with other RNAs and ligands (proteins, small metabolites, etc.). In order to fully understand RNA function it is necessary to define its spatial structure. Crystallography, nuclear magnetic resonance and cryogenic electron microscopy have demonstrated considerable success in determining the structures of biologically important RNA molecules. However, these powerful methods require large amounts of sample. Despite their limitations, chemical synthesis and in vitro transcription are usually employed to obtain milligram quantities of RNA for structural studies, delivering simple and effective methods for large-scale production of homogenous samples. The aim of this paper is to provide an overview of methods for large-scale RNA synthesis with emphasis on chemical synthesis and in vitro transcription. We also present our own results of testing the efficiency of these approaches in order to adapt the material acquisition strategy depending on the desired RNA construct.
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13
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Fedeles BI, Li D, Singh V. Structural Insights Into Tautomeric Dynamics in Nucleic Acids and in Antiviral Nucleoside Analogs. Front Mol Biosci 2022; 8:823253. [PMID: 35145998 PMCID: PMC8822119 DOI: 10.3389/fmolb.2021.823253] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 12/30/2021] [Indexed: 11/20/2022] Open
Abstract
DNA (2'-deoxyribonucleic acid) and RNA (ribonucleic acid) play diverse functional roles in biology and disease. Despite being comprised primarily of only four cognate nucleobases, nucleic acids can adopt complex three-dimensional structures, and RNA in particular, can catalyze biochemical reactions to regulate a wide variety of biological processes. Such chemical versatility is due in part to the phenomenon of nucleobase tautomerism, whereby the bases can adopt multiple, yet distinct isomeric forms, known as tautomers. For nucleobases, tautomers refer to structural isomers that differ from one another by the position of protons. By altering the position of protons on nucleobases, many of which play critical roles for hydrogen bonding and base pairing interactions, tautomerism has profound effects on the biochemical processes involving nucleic acids. For example, the transient formation of minor tautomers during replication could generate spontaneous mutations. These mutations could arise from the stabilization of mismatches, in the active site of polymerases, in conformations involving minor tautomers that are indistinguishable from canonical base pairs. In this review, we discuss the evidence for tautomerism in DNA, and its consequences to the fidelity of DNA replication. Also reviewed are RNA systems, such as the riboswitches and self-cleaving ribozymes, in which tautomerism plays a functional role in ligand recognition and catalysis, respectively. We also discuss tautomeric nucleoside analogs that are efficacious as antiviral drug candidates such as molnupiravir for coronaviruses and KP1212 for HIV. The antiviral efficacy of these analogs is due, in part, to their ability to exist in multiple tautomeric forms and induce mutations in the replicating viral genomes. From a technical standpoint, minor tautomers of nucleobases are challenging to identify directly because they are rare and interconvert on a fast, millisecond to nanosecond, time scale. Nevertheless, many approaches including biochemical, structural, computational and spectroscopic methods have been developed to study tautomeric dynamics in RNA and DNA systems, and in antiviral nucleoside analogs. An overview of these methods and their applications is included here.
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Affiliation(s)
- Bogdan I. Fedeles
- Departments of Chemistry and Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Deyu Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI, United States
| | - Vipender Singh
- Department of Biochemistry and Biophysics, Novartis Institute of Biomedical Research, Cambridge, MA, United States
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14
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Identifying proximal RNA interactions from cDNA-encoded crosslinks with ShapeJumper. PLoS Comput Biol 2021; 17:e1009632. [PMID: 34905538 PMCID: PMC8670686 DOI: 10.1371/journal.pcbi.1009632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 11/11/2021] [Indexed: 01/07/2023] Open
Abstract
SHAPE-JuMP is a concise strategy for identifying close-in-space interactions in RNA molecules. Nucleotides in close three-dimensional proximity are crosslinked with a bi-reactive reagent that covalently links the 2'-hydroxyl groups of the ribose moieties. The identities of crosslinked nucleotides are determined using an engineered reverse transcriptase that jumps across crosslinked sites, resulting in a deletion in the cDNA that is detected using massively parallel sequencing. Here we introduce ShapeJumper, a bioinformatics pipeline to process SHAPE-JuMP sequencing data and to accurately identify through-space interactions, as observed in complex JuMP datasets. ShapeJumper identifies proximal interactions with near-nucleotide resolution using an alignment strategy that is optimized to tolerate the unique non-templated reverse-transcription profile of the engineered crosslink-traversing reverse-transcriptase. JuMP-inspired strategies are now poised to replace adapter-ligation for detecting RNA-RNA interactions in most crosslinking experiments.
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15
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Dagenais P, Desjardins G, Legault P. An integrative NMR-SAXS approach for structural determination of large RNAs defines the substrate-free state of a trans-cleaving Neurospora Varkud Satellite ribozyme. Nucleic Acids Res 2021; 49:11959-11973. [PMID: 34718697 PMCID: PMC8599749 DOI: 10.1093/nar/gkab963] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 09/01/2021] [Accepted: 10/26/2021] [Indexed: 11/26/2022] Open
Abstract
The divide-and-conquer strategy is commonly used for protein structure determination, but its applications to high-resolution structure determination of RNAs have been limited. Here, we introduce an integrative approach based on the divide-and-conquer strategy that was undertaken to determine the solution structure of an RNA model system, the Neurospora VS ribozyme. NMR and SAXS studies were conducted on a minimal trans VS ribozyme as well as several isolated subdomains. A multi-step procedure was used for structure determination that first involved pairing refined NMR structures with SAXS data to obtain structural subensembles of the various subdomains. These subdomain structures were then assembled to build a large set of structural models of the ribozyme, which was subsequently filtered using SAXS data. The resulting NMR-SAXS structural ensemble shares several similarities with the reported crystal structures of the VS ribozyme. However, a local structural difference is observed that affects the global fold by shifting the relative orientation of the two three-way junctions. Thus, this finding highlights a global conformational change associated with substrate binding in the VS ribozyme that is likely critical for its enzymatic activity. Structural studies of other large RNAs should benefit from similar integrative approaches that allow conformational sampling of assembled fragments.
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Affiliation(s)
- Pierre Dagenais
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Box 6128, Downtown Station, Montreal, QC H3C 3J7, Quebec, Canada
| | - Geneviève Desjardins
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Box 6128, Downtown Station, Montreal, QC H3C 3J7, Quebec, Canada
| | - Pascale Legault
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Box 6128, Downtown Station, Montreal, QC H3C 3J7, Quebec, Canada
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16
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Peng H, Latifi B, Müller S, Lupták A, Chen IA. Self-cleaving ribozymes: substrate specificity and synthetic biology applications. RSC Chem Biol 2021; 2:1370-1383. [PMID: 34704043 PMCID: PMC8495972 DOI: 10.1039/d0cb00207k] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 06/14/2021] [Indexed: 12/22/2022] Open
Abstract
Various self-cleaving ribozymes appearing in nature catalyze the sequence-specific intramolecular cleavage of RNA and can be engineered to catalyze cleavage of appropriate substrates in an intermolecular fashion, thus acting as true catalysts. The mechanisms of the small, self-cleaving ribozymes have been extensively studied and reviewed previously. Self-cleaving ribozymes can possess high catalytic activity and high substrate specificity; however, substrate specificity is also engineerable within the constraints of the ribozyme structure. While these ribozymes share a common fundamental catalytic mechanism, each ribozyme family has a unique overall architecture and active site organization, indicating that several distinct structures yield this chemical activity. The multitude of catalytic structures, combined with some flexibility in substrate specificity within each family, suggests that such catalytic RNAs, taken together, could access a wide variety of substrates. Here, we give an overview of 10 classes of self-cleaving ribozymes and capture what is understood about their substrate specificity and synthetic applications. Evolution of these ribozymes in an RNA world might be characterized by the emergence of a new ribozyme family followed by rapid adaptation or diversification for specific substrates. Self-cleaving ribozymes have become important tools of synthetic biology. Here we summarize the substrate specificity and applications of the main classes of these ribozymes.![]()
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Affiliation(s)
- Huan Peng
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles CA 90095 USA
| | - Brandon Latifi
- Department of Pharmaceutical Sciences, University of California Irvine CA 92697 USA
| | - Sabine Müller
- Institute for Biochemistry, University Greifswald 17487 Greifswald Germany
| | - Andrej Lupták
- Department of Pharmaceutical Sciences, University of California Irvine CA 92697 USA
| | - Irene A Chen
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles CA 90095 USA
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17
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Liu D, Shao Y, Piccirilli JA, Weizmann Y. Structures of artificially designed discrete RNA nanoarchitectures at near-atomic resolution. SCIENCE ADVANCES 2021; 7:eabf4459. [PMID: 34550747 PMCID: PMC8457670 DOI: 10.1126/sciadv.abf4459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 08/02/2021] [Indexed: 05/11/2023]
Abstract
Although advances in nanotechnology have enabled the construction of complex and functional synthetic nucleic acid–based nanoarchitectures, high-resolution discrete structures are lacking because of the difficulty in obtaining good diffracting crystals. Here, we report the design and construction of RNA nanostructures based on homooligomerizable one-stranded tiles for x-ray crystallographic determination. We solved three structures to near-atomic resolution: a 2D parallelogram, a 3D nanobracelet unexpectedly formed from an RNA designed for a nanocage, and, eventually, a bona fide 3D nanocage designed with the guidance of the two previous structures. Structural details of their constituent motifs, such as kissing loops, branched kissing loops, and T-junctions, that resemble natural RNA motifs and resisted x-ray determination are revealed, providing insights into those natural motifs. This work unveils the largely unexplored potential of crystallography in gaining high-resolution feedback for nanoarchitectural design and suggests a route to investigate RNA motif structures by configuring them into nanoarchitectures.
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Affiliation(s)
- Di Liu
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Yaming Shao
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Joseph A. Piccirilli
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
| | - Yossi Weizmann
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
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18
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Yoon S, Harris ME. Beyond the Plateau: pL Dependence of Proton Inventories as a Tool for Studying Ribozyme and Ribonuclease Catalysis. Biochemistry 2021; 60:2810-2823. [PMID: 34495648 DOI: 10.1021/acs.biochem.1c00489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Acid/base catalysis is an important catalytic strategy used by ribonucleases and ribozymes; however, understanding the number and identity of functional groups involved in proton transfer remains challenging. The proton inventory (PI) technique analyzes the dependence of the enzyme reaction rate on the ratio of D2O to H2O and can provide information about the number of exchangeable sites that produce isotope effects and their magnitude. The Gross-Butler (GB) equation is used to evaluate H/D fractionation factors from PI data typically collected under conditions (i.e., a "plateau" in the pH-rate profile) assuming minimal change in active site residue ionization. However, restricting PI analysis to these conditions is problematic for many ribonucleases, ribozymes, and their variants due to ambiguity in the roles of active site residues, the lack of a plateau within the accessible pL range, or cooperative interactions between active site functional groups undergoing ionization. Here, we extend the integration of species distributions for alternative enzyme states in noncooperative models of acid/base catalysis into the GB equation, first used by Bevilacqua and colleagues for the HDV ribozyme, to develop a general population-weighted GB equation that allows simulation and global fitting of the three-dimensional relationship of the D2O ratio (n) versus pL versus kn/k0. Simulations using the GPW-GB equation of PI results for RNase A, HDVrz, and VSrz illustrate that data obtained at multiple selected pL values across the pL-rate profile can assist in the planning and interpreting of solvent isotope effect experiments to distinguish alternative mechanistic models.
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Affiliation(s)
- Suhyun Yoon
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Michael E Harris
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, United States
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19
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Christy TW, Giannetti CA, Houlihan G, Smola MJ, Rice GM, Wang J, Dokholyan NV, Laederach A, Holliger P, Weeks KM. Direct Mapping of Higher-Order RNA Interactions by SHAPE-JuMP. Biochemistry 2021; 60:1971-1982. [PMID: 34121404 PMCID: PMC8256721 DOI: 10.1021/acs.biochem.1c00270] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Higher-order structure governs function for many RNAs. However, discerning this structure for large RNA molecules in solution is an unresolved challenge. Here, we present SHAPE-JuMP (selective 2'-hydroxyl acylation analyzed by primer extension and juxtaposed merged pairs) to interrogate through-space RNA tertiary interactions. A bifunctional small molecule is used to chemically link proximal nucleotides in an RNA structure. The RNA cross-link site is then encoded into complementary DNA (cDNA) in a single, direct step using an engineered reverse transcriptase that "jumps" across cross-linked nucleotides. The resulting cDNAs contain a deletion relative to the native RNA sequence, which can be detected by sequencing, that indicates the sites of cross-linked nucleotides. SHAPE-JuMP measures RNA tertiary structure proximity concisely across large RNA molecules at nanometer resolution. SHAPE-JuMP is especially effective at measuring interactions in multihelix junctions and loop-to-helix packing, enables modeling of the global fold for RNAs up to several hundred nucleotides in length, facilitates ranking of structural models by consistency with through-space restraints, and is poised to enable solution-phase structural interrogation and modeling of complex RNAs.
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Affiliation(s)
- Thomas W. Christy
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Catherine A. Giannetti
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290
| | - Gillian Houlihan
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Matthew J. Smola
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290
| | - Greggory M. Rice
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290
| | - Jian Wang
- Departments of Pharmacology, and Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, PA 17033, USA
| | - Nikolay V. Dokholyan
- Departments of Pharmacology, and Biochemistry and Molecular Biology, Penn State University College of Medicine, Hershey, PA 17033, USA
- Departments of Chemistry, and Biomedical Engineering, Pennsylvania State University, University Park, PA 16802
| | - Alain Laederach
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Kevin M. Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290
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20
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Cortés-Guajardo C, Rojas-Hernández F, Paillao-Bustos R, Cepeda-Plaza M. Hydrated metal ion as a general acid in the catalytic mechanism of the 8-17 DNAzyme. Org Biomol Chem 2021; 19:5395-5402. [PMID: 34047747 DOI: 10.1039/d1ob00366f] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The RNA-cleaving 8-17 DNAzyme, which is a metalloenzyme that depends on divalent metal ions for its function, is the most studied catalytic DNA in terms of its mechanism. By the end of 2017, a report of the crystal structure of the enzyme-substrate complex in the presence of Pb2+ probed some of the previous findings and opened new questions, especially around the participation of the metal ion in the catalytic mechanism and the promiscuity exhibited by the enzyme in terms of the metal cofactor required for catalysis. In this article we explore the role of the divalent metal ion in the mechanism of the 8-17 DNAzyme as a general acid, by measuring the influence of pH over the activity of a slower variant of the enzyme in the presence of Pb2+. We replaced G14, which has been identified as a general base in the mechanism of the enzyme, by the unnatural analog 2-aminopurine, with a lower pKa value of the N1 group. With this approach, we obtained a bell-shaped pH-rate profile with experimental pKa values of 5.4 and 7.0. Comparing these results with previous pH-rate profiles in the presence of Mg2+, our findings suggest the stabilization of the 5'-O leaving group by the hydrated metal ion acting as a general acid, in addition to the activation of the 2'-OH nucleophile by the general base G14.
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21
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DasGupta S, Piccirilli JA. The Varkud Satellite Ribozyme: A Thirty-Year Journey through Biochemistry, Crystallography, and Computation. Acc Chem Res 2021; 54:2591-2602. [PMID: 33974386 DOI: 10.1021/acs.accounts.1c00052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The discovery of catalytic RNAs or ribozymes introduced a new class of enzymes to biology. In addition to their increasingly important roles in modern life, ribozymes are key players in the RNA World hypothesis, which posits that life started or flourished with RNA supporting both genetic and enzymatic functions. Therefore, investigations into the mechanisms of ribozyme function provide an exciting opportunity to examine the foundational principles of biological catalysis. Ribozymes are also attractive model systems to investigate the relationship between structure and function in RNA. Endonucleolytic ribozymes represent the largest class of catalytic RNA, of which the Varkud satellite (VS) ribozyme is structurally the most complex. The last ribozyme to be discovered by accident, the VS ribozyme had eluded structural determination for over two decades. When we solved the first crystal structures of the VS ribozyme, an extensive body of biochemical and biophysical data had accumulated over the years with which we could evaluate the functional relevance of the structure. Conversely, the structures provided a new perspective from which to reexamine the functional data and test new hypotheses. The VS ribozyme is organized in a modular fashion where independently folding domains assemble into the active conformation of the ribozyme via three-way junctions. Structures of the VS ribozyme in complex with its substrate at different stages of activation enabled us to map the structural reorganization of the substrate that must precede catalysis. In addition to defining the global architecture of the RNA, the essential interactions between the substrate and catalytic domains, and the rearrangements in the substrate prior to catalysis, these structures provided detailed snapshots of the ribozyme active site, revealing potential catalytic interactions. High resolution structures of the active site bolstered the view that the catalytic mechanism involved nucleobase-mediated general acid-base catalysis and uncovered additional catalytic interactions between the cleavage site and catalytic residues. Informed by the crystal structures of the VS ribozyme, an integrated experimental and computational approach identified the key players and essential interactions that define the active site of the ribozyme. This confluence of biochemical, structural, and computational studies revealed the catalytic mechanism of the ribozyme at unprecedented detail. Additionally, comparative analyses of the active site structures of the VS ribozyme and other nucleic acid-based endoribonucleases revealed common architectural motifs and strikingly similar catalytic strategies. In this Account, we document the progress of VS ribozyme research starting from its discovery and extending to the elucidation of its detailed catalytic mechanism 30 years later.
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Affiliation(s)
- Saurja DasGupta
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
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22
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Zn 2+-dependent DNAzymes that cleave all combinations of ribonucleotides. Commun Biol 2021; 4:221. [PMID: 33594202 PMCID: PMC7886857 DOI: 10.1038/s42003-021-01738-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 11/14/2020] [Indexed: 11/08/2022] Open
Abstract
Although several DNAzymes are known, their utility is limited by a narrow range of substrate specificity. Here, we report the isolation of two zinc-dependent DNAzymes, ZincDz1 and ZincDz2, which exhibit compact catalytic core sequences with highly versatile hydrolysis activity. They were selected through in vitro selection followed by deep sequencing analysis. Despite their sequence similarity, each DNAzyme showed different Zn2+-concentration and pH-dependent reaction profiles, and cleaved the target RNA sequences at different sites. Using various substrate RNA sequences, we found that the cleavage sequence specificity of ZincDz2 and its highly active mutant ZincDz2-v2 to be 5'-rN↓rNrPu-3'. Furthermore, we demonstrated that the designed ZincDz2 could cut microRNA miR-155 at three different sites. These DNAzymes could be useful in a broad range of applications in the fields of medicine and biotechnology.
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23
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Zhang D, Li J, Chen SJ. IsRNA1: De Novo Prediction and Blind Screening of RNA 3D Structures. J Chem Theory Comput 2021; 17:1842-1857. [PMID: 33560836 DOI: 10.1021/acs.jctc.0c01148] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Modeling structures and functions of large ribonucleic acid (RNAs) especially with complicated topologies is highly challenging due to the inefficiency of large conformational sampling and the presence of complicated tertiary interactions. To address this problem, one highly promising approach is coarse-grained modeling. Here, following an iterative simulated reference state approach to decipher the correlations between different structural parameters, we developed a potent coarse-grained RNA model named as IsRNA1 for RNA studies. Molecular dynamics simulations in the IsRNA1 can predict the native structures of small RNAs from a sequence and fold medium-sized RNAs into near-native tertiary structures with the assistance of secondary structure constraints. A large-scale benchmark test on RNA 3D structure prediction shows that IsRNA1 exhibits improved performance for relatively large RNAs of complicated topologies, such as large stem-loop structures and structures containing long-range tertiary interactions. The advantages of IsRNA1 include the consideration of the correlations between the different structural variables, the appropriate characterization of canonical base-pairing and base-stacking interactions, and the better sampling for the backbone conformations. Moreover, a blind screening protocol was developed based on IsRNA1 to identify good structural models from a pool of candidates without prior knowledge of the native structures.
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Affiliation(s)
- Dong Zhang
- Department of Physics, Department of Biochemistry, and Institute of Data Science and Informatics, University of Missouri, Columbia, Missouri 65211, United States
| | - Jun Li
- Department of Physics, Department of Biochemistry, and Institute of Data Science and Informatics, University of Missouri, Columbia, Missouri 65211, United States
| | - Shi-Jie Chen
- Department of Physics, Department of Biochemistry, and Institute of Data Science and Informatics, University of Missouri, Columbia, Missouri 65211, United States
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24
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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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25
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Watkins AM, Rangan R, Das R. FARFAR2: Improved De Novo Rosetta Prediction of Complex Global RNA Folds. Structure 2020; 28:963-976.e6. [PMID: 32531203 PMCID: PMC7415647 DOI: 10.1016/j.str.2020.05.011] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 04/27/2020] [Accepted: 05/20/2020] [Indexed: 01/01/2023]
Abstract
Predicting RNA three-dimensional structures from sequence could accelerate understanding of the growing number of RNA molecules being discovered across biology. Rosetta's Fragment Assembly of RNA with Full-Atom Refinement (FARFAR) has shown promise in community-wide blind RNA-Puzzle trials, but lack of a systematic and automated benchmark has left unclear what limits FARFAR performance. Here, we benchmark FARFAR2, an algorithm integrating RNA-Puzzle-inspired innovations with updated fragment libraries and helix modeling. In 16 of 21 RNA-Puzzles revisited without experimental data or expert intervention, FARFAR2 recovers native-like structures more accurate than models submitted during the RNA-Puzzles trials. Remaining bottlenecks include conformational sampling for >80-nucleotide problems and scoring function limitations more generally. Supporting these conclusions, preregistered blind models for adenovirus VA-I RNA and five riboswitch complexes predicted native-like folds with 3- to 14 Å root-mean-square deviation accuracies. We present a FARFAR2 webserver and three large model archives (FARFAR2-Classics, FARFAR2-Motifs, and FARFAR2-Puzzles) to guide future applications and advances.
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Affiliation(s)
- Andrew Martin Watkins
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ramya Rangan
- Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | - Rhiju Das
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA; Biophysics Program, Stanford University, Stanford, CA 94305, USA.
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26
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Structural Insights into RNA Dimerization: Motifs, Interfaces and Functions. Molecules 2020; 25:molecules25122881. [PMID: 32585844 PMCID: PMC7357161 DOI: 10.3390/molecules25122881] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 12/26/2022] Open
Abstract
In comparison with the pervasive use of protein dimers and multimers in all domains of life, functional RNA oligomers have so far rarely been observed in nature. Their diminished occurrence contrasts starkly with the robust intrinsic potential of RNA to multimerize through long-range base-pairing ("kissing") interactions, self-annealing of palindromic or complementary sequences, and stable tertiary contact motifs, such as the GNRA tetraloop-receptors. To explore the general mechanics of RNA dimerization, we performed a meta-analysis of a collection of exemplary RNA homodimer structures consisting of viral genomic elements, ribozymes, riboswitches, etc., encompassing both functional and fortuitous dimers. Globally, we found that domain-swapped dimers and antiparallel, head-to-tail arrangements are predominant architectural themes. Locally, we observed that the same structural motifs, interfaces and forces that enable tertiary RNA folding also drive their higher-order assemblies. These feature prominently long-range kissing loops, pseudoknots, reciprocal base intercalations and A-minor interactions. We postulate that the scarcity of functional RNA multimers and limited diversity in multimerization motifs may reflect evolutionary constraints imposed by host antiviral immune surveillance and stress sensing. A deepening mechanistic understanding of RNA multimerization is expected to facilitate investigations into RNA and RNP assemblies, condensates, and granules and enable their potential therapeutical targeting.
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27
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Duan J, Wang X, Kizer ME. Biotechnological and Therapeutic Applications of Natural Nucleic Acid Structural Motifs. Top Curr Chem (Cham) 2020; 378:26. [PMID: 32067108 DOI: 10.1007/s41061-020-0290-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/11/2020] [Indexed: 11/28/2022]
Abstract
Genetic information and the blueprint of life are stored in the form of nucleic acids. The primary sequence of DNA, read from the canonical double helix, provides the code for RNA and protein synthesis. Yet these already-information-rich molecules have higher-order structures which play critical roles in transcription and translation. Uncovering the sequences, parameters, and conditions which govern the formation of these structural motifs has allowed researchers to study them and to utilize them in biotechnological and therapeutic applications in vitro and in vivo. This review covers both DNA and RNA structural motifs found naturally in biological systems including catalytic nucleic acids, non-coding RNA, aptamers, G-quadruplexes, i-motifs, and Holliday junctions. For each category, an overview of the structural characteristics, biological prevalence, and function will be discussed. The biotechnological and therapeutic applications of these structural motifs are highlighted. Future perspectives focus on the addition of proteins and unnatural modifications to enhance structural stability for greater applicability.
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Affiliation(s)
- Jinwei Duan
- Department of Chemistry and Materials Science, College of Sciences, Chang'an University, Xi'an, 710064, Shaanxi, People's Republic of China.
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Xing Wang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Holonyak Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Megan E Kizer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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28
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Gaines CS, Piccirilli JA, York DM. The L-platform/L-scaffold framework: a blueprint for RNA-cleaving nucleic acid enzyme design. RNA (NEW YORK, N.Y.) 2020; 26:111-125. [PMID: 31776179 PMCID: PMC6961537 DOI: 10.1261/rna.071894.119] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 11/14/2019] [Indexed: 05/13/2023]
Abstract
We develop an L-platform/L-scaffold framework we hypothesize may serve as a blueprint to facilitate site-specific RNA-cleaving nucleic acid enzyme design. Building on the L-platform motif originally described by Suslov and coworkers, we identify new critical scaffolding elements required to anchor a conserved general base guanine ("L-anchor") and bind functionally important metal ions at the active site ("L-pocket"). Molecular simulations, together with a broad range of experimental structural and functional data, connect the L-platform/L-scaffold elements to necessary and sufficient conditions for catalytic activity. We demonstrate that the L-platform/L-scaffold framework is common to five of the nine currently known naturally occurring ribozyme classes (Twr, HPr, VSr, HHr, Psr), and intriguingly from a design perspective, the framework also appears in an artificially engineered DNAzyme (8-17dz). The flexibility of the L-platform/L-scaffold framework is illustrated on these systems, highlighting modularity and trends in the variety of known general acid moieties that are supported. These trends give rise to two distinct catalytic paradigms, building on the classifications proposed by Wilson and coworkers and named for the implicated general base and acid. The "G + A" paradigm (Twr, HPr, VSr) exclusively utilizes nucleobase residues for chemistry, and the "G + M + " paradigm (HHr, 8-17dz, Psr) involves structuring of the "L-pocket" metal ion binding site for recruitment of a divalent metal ion that plays an active role in the chemical steps of the reaction. Finally, the modularity of the L-platform/L-scaffold framework is illustrated in the VS ribozyme where the "L-pocket" assumes the functional role of the "L-anchor" element, highlighting a distinct mechanism, but one that is functionally linked with the hammerhead ribozyme.
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Affiliation(s)
- Colin S Gaines
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Joseph A Piccirilli
- Department of Biochemistry and Molecular Biology and Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
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29
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Magnus M, Antczak M, Zok T, Wiedemann J, Lukasiak P, Cao Y, Bujnicki JM, Westhof E, Szachniuk M, Miao Z. RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools. Nucleic Acids Res 2020; 48:576-588. [PMID: 31799609 PMCID: PMC7145511 DOI: 10.1093/nar/gkz1108] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/06/2019] [Accepted: 11/15/2019] [Indexed: 12/12/2022] Open
Abstract
Significant improvements have been made in the efficiency and accuracy of RNA 3D structure prediction methods during the succeeding challenges of RNA-Puzzles, a community-wide effort on the assessment of blind prediction of RNA tertiary structures. The RNA-Puzzles contest has shown, among others, that the development and validation of computational methods for RNA fold prediction strongly depend on the benchmark datasets and the structure comparison algorithms. Yet, there has been no systematic benchmark set or decoy structures available for the 3D structure prediction of RNA, hindering the standardization of comparative tests in the modeling of RNA structure. Furthermore, there has not been a unified set of tools that allows deep and complete RNA structure analysis, and at the same time, that is easy to use. Here, we present RNA-Puzzles toolkit, a computational resource including (i) decoy sets generated by different RNA 3D structure prediction methods (raw, for-evaluation and standardized datasets), (ii) 3D structure normalization, analysis, manipulation, visualization tools (RNA_format, RNA_normalizer, rna-tools) and (iii) 3D structure comparison metric tools (RNAQUA, MCQ4Structures). This resource provides a full list of computational tools as well as a standard RNA 3D structure prediction assessment protocol for the community.
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Affiliation(s)
- Marcin Magnus
- International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
- ReMedy-International Research Agenda Unit, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Maciej Antczak
- Institute of Computing Science & European Centre for Bioinformatics and Genomics, Poznan University of Technology, 60-965 Poznan, Poland
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Tomasz Zok
- Institute of Computing Science & European Centre for Bioinformatics and Genomics, Poznan University of Technology, 60-965 Poznan, Poland
| | - Jakub Wiedemann
- Institute of Computing Science & European Centre for Bioinformatics and Genomics, Poznan University of Technology, 60-965 Poznan, Poland
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Piotr Lukasiak
- Institute of Computing Science & European Centre for Bioinformatics and Genomics, Poznan University of Technology, 60-965 Poznan, Poland
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Yang Cao
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, PR China
| | - Janusz M Bujnicki
- International Institute of Molecular and Cell Biology in Warsaw, 02-109 Warsaw, Poland
- Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Eric Westhof
- Architecture et Réactivité de l’ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 12 allée Konrad Roentgen, 67084 Strasbourg, France
| | - Marta Szachniuk
- Institute of Computing Science & European Centre for Bioinformatics and Genomics, Poznan University of Technology, 60-965 Poznan, Poland
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Zhichao Miao
- Translational Research Institute of Brain and Brain-Like Intelligence and Department of Anesthesiology, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai 200081, China
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
- Newcastle Fibrosis Research Group, Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
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30
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Confluence of theory and experiment reveals the catalytic mechanism of the Varkud satellite ribozyme. Nat Chem 2020; 12:193-201. [PMID: 31959957 PMCID: PMC7389185 DOI: 10.1038/s41557-019-0391-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 11/13/2019] [Indexed: 11/09/2022]
Abstract
The Varkud satellite ribozyme catalyses site-specific RNA cleavage and ligation, and serves as an important model system to understand RNA catalysis. Here, we combine stereospecific phosphorothioate substitution, precision nucleobase mutation and linear free-energy relationship measurements with molecular dynamics, molecular solvation theory and ab initio quantum mechanical/molecular mechanical free-energy simulations to gain insight into the catalysis. Through this confluence of theory and experiment, we unify the existing body of structural and functional data to unveil the catalytic mechanism in unprecedented detail, including the degree of proton transfer in the transition state. Further, we provide evidence for a critical Mg2+ in the active site that interacts with the scissile phosphate and anchors the general base guanine in position for nucleophile activation. This novel role for Mg2+ adds to the diversity of known catalytic RNA strategies and unifies functional features observed in the Varkud satellite, hairpin and hammerhead ribozyme classes.
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31
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Abstract
Molecular crowding promotes RNA folding and catalysis and could have played vital roles in the evolution of primordial ribozymes and protocells.
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Affiliation(s)
- Saurja DasGupta
- Howard Hughes Medical Institute
- Massachusetts General Hospital
- Boston
- USA
- Department of Molecular Biology
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32
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Huang L, Wang J, Watkins AM, Das R, Lilley DMJ. Structure and ligand binding of the glutamine-II riboswitch. Nucleic Acids Res 2019; 47:7666-7675. [PMID: 31216023 PMCID: PMC6698751 DOI: 10.1093/nar/gkz539] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 05/31/2019] [Accepted: 06/06/2019] [Indexed: 12/14/2022] Open
Abstract
We have determined the structure of the glutamine-II riboswitch ligand binding domain using X-ray crystallography. The structure was solved using a novel combination of homology modeling and molecular replacement. The structure comprises three coaxial helical domains, the central one of which is a pseudoknot with partial triplex character. The major groove of this helix provides the binding site for L-glutamine, which is extensively hydrogen bonded to the RNA. Atomic mutation of the RNA at the ligand binding site leads to loss of binding shown by isothermal titration calorimetry, explaining the specificity of the riboswitch. A metal ion also plays an important role in ligand binding. This is directly bonded to a glutamine carboxylate oxygen atom, and its remaining inner-sphere water molecules make hydrogen bonding interactions with the RNA.
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Affiliation(s)
- Lin Huang
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Jia Wang
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Andrew M Watkins
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rhiju Das
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
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33
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Ganguly A, Weissman BP, Piccirilli JA, York DM. Evidence for a Catalytic Strategy to Promote Nucleophile Activation in Metal-Dependent RNA-Cleaving Ribozymes and 8-17 DNAzyme. ACS Catal 2019; 9:10612-10617. [PMID: 31840007 PMCID: PMC6902279 DOI: 10.1021/acscatal.9b02035] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 09/04/2019] [Indexed: 12/30/2022]
Abstract
An unique catalytic strategy was recently reported for the glmS ribozyme [Bingaman et al., Nat. Chem. Biol.2017, 13, 439-445] that involves promotion of productive hydrogen bonding of the O2' nucleophile to facilitate its activation. We provide broad evidence of this strategy in the hammerhead, pistol, and VS ribozymes and 8-17 DNAzyme, enabled by a functionally important divalent metal ion that interacts with the scissile phosphate and disrupts nonproductive competitive hydrogen bonding with the O2' nucleophile. This strategy, designated tertiary gamma (3°γ) catalysis, illustrates an additional role for divalent ions in ribozyme catalysis.
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Affiliation(s)
- Abir Ganguly
- Laboratory
for Biomolecular Simulation Research, Rutgers,
The State University of New Jersey, Piscataway, New Jersey 08854-8087, United States
- Institute
for Quantitative Biomedicine, Rutgers, The
State University of New Jersey, Piscataway, New Jersey 08854-8087, United States
| | - Benjamin P. Weissman
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Joseph A. Piccirilli
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
- Department
of Biochemistry and Molecular Biology, The
University of Chicago, Chicago, Illinois 60637, United States
| | - Darrin M. York
- Laboratory
for Biomolecular Simulation Research, Rutgers,
The State University of New Jersey, Piscataway, New Jersey 08854-8087, United States
- Institute
for Quantitative Biomedicine, Rutgers, The
State University of New Jersey, Piscataway, New Jersey 08854-8087, United States
- Department
of Chemistry and Chemical Biology, Rutgers,
The State University of New Jersey, Piscataway, New Jersey 08854-8087, United States
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34
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Maurel MC, Leclerc F, Hervé G. Ribozyme Chemistry: To Be or Not To Be under High Pressure. Chem Rev 2019; 120:4898-4918. [DOI: 10.1021/acs.chemrev.9b00457] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marie-Christine Maurel
- Institut de Systématique, Evolution, Biodiversité (ISYEB), CNRS, Sorbonne Université, Muséum National d’Histoire Naturelle, EPHE, F-75005 Paris, France
| | - Fabrice Leclerc
- Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Université Paris Sud, F-91198 Gif-sur-Yvette, France
| | - Guy Hervé
- Laboratoire BIOSIPE, Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, Campus Pierre et Marie Curie, F-75005 Paris, France
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35
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Suddala KC, Zhang J. High-affinity recognition of specific tRNAs by an mRNA anticodon-binding groove. Nat Struct Mol Biol 2019; 26:1114-1122. [PMID: 31792448 PMCID: PMC6903423 DOI: 10.1038/s41594-019-0335-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 10/21/2019] [Indexed: 11/10/2022]
Abstract
T-box riboswitches are modular bacterial noncoding RNAs that sense and regulate amino acid availability through direct interactions with tRNAs. Between the 5' anticodon-binding stem I domain and the 3' amino acid sensing domains of most T-boxes lies the stem II domain of unknown structure and function. Here, we report a 2.8-Å cocrystal structure of the Nocardia farcinica ileS T-box in complex with its cognate tRNAIle. The structure reveals a perpendicularly arranged ultrashort stem I containing a K-turn and an elongated stem II bearing an S-turn. Both stems rest against a compact pseudoknot, dock via an extended ribose zipper and jointly create a binding groove specific to the anticodon of its cognate tRNA. Contrary to proposed distal contacts to the tRNA elbow region, stem II locally reinforces the codon-anticodon interactions between stem I and tRNA, achieving low-nanomolar affinity. This study illustrates how mRNA junctions can create specific binding sites for interacting RNAs of prescribed sequence and structure.
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Affiliation(s)
- Krishna C Suddala
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Jinwei Zhang
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA.
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36
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Kostenbader K, York DM. Molecular simulations of the pistol ribozyme: unifying the interpretation of experimental data and establishing functional links with the hammerhead ribozyme. RNA (NEW YORK, N.Y.) 2019; 25:1439-1456. [PMID: 31363004 PMCID: PMC6795133 DOI: 10.1261/rna.071944.119] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/11/2019] [Indexed: 05/27/2023]
Abstract
The pistol ribozyme (Psr) is among the most recently discovered RNA enzymes and has been the subject of experiments aimed at elucidating the mechanism. Recent biochemical studies have revealed exciting clues about catalytic interactions in the active site not apparent from available crystallographic data. The present work unifies the interpretation of the existing body of structural and functional data on Psr by providing a dynamical model for the catalytically active state in solution from molecular simulation. Our results suggest that a catalytic Mg2+ ion makes inner-sphere contact with G33:N7 and outer-sphere coordination to the pro-RP of the scissile phosphate, promoting electrostatic stabilization of the dianionic transition state and neutralization of the developing charge of the leaving group through a metal-coordinated water molecule that is made more acidic by a hydrogen bond donated from the 2'OH of P32. This model is consistent with experimental activity-pH and mutagenesis data, including sensitivity to G33(7cG) and phosphorothioate substitution/metal ion rescue. The model suggests several experimentally testable predictions, including the response of cleavage activity to mutations at G42 and P32 positions in the ribozyme, and thio substitutions of the substrate in the presence of different divalent metal ions. Further, the model identifies striking similarities of Psr to the hammerhead ribozyme (HHr), including similar global fold, organization of secondary structure around an active site three-way junction, catalytic metal ion binding mode, and guanine general base. However, the specific binding mode and role of the Mg2+ ion, as well as a conserved 2'-OH in the active site, are interrelated but subtly different between the ribozymes.
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Affiliation(s)
- Ken Kostenbader
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-8076, USA
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-8076, USA
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37
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Weinberg CE, Weinberg Z, Hammann C. Novel ribozymes: discovery, catalytic mechanisms, and the quest to understand biological function. Nucleic Acids Res 2019; 47:9480-9494. [PMID: 31504786 PMCID: PMC6765202 DOI: 10.1093/nar/gkz737] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 08/08/2019] [Accepted: 08/21/2019] [Indexed: 12/21/2022] Open
Abstract
Small endonucleolytic ribozymes promote the self-cleavage of their own phosphodiester backbone at a specific linkage. The structures of and the reactions catalysed by members of individual families have been studied in great detail in the past decades. In recent years, bioinformatics studies have uncovered a considerable number of new examples of known catalytic RNA motifs. Importantly, entirely novel ribozyme classes were also discovered, for most of which both structural and biochemical information became rapidly available. However, for the majority of the new ribozymes, which are found in the genomes of a variety of species, a biological function remains elusive. Here, we concentrate on the different approaches to find catalytic RNA motifs in sequence databases. We summarize the emerging principles of RNA catalysis as observed for small endonucleolytic ribozymes. Finally, we address the biological functions of those ribozymes, where relevant information is available and common themes on their cellular activities are emerging. We conclude by speculating on the possibility that the identification and characterization of proteins that we hypothesize to be endogenously associated with catalytic RNA might help in answering the ever-present question of the biological function of the growing number of genomically encoded, small endonucleolytic ribozymes.
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Affiliation(s)
- Christina E Weinberg
- Institute for Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany
| | - Zasha Weinberg
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Leipzig University, Härtelstraße 16–18, 04107 Leipzig, Germany
| | - Christian Hammann
- Ribogenetics & Biochemistry, Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
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38
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Girard N, Dagenais P, Lacroix-Labonté J, Legault P. A multi-axial RNA joint with a large range of motion promotes sampling of an active ribozyme conformation. Nucleic Acids Res 2019; 47:3739-3751. [PMID: 30993347 PMCID: PMC6468304 DOI: 10.1093/nar/gkz098] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 01/17/2019] [Accepted: 02/12/2019] [Indexed: 12/21/2022] Open
Abstract
Investigating the dynamics of structural elements in functional RNAs is important to better understand their mechanism and for engineering RNAs with novel functions. Previously, we performed rational engineering studies with the Varkud satellite (VS) ribozyme and switched its specificity toward non-natural hairpin substrates through modification of a critical kissing-loop interaction (KLI). We identified functional VS ribozyme variants with surrogate KLIs (ribosomal RNA L88/L22 and human immunodeficiency virus-1 TAR/TAR*), but they displayed ∼100-fold lower cleavage activity. Here, we characterized the dynamics of KLIs to correlate dynamic properties with function and improve the activity of designer ribozymes. Using temperature replica exchange molecular dynamics, we determined that the natural KLI in the VS ribozyme supports conformational sampling of its closed and active state, whereas the surrogate KLIs display more restricted motions. Based on in vitro selection, the cleavage activity of a VS ribozyme variant with the TAR/TAR* KLI could be markedly improved by partly destabilizing the KLI but increasing conformation sampling. We formulated a mechanistic model for substrate binding in which the KLI dynamics contribute to formation of the active site. Our model supports the modular nature of RNA in which subdomain structure and dynamics contribute to define the thermodynamics and kinetics relevant to RNA function.
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Affiliation(s)
- Nicolas Girard
- Département de biochimie et médecine moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC, H3C 3J7, Canada
| | - Pierre Dagenais
- Département de biochimie et médecine moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC, H3C 3J7, Canada
| | - Julie Lacroix-Labonté
- Département de biochimie et médecine moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC, H3C 3J7, Canada
| | - Pascale Legault
- Département de biochimie et médecine moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC, H3C 3J7, Canada
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39
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Plebanek A, Larnerd C, Popović M, Wei C, Pohorille A, Ditzler MA. Big on Change, Small on Innovation: Evolutionary Consequences of RNA Sequence Duplication. J Mol Evol 2019; 87:240-253. [PMID: 31435687 PMCID: PMC6711949 DOI: 10.1007/s00239-019-09906-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/06/2019] [Indexed: 01/11/2023]
Abstract
The potential for biopolymers to evolve new structures has important consequences for their ability to optimize function and our attempts to reconstruct their evolutionary histories. Prior work with in vitro systems suggests that structural remodeling of RNA is difficult to achieve through the accumulation of point mutations or through recombination events. Sequence duplication may represent an alternative mechanism that can more readily lead to the evolution of new structures. Structural and sequence elements in many RNAs and proteins appear to be the products of duplication events, indicating that this mechanism plays a major role in molecular evolution. Despite the potential significance of this mechanism, little experimental data is available concerning the structural and evolutionary consequences of duplicating biopolymer sequences. To assess the structural consequences of sequence duplication on the evolution of RNA, we mutagenized an RNA sequence containing two copies of an ATP aptamer and subjected the resulting population to multiple in vitro evolution experiments. We identified multiple routes by which duplication, followed by the accumulation of functional point mutations, allowed our populations to sample two entirely different secondary structures. The two structures have no base pairs in common, but both structures contain two copies of the same ATP-binding motif. We do not observe the emergence of any other functional secondary structures beyond these two. Although this result suggests a limited capacity for duplication to support short-term functional innovation, major changes in secondary structure, like the one observed here, should be given careful consideration as they are likely to frustrate attempts to infer deep evolutionary histories of functional RNAs.
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Affiliation(s)
- Andrew Plebanek
- Exobiology Branch, Space Science and Astrobiology Division, NASA Ames Research Center, Bldg N239 Mail Stop 239-4, Moffett Field, CA, 94035, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Caleb Larnerd
- NASA Internship Program, NASA Ames Research Center, Moffett Field, CA, 94035, USA
| | - Milena Popović
- Exobiology Branch, Space Science and Astrobiology Division, NASA Ames Research Center, Bldg N239 Mail Stop 239-4, Moffett Field, CA, 94035, USA.,Center for the Emergence of Life, NASA Ames Research Center, Moffett Field, CA, 94035, USA.,Blue Marble Space Institute of Science, Seattle, WA, 98145, USA
| | - Chenyu Wei
- Exobiology Branch, Space Science and Astrobiology Division, NASA Ames Research Center, Bldg N239 Mail Stop 239-4, Moffett Field, CA, 94035, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94143, USA.,Center for the Emergence of Life, NASA Ames Research Center, Moffett Field, CA, 94035, USA
| | - Andrew Pohorille
- Exobiology Branch, Space Science and Astrobiology Division, NASA Ames Research Center, Bldg N239 Mail Stop 239-4, Moffett Field, CA, 94035, USA.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, 94143, USA.,Center for the Emergence of Life, NASA Ames Research Center, Moffett Field, CA, 94035, USA
| | - Mark A Ditzler
- Exobiology Branch, Space Science and Astrobiology Division, NASA Ames Research Center, Bldg N239 Mail Stop 239-4, Moffett Field, CA, 94035, USA. .,Center for the Emergence of Life, NASA Ames Research Center, Moffett Field, CA, 94035, USA.
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40
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Abstract
The nucleolytic ribozymes carry out site-specific RNA cleavage reactions by nucleophilic attack of the 2'-oxygen atom on the adjacent phosphorus with an acceleration of a million-fold or greater. A major part of this arises from concerted general acid-base catalysis. Recent identification of new ribozymes has expanded the group to a total of nine and this provides a new opportunity to identify sub-groupings according to the nature of the general base and acid. These include nucleobases, hydrated metal ions, and 2'-hydroxyl groups. Evolution has selected a number of different combinations of these elements that lead to efficient catalysis. These differences provide a new mechanistic basis for classifying these ribozymes.
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Affiliation(s)
- David M.J. Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, UK
- School of Life Sciences, Xiamen University, Xiamen, China
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41
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Gaines CS, Giese TJ, York DM. Cleaning Up Mechanistic Debris Generated by Twister Ribozymes Using Computational RNA Enzymology. ACS Catal 2019; 9:5803-5815. [PMID: 31328021 PMCID: PMC6641568 DOI: 10.1021/acscatal.9b01155] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The catalytic properties of RNA have been a subject of fascination and intense research since their discovery over 30 years ago. Very recently, several classes of nucleolytic ribozymes have emerged and been characterized structurally. Among these, the twister ribozyme has been center-stage, and a topic of debate about its architecture and mechanism owing to conflicting interpretations of different crystal structures, and in some cases conflicting interpretations of the same functional data. In the present work, we attempt to clean up the mechanistic "debris" generated by twister ribozymes using a comprehensive computational RNA enzymology approach aimed to provide a unified interpretation of existing structural and functional data. Simulations in the crystalline environment and in solution provide insight into the origins of observed differences in crystal structures, and coalesce on a common active site architecture, and dynamical ensemble in solution. We use GPU-accelerated free energy methods with enhanced sampling to ascertain microscopic nucleobase pK a values of the implicated general acid and base, from which predicted activity-pH profiles can be compared directly with experiments. Next, ab initio quantum mechanical/molecular mechanical (QM/MM) simulations with full dynamic solvation under periodic boundary conditions are used to determine mechanistic pathways through multi-dimensional free energy landscapes for the reaction. We then characterize the rate-controlling transition state, and make predictions about kinetic isotope effects and linear free energy relations. Computational mutagenesis is performed to explain the origin of rate effects caused by chemical modifications and make experimentally testable predictions. Finally, we provide evidence that helps to resolve conflicting issues related to the role of metal ions in catalysis. Throughout each stage, we highlight how a conserved L-platform structural motif, to- gether with a key L-anchor residue, forms the characteristic active site scaffold enabling each of the catalytic strategies to come together not only for the twister ribozyme, but the majority of the known small nucleolytic ribozyme classes.
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Affiliation(s)
- Colin S. Gaines
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Timothy J. Giese
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Darrin M. York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
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42
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Kumar N, Marx D. Mechanistic role of nucleobases in self-cleavage catalysis of hairpin ribozyme at ambient versus high-pressure conditions. Phys Chem Chem Phys 2019; 20:20886-20898. [PMID: 30067263 DOI: 10.1039/c8cp03142h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Ribozymes catalyze the site-specific self-cleavage of intramolecular phosphodiester bonds. Initially thought to act as metalloenzymes, they are now known to be functional even in the absence of divalent metal ions and specific nucleobases directly participate in the self-cleavage reaction. Here, we use extensive replica exchange molecular dynamics simulations to probe the precise mechanistic role of nucleobases by simulating precatalytic reactant and active precursor states of a hairpin ribozyme along its reaction path at ambient as well as high-pressure conditions. The results provide novel key insights into the self-cleavage of ribozymes. We find that deprotonation of the hydroxyl group is crucial and might be the penultimate step to the self-cleavage. The G8 nucleobase is found to stabilize the activated precursor into inline arrangement for facile nucleophilic attack of the scissile phosphate only after deprotonation of the hydroxyl group. The protonated A38 nucleobase, in contrast, mainly acts a proton donor to the O5'-oxygen leaving group that eventually leads to the self-cleavage. Indeed, systematic high-pressure simulations of catalytically relevant states confirm these findings and, moreover, provide support to the role of ribozymes as piezophilic biocatalysts with regard to their relevance in early life under extreme conditions in the realm of RNA world hypothesis.
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Affiliation(s)
- Narendra Kumar
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany.
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43
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Abstract
Self-cleaving ribozymes are RNAs that catalyze position-specific cleavage of their phosphodiester backbone. The cleavage site of the newly discovered hatchet ribozyme is located at the very 5′ end of its consensus secondary structure motif. Here we report on the 2.1-Å crystal structure of the hatchet ribozyme in the product state, which defines its intricate tertiary fold and identifies key residues lining the catalytic pocket. This in turn has allowed us to propose a model of the precatalytic state structure and a role in catalysis for a conserved guanine. This study therefore provides a structure-based platform toward an improved understanding of the catalytic mechanism of hatchet ribozymes. Small self-cleaving ribozymes catalyze site-specific cleavage of their own phosphodiester backbone with implications for viral genome replication, pre-mRNA processing, and alternative splicing. We report on the 2.1-Å crystal structure of the hatchet ribozyme product, which adopts a compact pseudosymmetric dimeric scaffold, with each monomer stabilized by long-range interactions involving highly conserved nucleotides brought into close proximity of the scissile phosphate. Strikingly, the catalytic pocket contains a cavity capable of accommodating both the modeled scissile phosphate and its flanking 5′ nucleoside. The resulting modeled precatalytic conformation incorporates a splayed-apart alignment at the scissile phosphate, thereby providing structure-based insights into the in-line cleavage mechanism. We identify a guanine lining the catalytic pocket positioned to contribute to cleavage chemistry. The functional relevance of structure-based insights into hatchet ribozyme catalysis is strongly supported by cleavage assays monitoring the impact of selected nucleobase and atom-specific mutations on ribozyme activity.
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44
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Zhang H, Keane SC. Advances that facilitate the study of large RNA structure and dynamics by nuclear magnetic resonance spectroscopy. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1541. [PMID: 31025514 PMCID: PMC7169810 DOI: 10.1002/wrna.1541] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 01/18/2019] [Accepted: 04/02/2019] [Indexed: 12/22/2022]
Abstract
The characterization of functional yet nonprotein coding (nc) RNAs has expanded the role of RNA in the cell from a passive player in the central dogma of molecular biology to an active regulator of gene expression. The misregulation of ncRNA function has been linked with a variety of diseases and disorders ranging from cancers to neurodegeneration. However, a detailed molecular understanding of how ncRNAs function has been limited; due, in part, to the difficulties associated with obtaining high-resolution structures of large RNAs. Tertiary structure determination of RNA as a whole is hampered by various technical challenges, all of which are exacerbated as the size of the RNA increases. Namely, RNAs tend to be highly flexible and dynamic molecules, which are difficult to crystallize. Biomolecular nuclear magnetic resonance (NMR) spectroscopy offers a viable alternative to determining the structure of large RNA molecules that do not readily crystallize, but is itself hindered by some technical limitations. Recently, a series of advancements have allowed the biomolecular NMR field to overcome, at least in part, some of these limitations. These advances include improvements in sample preparation strategies as well as methodological improvements. Together, these innovations pave the way for the study of ever larger RNA molecules that have important biological function. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
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Affiliation(s)
- Huaqun Zhang
- Biophysics Program, University of Michigan, Ann Arbor, Michigan
| | - Sarah C Keane
- Biophysics Program, University of Michigan, Ann Arbor, Michigan.,Department of Chemistry, University of Michigan, Ann Arbor, Michigan
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45
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Maurel MC, Leclerc F, Vergne J, Zaccai G. RNA Back and Forth: Looking through Ribozyme and Viroid Motifs. Viruses 2019; 11:E283. [PMID: 30901893 PMCID: PMC6466107 DOI: 10.3390/v11030283] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 03/14/2019] [Accepted: 03/18/2019] [Indexed: 12/28/2022] Open
Abstract
Current cellular facts allow us to follow the link from chemical to biochemical metabolites, from the ancient to the modern world. In this context, the "RNA world" hypothesis proposes that early in the evolution of life, the ribozyme was responsible for the storage and transfer of genetic information and for the catalysis of biochemical reactions. Accordingly, the hammerhead ribozyme (HHR) and the hairpin ribozyme belong to a family of endonucleolytic RNAs performing self-cleavage that might occur during replication. Furthermore, regarding the widespread occurrence of HHRs in several genomes of modern organisms (from mammals to small parasites and elsewhere), these small ribozymes have been regarded as living fossils of a primitive RNA world. They fold into 3D structures that generally require long-range intramolecular interactions to adopt the catalytically active conformation under specific physicochemical conditions. By studying viroids as plausible remains of ancient RNA, we recently demonstrated that they replicate in non-specific hosts, emphasizing their adaptability to different environments, which enhanced their survival probability over the ages. All these results exemplify ubiquitous features of life. Those are the structural and functional versatility of small RNAs, ribozymes, and viroids, as well as their diversity and adaptability to various extreme conditions. All these traits must have originated in early life to generate novel RNA populations.
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Affiliation(s)
- Marie-Christine Maurel
- Sorbonne Université, Museum National d'Histoire Naturelle, CNRS MNHN UMR 7205, Institut de Systématique, Evolution, Biodiversité, ISYEB, F-75005 Paris, France.
| | - Fabrice Leclerc
- Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Université Paris Sud, F-91198 Gif-sur-Yvette, France.
| | - Jacques Vergne
- Sorbonne Université, Museum National d'Histoire Naturelle, CNRS MNHN UMR 7205, Institut de Systématique, Evolution, Biodiversité, ISYEB, F-75005 Paris, France.
| | - Giuseppe Zaccai
- Institut de Biologie Structurale CNRS-CEA-UGA, F-380447 Grenoble, France, and Institut Laue Langevin, 71 Avenue des Martyrs, F-38042 Grenoble, France.
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46
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Nomura Y, Roston D, Montemayor EJ, Cui Q, Butcher SE. Structural and mechanistic basis for preferential deadenylation of U6 snRNA by Usb1. Nucleic Acids Res 2018; 46:11488-11501. [PMID: 30215753 PMCID: PMC6265477 DOI: 10.1093/nar/gky812] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 08/27/2018] [Accepted: 08/29/2018] [Indexed: 01/08/2023] Open
Abstract
Post-transcriptional modification of snRNA is central to spliceosome function. Usb1 is an exoribonuclease that shortens the oligo-uridine tail of U6 snRNA, resulting in a terminal 2',3' cyclic phosphate group in most eukaryotes, including humans. Loss of function mutations in human Usb1 cause the rare disorder poikiloderma with neutropenia (PN), and result in U6 snRNAs with elongated 3' ends that are aberrantly adenylated. Here, we show that human Usb1 removes 3' adenosines with 20-fold greater efficiency than uridines, which explains the presence of adenylated U6 snRNAs in cells lacking Usb1. We determined three high-resolution co-crystal structures of Usb1: wild-type Usb1 bound to the substrate analog adenosine 5'-monophosphate, and an inactive mutant bound to RNAs with a 3' terminal adenosine and uridine. These structures, along with QM/MM MD simulations of the catalytic mechanism, illuminate the molecular basis for preferential deadenylation of U6 snRNA. The extent of Usb1 processing is influenced by the secondary structure of U6 snRNA.
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Affiliation(s)
- Yuichiro Nomura
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Daniel Roston
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Eric J Montemayor
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Qiang Cui
- Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Samuel E Butcher
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
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47
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Shelke SA, Shao Y, Laski A, Koirala D, Weissman BP, Fuller JR, Tan X, Constantin TP, Waggoner AS, Bruchez MP, Armitage BA, Piccirilli JA. Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif. Nat Commun 2018; 9:4542. [PMID: 30382099 PMCID: PMC6208384 DOI: 10.1038/s41467-018-06942-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 09/26/2018] [Indexed: 12/24/2022] Open
Abstract
The DIR2s RNA aptamer, a second-generation, in-vitro selected binder to dimethylindole red (DIR), activates the fluorescence of cyanine dyes, DIR and oxazole thiazole blue (OTB), allowing detection of two well-resolved emission colors. Using Fab BL3-6 and its cognate hairpin as a crystallization module, we solved the crystal structures of both the apo and OTB-SO3 bound forms of DIR2s at 2.0 Å and 1.8 Å resolution, respectively. DIR2s adopts a compact, tuning fork-like architecture comprised of a helix and two short stem-loops oriented in parallel to create the ligand binding site through tertiary interactions. The OTB-SO3 fluorophore binds in a planar conformation to a claw-like structure formed by a purine base-triple, which provides a stacking platform for OTB-SO3, and an unpaired nucleotide, which partially caps the binding site from the top. The absence of a G-quartet or base tetrad makes the DIR2s aptamer unique among fluorogenic RNAs with known 3D structure. The DIR2s RNA aptamer activates the fluorescence of cyanine dyes allowing detection of two well-resolved emission colors. Here authors solve the crystal structures of the apo and OTB-SO3 fluorophore-bound DIR2s and show how the fluorophore ligand is bound.
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Affiliation(s)
- Sandip A Shelke
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Yaming Shao
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Artur Laski
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Deepak Koirala
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | | | - James R Fuller
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Xiaohong Tan
- Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Tudor P Constantin
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Alan S Waggoner
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Marcel P Bruchez
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Bruce A Armitage
- Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Joseph A Piccirilli
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA. .,Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA.
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48
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Yang L, Zhong Z, Tong C, Jia H, Liu Y, Chen G. Single-Molecule Mechanical Folding and Unfolding of RNA Hairpins: Effects of Single A-U to A·C Pair Substitutions and Single Proton Binding and Implications for mRNA Structure-Induced -1 Ribosomal Frameshifting. J Am Chem Soc 2018; 140:8172-8184. [PMID: 29884019 DOI: 10.1021/jacs.8b02970] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A wobble A·C pair can be protonated at near physiological pH to form a more stable wobble A+·C pair. Here, we constructed an RNA hairpin (rHP) and three mutants with one A-U base pair substituted with an A·C mismatch on the top (near the loop, U22C), middle (U25C), and bottom (U29C) positions of the stem, respectively. Our results on single-molecule mechanical (un)folding using optical tweezers reveal the destabilization effect of A-U to A·C pair substitution and protonation-dependent enhancement of mechanical stability facilitated through an increased folding rate, or decreased unfolding rate, or both. Our data show that protonation may occur rapidly upon the formation of an apparent mechanical folding transition state. Furthermore, we measured the bulk -1 ribosomal frameshifting efficiencies of the hairpins by a cell-free translation assay. For the mRNA hairpins studied, -1 frameshifting efficiency correlates with mechanical unfolding force at equilibrium and folding rate at around 15 pN. U29C has a frameshifting efficiency similar to that of rHP (∼2%). Accordingly, the bottom 2-4 base pairs of U29C may not form under a stretching force at pH 7.3, which is consistent with the fact that the bottom base pairs of the hairpins may be disrupted by ribosome at the slippery site. U22C and U25C have a similar frameshifting efficiency (∼1%), indicating that both unfolding and folding rates of an mRNA hairpin in a crowded environment may affect frameshifting. Our data indicate that mechanical (un)folding of RNA hairpins may mimic how mRNAs unfold and fold in the presence of translating ribosomes.
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Affiliation(s)
- Lixia Yang
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Zhensheng Zhong
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371.,School of Physics, and State Key Laboratory of Optoelectronic Materials and Technologies , Sun Yat-sen University , Guangzhou 510275 , People's Republic of China
| | - Cailing Tong
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Huan Jia
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Yiran Liu
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , Singapore 637371
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49
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Abstract
An artificially evolved ribozyme can catalyse the synthesis of RNA by using trinucleotide triphosphates as building blocks.
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Affiliation(s)
- Antony Crisp
- Center for Integrated Protein Science, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Thomas Carell
- Center for Integrated Protein Science, Ludwig-Maximilians-Universität München, Munich, Germany
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50
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Attwater J, Raguram A, Morgunov AS, Gianni E, Holliger P. Ribozyme-catalysed RNA synthesis using triplet building blocks. eLife 2018; 7:35255. [PMID: 29759114 PMCID: PMC6003772 DOI: 10.7554/elife.35255] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 05/09/2018] [Indexed: 12/18/2022] Open
Abstract
RNA-catalyzed RNA replication is widely believed to have supported a primordial biology. However, RNA catalysis is dependent upon RNA folding, and this yields structures that can block replication of such RNAs. To address this apparent paradox, we have re-examined the building blocks used for RNA replication. We report RNA-catalysed RNA synthesis on structured templates when using trinucleotide triphosphates (triplets) as substrates, catalysed by a general and accurate triplet polymerase ribozyme that emerged from in vitro evolution as a mutualistic RNA heterodimer. The triplets cooperatively invaded and unraveled even highly stable RNA secondary structures, and support non-canonical primer-free and bidirectional modes of RNA synthesis and replication. Triplet substrates thus resolve a central incongruity of RNA replication, and here allow the ribozyme to synthesise its own catalytic subunit ‘+’ and ‘–’ strands in segments and assemble them into a new active ribozyme. Life as we know it relies on three types of molecules: DNA, which stores genetic information; proteins that carry out the chemical reactions necessary for life; and RNA, which relays information between the two. However, some scientists think that before life adopted DNA and proteins, it relied primarily on RNA. Like DNA, strands of RNA contain genetic data. Yet, some RNA strands can also fold to form ribozymes, 3D structures that could have guided life’s chemical processes the way proteins do now. For early life to be built on RNA, though, this molecule must have had the ability to make copies of itself. This duplication is a chemical reaction that could be driven by an ‘RNA replicase’ ribozyme. RNA strands are made of four different letters attached to each other in a specific order. When RNA is copied, one strand acts as a template, and a replicase ribozyme would accurately guide which letters are added to the strand under construction. However, no replicase ribozyme has been observed in existing life forms; this has led scientists to try to artificially create RNA replicase ribozymes that could copy themselves. Until now, the best approaches have assumed that a replicase would add building blocks formed of a single letter one by one to grow a new strand. Yet, although ribozymes can be made to copy straight RNA templates this way, folded RNA templates – including the replicase ribozyme itself – impede copying. In this apparent paradox, a ribozyme needs to fold to copy RNA, but when folded, is itself copied poorly. Here, Attwater et al. wondered if choosing different building blocks might overcome this contradiction. Biochemical techniques were used to engineer a ribozyme that copies RNA strands by adding letters not one-by-one, but three-by-three. Using three-letter ‘triplet’ building blocks, this new ribozyme can copy various folded RNA strands, including the active part of its own sequence. This is because triplet building blocks have different, and sometimes unexpected, chemical properties compared to single-letter blocks. For example, these triplets work together to bind tightly to RNA strands and unravel structures that block RNA copying. All life on Earth today uses a triplet RNA code to make proteins from DNA, and these experiments showed how RNA triplets might have helped RNA sustain early life forms. Further work is now needed to improve the ribozyme designed by Attwater et al. for efficient self-copying.
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Affiliation(s)
- James Attwater
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Aditya Raguram
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Alexey S Morgunov
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Edoardo Gianni
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
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