1
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Acquisition of Dual Ribozyme-Functions in Nonfunctional Short Hairpin RNAs through Kissing-Loop Interactions. LIFE (BASEL, SWITZERLAND) 2022; 12:life12101561. [PMID: 36294996 PMCID: PMC9604999 DOI: 10.3390/life12101561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/30/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022]
Abstract
The acquisition of functions via the elongation of nucleotides is an important factor in the development of the RNA world. In our previous study, we found that the introduction of complementary seven-membered kissing loops into inactive R3C ligase ribozymes revived their ligation activity. In this study, we applied the kissing complex formation-induced rearrangement of RNAs to two nonfunctional RNAs by introducing complementary seven-membered loops into each of them. By combining these two forms of RNAs, the ligase activity (derived from the R3C ligase ribozyme) as well as cleavage activity (derived from the hammerhead ribozyme) was obtained. Thus, effective RNA evolution toward the formation of a life system may require the achievement of “multiple” functions via kissing-loop interactions, as indicated in this study. Our results point toward the versatility of kissing-loop interactions in the evolution of RNA, i.e., two small nonfunctional RNAs can gain dual functions via a kissing-loop interaction.
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2
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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: 17] [Impact Index Per Article: 5.7] [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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3
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Assembly factors chaperone ribosomal RNA folding by isolating helical junctions that are prone to misfolding. Proc Natl Acad Sci U S A 2021; 118:2101164118. [PMID: 34135123 DOI: 10.1073/pnas.2101164118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
While RNAs are known to misfold, the underlying molecular causes have been mainly studied in fragments of biologically relevant larger RNAs. As these small RNAs are dominated by secondary structures, misfolding of these secondary structures remains the most-explored cause for global RNA misfolding. Conversely, how RNA chaperones function in a biological context to promote native folding beyond duplex annealing remains unknown. Here, in a combination of dimethylsulfate mutational profiling with sequencing (DMS-MaPseq), structural analyses, biochemical experiments, and yeast genetics, we show that three-helix junctions are prone to misfolding during assembly of the small ribosomal subunit in vivo. We identify ubiquitous roles for ribosome assembly factors in chaperoning their folding by preventing the formation of premature tertiary interactions, which otherwise kinetically trap misfolded junctions, thereby blocking further progress in the assembly cascade. While these protein chaperones act indirectly by binding the interaction partners of junctions, our analyses also suggest direct roles for small nucleolar RNAs (snoRNAs) in binding and chaperoning helical junctions during transcription. While these assembly factors do not utilize energy to ameliorate misfolding, our data demonstrate how their dissociation renders reversible folding steps irreversible, thereby driving native folding and assembly and setting up a timer that dictates the propensity of misfolded intermediates to escape quality control. Finally, the data demonstrate that RNA chaperones act locally on individual tertiary interactions, in contrast to protein chaperones, which globally unfold misfolded proteins.
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4
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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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5
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Dagenais P, Legault P. In Vitro Selection of Varkud Satellite Ribozyme Variants that Cleave a Modified Stem-Loop Substrate. Methods Mol Biol 2021; 2167:61-77. [PMID: 32712915 DOI: 10.1007/978-1-0716-0716-9_5] [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] [Indexed: 06/11/2023]
Abstract
In vitro selection is an established approach to create artificial ribozymes with defined activities or to modify the properties of naturally occurring ribozymes. For the Varkud satellite ribozyme of Neurospora, an in vitro selection protocol based on its phosphodiester bond cleavage activity has not been previously reported. Here, we describe a simple protocol for cleavage-based in vitro selection that we recently used to identify variants of the Varkud satellite ribozyme able to target and cleave a non-natural stem-loop substrate derived from the HIV-1 TAR RNA. It allows quick selection of active ribozyme variants from the transcription reaction based on the size of the self-cleavage product without the need for RNA labeling. This results in a streamlined procedure that is easily adaptable to engineer ribozymes with new activities.
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Affiliation(s)
- Pierre Dagenais
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC, Canada
| | - Pascale Legault
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC, Canada.
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6
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Light-controlled twister ribozyme with single-molecule detection resolves RNA function in time and space. Proc Natl Acad Sci U S A 2020; 117:12080-12086. [PMID: 32430319 DOI: 10.1073/pnas.2003425117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Small ribozymes such as Oryza sativa twister spontaneously cleave their own RNA when the ribozyme folds into its active conformation. The coupling between twister folding and self-cleavage has been difficult to study, however, because the active ribozyme rapidly converts to product. Here, we describe the synthesis of a photocaged nucleotide that releases guanosine within microseconds upon photosolvolysis with blue light. Application of this tool to O. sativa twister achieved the spatial (75 µm) and temporal (≤30 ms) control required to resolve folding and self-cleavage events when combined with single-molecule fluorescence detection of the ribozyme folding pathway. Real-time observation of single ribozymes after photo-deprotection showed that the precleaved folded state is unstable and quickly unfolds if the RNA does not react. Kinetic analysis showed that Mg2+ and Mn2+ ions increase ribozyme efficiency by making transitions to the high energy active conformation more probable, rather than by stabilizing the folded ground state or the cleaved product. This tool for light-controlled single RNA folding should offer precise and rapid control of other nucleic acid systems.
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7
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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: 27] [Impact Index Per Article: 6.8] [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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8
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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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9
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DasGupta S, Suslov NB, Piccirilli JA. Structural Basis for Substrate Helix Remodeling and Cleavage Loop Activation in the Varkud Satellite Ribozyme. J Am Chem Soc 2017; 139:9591-9597. [PMID: 28625058 PMCID: PMC5929484 DOI: 10.1021/jacs.7b03655] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The Varkud satellite (VS) ribozyme catalyzes site-specific RNA cleavage and ligation reactions. Recognition of the substrate involves a kissing loop interaction between the substrate and the catalytic domain of the ribozyme, resulting in a rearrangement of the substrate helix register into a so-called "shifted" conformation that is critical for substrate binding and activation. We report a 3.3 Å crystal structure of the complete ribozyme that reveals the active, shifted conformation of the substrate, docked into the catalytic domain of the ribozyme. Comparison to previous NMR structures of isolated, inactive substrates provides a physical description of substrate remodeling, and implicates roles for tertiary interactions in catalytic activation of the cleavage loop. Similarities to the hairpin ribozyme cleavage loop activation suggest general strategies to enhance fidelity in RNA folding and ribozyme cleavage.
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Affiliation(s)
- Saurja DasGupta
- Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA
| | - Nikolai B. Suslov
- 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
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10
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Dagenais P, Girard N, Bonneau E, Legault P. Insights into RNA structure and dynamics from recent NMR and X-ray studies of the Neurospora Varkud satellite ribozyme. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [PMID: 28382748 PMCID: PMC5573960 DOI: 10.1002/wrna.1421] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 02/21/2017] [Accepted: 03/08/2017] [Indexed: 12/31/2022]
Abstract
Despite the large number of noncoding RNAs and their importance in several biological processes, our understanding of RNA structure and dynamics at atomic resolution is still very limited. Like many other RNAs, the Neurospora Varkud satellite (VS) ribozyme performs its functions through dynamic exchange of multiple conformational states. More specifically, the VS ribozyme recognizes and cleaves its stem-loop substrate via a mechanism that involves several structural transitions within its stem-loop substrate. The recent publications of high-resolution structures of the VS ribozyme, obtained by NMR spectroscopy and X-ray crystallography, offer an opportunity to integrate the data and closely examine the structural and dynamic properties of this model RNA system. Notably, these investigations provide a valuable example of the divide-and-conquer strategy for structural and dynamic characterization of a large RNA, based on NMR structures of several individual subdomains. The success of this divide-and-conquer approach reflects the modularity of RNA architecture and the great care taken in identifying the independently-folding modules. Together with previous biochemical and biophysical characterizations, the recent NMR and X-ray studies provide a coherent picture into how the VS ribozyme recognizes its stem-loop substrate. Such in-depth characterization of this RNA enzyme will serve as a model for future structural and engineering studies of dynamic RNAs and may be particularly useful in planning divide-and-conquer investigations. WIREs RNA 2017, 8:e1421. doi: 10.1002/wrna.1421 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Pierre Dagenais
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Canada
| | - Nicolas Girard
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Canada
| | - Eric Bonneau
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Canada
| | - Pascale Legault
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Canada
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11
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Lacroix-Labonté J, Girard N, Dagenais P, Legault P. Rational engineering of the Neurospora VS ribozyme to allow substrate recognition via different kissing-loop interactions. Nucleic Acids Res 2016; 44:6924-34. [PMID: 27166370 PMCID: PMC5001590 DOI: 10.1093/nar/gkw401] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 04/30/2016] [Indexed: 12/24/2022] Open
Abstract
The Neurospora VS ribozyme is a catalytic RNA that has the unique ability to specifically recognize and cleave a stem-loop substrate through formation of a highly stable kissing-loop interaction (KLI). In order to explore the engineering potential of the VS ribozyme to cleave alternate substrates, we substituted the wild-type KLI by other known KLIs using an innovative engineering method that combines rational and combinatorial approaches. A bioinformatic search of the protein data bank was initially performed to identify KLIs that are structurally similar to the one found in the VS ribozyme. Next, substrate/ribozyme (S/R) pairs that incorporate these alternative KLIs were kinetically and structurally characterized. Interestingly, several of the resulting S/R pairs allowed substrate cleavage with substantial catalytic efficiency, although with reduced activity compared to the reference S/R pair. Overall, this study describes an innovative approach for RNA engineering and establishes that the KLI of the trans VS ribozyme can be adapted to cleave other folded RNA substrates.
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Affiliation(s)
- Julie Lacroix-Labonté
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC H3C 3J7, Canada
| | - 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
| | - 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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12
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Prieto F, Su Z, Leitch JJ, Rueda M, Lipkowski J. Quantitative Subtractively Normalized Interfacial Fourier Transform Infrared Reflection Spectroscopy Study of the Adsorption of Adenine on Au(111) Electrodes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:3827-3835. [PMID: 27040121 DOI: 10.1021/acs.langmuir.6b00635] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Quantitative subtractively normalized interfacial Fourier transform infrared reflection spectroscopy (SNIFTIRS) was used to determine the molecular orientation and identify the metal-molecular interactions responsible for the adsorption of adenine from the bulk electrolyte solution onto the surface of the Au(111) electrode. The recorded p-polarized IR spectra of the adsorbed species were subtracted from the collected s-polarized IR spectra to remove the IR contributions of the vibrational bands of the desorbed molecules that are located within the thin layer cavity of the spectroelectrochemical cell. The intense IR band around 1640 cm(-1), which is assigned to the pyrimidine ring stretching vibrations of the C5-C6 and C6-N10 bonds, and the IR band at 1380 cm(-1), which results from a combination of the ring stretching vibration of the C5-C7 bond and the in-plane CH bending vibration, were selected for the quantitative analysis measurements. The transition dipoles of these bands were evaluated by DFT calculations. Their orientations differed by 85 ± 5°. The tilt angles of adsorbed adenine molecules were calculated from the intensity of these two vibrations at different potentials. The results indicate that the molecular plane is tilted at an angle of 40° with respect to the surface normal of the electrode and rotates by 16° around its normal axis with increasing electrode potential. This orientation results from the chemical interaction between the N10 and gold atoms coupled with the π-π parallel stacking interactions between the adjacent adsorbed molecules. Furthermore, the changes in the molecular plane rotation with the electric field suggests that the N1 atom of adenine must also participate in the interaction between the molecule and metal.
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Affiliation(s)
- Francisco Prieto
- Department of Physical Chemistry, University of Seville , c/Professor Garcia Gonzalez 2, 41012 Seville, Spain
| | - Zhangfei Su
- Electrochemistry Technology Centre, Department of Chemistry, College of Physical & Engineering Science, University of Guelph , Guelph, Ontario, Canada N1G 2W1
| | - J Jay Leitch
- Electrochemistry Technology Centre, Department of Chemistry, College of Physical & Engineering Science, University of Guelph , Guelph, Ontario, Canada N1G 2W1
| | - Manuela Rueda
- Department of Physical Chemistry, University of Seville , c/Professor Garcia Gonzalez 2, 41012 Seville, Spain
| | - Jacek Lipkowski
- Electrochemistry Technology Centre, Department of Chemistry, College of Physical & Engineering Science, University of Guelph , Guelph, Ontario, Canada N1G 2W1
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13
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Jimenez RM, Polanco JA, Lupták A. Chemistry and Biology of Self-Cleaving Ribozymes. Trends Biochem Sci 2015; 40:648-661. [PMID: 26481500 DOI: 10.1016/j.tibs.2015.09.001] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 08/28/2015] [Accepted: 09/01/2015] [Indexed: 11/26/2022]
Abstract
Self-cleaving ribozymes were discovered 30 years ago, but their biological distribution and catalytic mechanisms are only beginning to be defined. Each ribozyme family is defined by a distinct structure, with unique active sites accelerating the same transesterification reaction across the families. Biochemical studies show that general acid-base catalysis is the most common mechanism of self-cleavage, but metal ions and metabolites can be used as cofactors. Ribozymes have been discovered in highly diverse genomic contexts throughout nature, from viroids to vertebrates. Their biological roles include self-scission during rolling-circle replication of RNA genomes, co-transcriptional processing of retrotransposons, and metabolite-dependent gene expression regulation in bacteria. Other examples, including highly conserved mammalian ribozymes, suggest that many new biological roles are yet to be discovered.
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Affiliation(s)
- Randi M Jimenez
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - Julio A Polanco
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - Andrej Lupták
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA; Department of Pharmaceutical Sciences, University of California, Irvine, CA, USA; Department of Chemistry, University of California, Irvine, CA, USA.
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14
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Abstract
Varkud Satellite (VS) ribozyme mediates rolling circle replication of a plasmid found in the Neurospora mitochondria. We report crystal structures of this ribozyme at 3.1Å resolution, revealing an intertwined dimer formed by an exchange of substrate helices. Within each protomer, an arrangement of three-way helical junctions organizes seven helices into a global fold that creates a docking site for the substrate helix of the other protomer, resulting in the formation of two active sites in trans. This mode of RNA-RNA association resembles the process of domain swapping in proteins and has implications for RNA regulation and evolution. Within each active site, adenine and guanine nucleobases abut the scissile phosphate, poised to serve direct roles in catalysis. Similarities to the active sites of the hairpin and hammerhead ribozymes highlight the functional significance of active site features, underscore the ability of RNA to access functional architectures from distant regions of sequence space, and suggest convergent evolution.
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15
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Lussier A, Bastet L, Chauvier A, Lafontaine DA. A kissing loop is important for btuB riboswitch ligand sensing and regulatory control. J Biol Chem 2015; 290:26739-51. [PMID: 26370077 DOI: 10.1074/jbc.m115.684134] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Indexed: 12/18/2022] Open
Abstract
RNA-based genetic regulation is exemplified by metabolite-binding riboswitches that modulate gene expression through conformational changes. Crystal structures show that the Escherichia coli btuB riboswitch contains a kissing loop interaction that is in close proximity to the bound ligand. To analyze the role of the kissing loop interaction in the riboswitch regulatory mechanism, we used RNase H cleavage assays to probe the structure of nascent riboswitch transcripts produced by the E. coli RNA polymerase. By monitoring the folding of the aptamer, kissing loop, and riboswitch expression platform, we established the conformation of each structural component in the absence or presence of bound adenosylcobalamin. We found that the kissing loop interaction is not essential for ligand binding. However, we showed that kissing loop formation improves ligand binding efficiency and is required to couple ligand binding to the riboswitch conformational changes involved in regulating gene expression. These results support a mechanism by which the btuB riboswitch modulates the formation of a tertiary structure to perform metabolite sensing and regulate gene expression.
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Affiliation(s)
- Antony Lussier
- From the Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Québec J1K 2R1, Canada
| | - Laurène Bastet
- From the Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Québec J1K 2R1, Canada
| | - Adrien Chauvier
- From the Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Québec J1K 2R1, Canada
| | - Daniel A Lafontaine
- From the Department of Biology, Faculty of Science, RNA Group, Université de Sherbrooke, Sherbrooke, Québec J1K 2R1, Canada
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16
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Bonneau E, Girard N, Lemieux S, Legault P. The NMR structure of the II-III-VI three-way junction from the Neurospora VS ribozyme reveals a critical tertiary interaction and provides new insights into the global ribozyme structure. RNA (NEW YORK, N.Y.) 2015; 21:1621-32. [PMID: 26124200 PMCID: PMC4536322 DOI: 10.1261/rna.052076.115] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 06/08/2015] [Indexed: 05/04/2023]
Abstract
As part of an effort to structurally characterize the complete Neurospora VS ribozyme, NMR solution structures of several subdomains have been previously determined, including the internal loops of domains I and VI, the I/V kissing-loop interaction and the III-IV-V junction. Here, we expand this work by determining the NMR structure of a 62-nucleotide RNA (J236) that encompasses the VS ribozyme II-III-VI three-way junction and its adjoining stems. In addition, we localize Mg(2+)-binding sites within this structure using Mn(2+)-induced paramagnetic relaxation enhancement. The NMR structure of the J236 RNA displays a family C topology with a compact core stabilized by continuous stacking of stems II and III, a cis WC/WC G•A base pair, two base triples and two Mg(2+) ions. Moreover, it reveals a remote tertiary interaction between the adenine bulges of stems II and VI. Additional NMR studies demonstrate that both this bulge-bulge interaction and Mg(2+) ions are critical for the stable folding of the II-III-VI junction. The NMR structure of the J236 RNA is consistent with biochemical studies on the complete VS ribozyme, but not with biophysical studies performed with a minimal II-III-VI junction that does not contain the II-VI bulge-bulge interaction. Together with previous NMR studies, our findings provide important new insights into the three-dimensional architecture of this unique ribozyme.
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Affiliation(s)
- Eric Bonneau
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Nicolas Girard
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Sébastien Lemieux
- Département d'Informatique et de Recherche Opérationnelle et Institut de Recherche en Immunologie et en Cancérologie, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
| | - Pascale Legault
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
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17
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Bonneau E, Legault P. Nuclear magnetic resonance structure of the III-IV-V three-way junction from the Varkud satellite ribozyme and identification of magnesium-binding sites using paramagnetic relaxation enhancement. Biochemistry 2014; 53:6264-75. [PMID: 25238589 DOI: 10.1021/bi500826n] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The VS ribozyme is a catalytic RNA found within some natural isolates of Neurospora that is being used as a model system to improve our understanding of RNA structure, catalysis, and engineering. The catalytic domain contains five helical domains (SLII-SLVI) that are organized by two three-way junctions. The III-IV-V junction is required for high-affinity binding of the substrate domain (SLI) through formation of a kissing loop interaction with SLV. Here, we determine the high-resolution nuclear magnetic resonance (NMR) structure of a 47-nucleotide RNA containing the III-IV-V junction (J345). The J345 RNA adopts a Y-shaped fold typical of the family C three-way junctions, with coaxial stacking between stems III and IV and an acute angle between stems III and V. The NMR structure reveals that the core of the III-IV-V junction contains four stacked base triples, a U-turn motif, a cross-strand stacking interaction, an A-minor interaction, and a ribose zipper. In addition, the NMR structure shows that the cCUUGg tetraloop used to stabilize stem IV adopts a novel RNA tetraloop fold, different from the known gCUUGc tetraloop structure. Using Mn(2+)-induced paramagnetic relaxation enhancement, we identify six Mg(2+)-binding sites within J345, including one associated with the cCUUGg tetraloop and two with the junction core. The NMR structure of J345 likely represents the conformation of the III-IV-V junction in the context of the active VS ribozyme and suggests that this junction functions as a dynamic hinge that contributes to substrate recognition and catalysis. Moreover, this study highlights a new role for family C three-way junctions in long-range tertiary interactions.
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Affiliation(s)
- Eric Bonneau
- Département de Biochimie et Médecine Moléculaire, Université de Montréal , C.P. 6128, Succursale Centre-Ville, Montréal, QC, Canada H3C 3J7
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18
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Bouchard P, Legault P. A remarkably stable kissing-loop interaction defines substrate recognition by the Neurospora Varkud Satellite ribozyme. RNA (NEW YORK, N.Y.) 2014; 20:1451-64. [PMID: 25051972 PMCID: PMC4138328 DOI: 10.1261/rna.046144.114] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 06/03/2014] [Indexed: 05/20/2023]
Abstract
Kissing loops are tertiary structure elements that often play key roles in functional RNAs. In the Neurospora VS ribozyme, a kissing-loop interaction between the stem-loop I (SLI) substrate and stem-loop V (SLV) of the catalytic domain is known to play an important role in substrate recognition. In addition, this I/V kissing-loop interaction is associated with a helix shift in SLI that activates the substrate for catalysis. To better understand the role of this kissing-loop interaction in substrate recognition and activation by the VS ribozyme, we performed a thermodynamic characterization by isothermal titration calorimetry using isolated SLI and SLV stem-loops. We demonstrate that preshifted SLI variants have higher affinity for SLV than shiftable SLI variants, with an energetic cost of 1.8-3 kcal/mol for the helix shift in SLI. The affinity of the preshifted SLI for SLV is remarkably high, the interaction being more stable by 7-8 kcal/mol than predicted for a comparable duplex containing three Watson-Crick base pairs. The structural basis of this remarkable stability is discussed in light of previous NMR studies. Comparative thermodynamic studies reveal that kissing-loop complexes containing 6-7 Watson-Crick base pairs are as stable as predicted from comparable RNA duplexes; however, those with 2-3 Watson-Crick base pairs are more stable than predicted. Interestingly, the stability of SLI/ribozyme complexes is similar to that of SLI/SLV complexes. Thus, the I/V kissing loop interaction represents the predominant energetic contribution to substrate recognition by the trans-cleaving VS ribozyme.
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Affiliation(s)
- Patricia Bouchard
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC, Canada H3C 3J7
| | - Pascale Legault
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC, Canada H3C 3J7
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19
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Bonneau E, Legault P. NMR localization of divalent cations at the active site of the Neurospora VS ribozyme provides insights into RNA-metal-ion interactions. Biochemistry 2014; 53:579-90. [PMID: 24364590 PMCID: PMC3906864 DOI: 10.1021/bi401484a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Metal cations represent key elements of RNA structure and function. In the Neurospora VS ribozyme, metal cations play diverse roles; they are important for substrate recognition, formation of the active site, and shifting the pKa's of two key nucleobases that contribute to the general acid-base mechanism. Recently, we determined the NMR structure of the A730 loop of the VS ribozyme active site (SLVI) that contributes the general acid (A756) in the enzymatic mechanism of the cleavage reaction. Our studies showed that magnesium (Mg(2+)) ions are essential to stabilize the formation of the S-turn motif within the A730 loop that exposes the A756 nucleobase for catalysis. In this article, we extend these NMR investigations by precisely mapping the Mg(2+)-ion binding sites using manganese-induced paramagnetic relaxation enhancement and cadmium-induced chemical-shift perturbation of phosphorothioate RNAs. These experiments identify five Mg(2+)-ion binding sites within SLVI. Four Mg(2+) ions in SLVI are associated with known RNA structural motifs, including the G-U wobble pair and the GNRA tetraloop, and our studies reveal novel insights about Mg(2+) ion binding to these RNA motifs. Interestingly, one Mg(2+) ion is specifically associated with the S-turn motif, confirming its structural role in the folding of the A730 loop. This Mg(2+) ion is likely important for formation of the active site and may play an indirect role in catalysis.
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Affiliation(s)
- Eric Bonneau
- Département de Biochimie et Médecine Moléculaire, Université de Montréal , C.P. 6128, Succursale Centre-Ville, Montréal, Québec H3C 3J7, Canada
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20
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Bianchi C, Zangi R. Dual base-flipping of cytosines in a CpG dinucleotide sequence. Biophys Chem 2013; 187-188:14-22. [PMID: 24469333 DOI: 10.1016/j.bpc.2013.12.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 12/18/2013] [Accepted: 12/18/2013] [Indexed: 12/30/2022]
Abstract
Simultaneous flipped-out conformation of two neighboring bases on opposite strands of DNAs has been observed in several X-ray structures. It has also been detected for two cytosines on opposite strands in different contexts of CpG sites. In this paper, we study by MD simulations the dual base flipping of the two cytosines in hemi-methylated CpG site. We calculate the potential of mean force of flipping-out the unmethylated cytosine in three model systems. The first is for DNA bound to the regulatory protein UHRF1. In this case, the methyl-cytosine on the complementary strand is flipped-out into the binding pocket of the SRA domain of the protein. The other two systems are for unbound DNAs in which the methyl-cytosine is either intra-helical or extra-helical. We find that when the methyl-cytosine is flipped-out it is easier to flip-out the other (unmethylated) cytosine on the opposite strand by about 14-16kJ/mol. This lower penalty for dual-base flipping is observed for both the bound and unbound states of the DNA. Analyses of the hydrogen bond network and stacking interactions within the CpG site indicate that the lower penalty is due to stabilization of the dual-base flipped-out conformation via interactions involving the orphan guanines. The results presented in this paper suggest that the extra-helical conformation of the methyl-cytosine recognized by UHRF1 can facilitate the base-flipping process of the target cytosine to be methylated by Dnmt1.
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Affiliation(s)
- Caterina Bianchi
- Department of Organic Chemistry I, University of the Basque Country UPV/EHU, Avenida de Tolosa 72, 20018 San Sebastian, Spain
| | - Ronen Zangi
- Department of Organic Chemistry I, University of the Basque Country UPV/EHU, Avenida de Tolosa 72, 20018 San Sebastian, Spain; IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain.
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21
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Bouchard P, Legault P. Structural insights into substrate recognition by the Neurospora Varkud satellite ribozyme: importance of U-turns at the kissing-loop junction. Biochemistry 2013; 53:258-69. [PMID: 24325625 PMCID: PMC3893828 DOI: 10.1021/bi401491g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
![]()
Substrate
recognition by the Neurospora Varkud
satellite ribozyme depends on the formation of a magnesium-dependent
kissing-loop interaction between the stem-loop I (SLI) substrate and
stem-loop V (SLV) of the catalytic domain. From mutagenesis studies,
it has been established that this I/V kissing-loop interaction involves
three Watson–Crick base pairs and is associated with a structural
rearrangement of the SLI substrate that facilitates catalysis. Here,
we report the NMR structural characterization of this I/V kissing-loop
using isolated stem-loops. NMR studies were performed on different
SLI/SLV complexes containing a common SLV and shiftable, preshifted,
or double-stranded SLI variants. These studies confirm the presence
of three Watson–Crick base pairs at the kissing-loop junction
and provide evidence for the structural rearrangement of shiftable
SLI variants upon SLV binding. NMR structure determination of an SLI/SLV
complex demonstrates that both the SLI and SLV loops adopt U-turn
structures, which facilitates intermolecular Watson–Crick base
pairing. Several other interactions at the I/V interface, including
base triples and base stacking, help create a continuously stacked
structure. These NMR studies provide a structural basis to understand
the stability of the I/V kissing-loop interaction and lead us to propose
a kinetic model for substrate activation in the VS ribozyme.
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Affiliation(s)
- Patricia Bouchard
- Département de Biochimie et Médecine Moléculaire, Université de Montréal , C.P. 6128, Succursale Centre-Ville, Montréal, Quebec H3C 3J7, Canada
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22
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Pabit SA, Sutton JL, Chen H, Pollack L. Role of ion valence in the submillisecond collapse and folding of a small RNA domain. Biochemistry 2013; 52:1539-46. [PMID: 23398396 DOI: 10.1021/bi3016636] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Following the addition of ions to trigger folding, RNA molecules undergo a transition from rigid, extended states to a compact ensemble. Determining the time scale for this collapse provides important insights into electrostatic contributions to RNA folding; however, it can be challenging to isolate the effects of purely nonspecific collapse, e.g., relaxation due to backbone charge compensation, from the concurrent formation of some tertiary contacts. To solve this problem, we decoupled nonspecific collapse from tertiary folding using a single-point mutation to eliminate tertiary contacts in the small RNA subdomain known as tP5abc. Microfluidic mixing with microsecond time resolution and Förster resonance energy transfer detection provides insight into the ionic strength-dependent transition from extended to compact ensembles. Differences in reaction rates are detected when folding is initiated by monovalent or divalent ions, consistent with equilibrium measurements illustrating the enhanced screening of divalent ions relative to monovalent ions at the same ionic strength. Ion-driven collapse is fast, and a comparison of the collapse time of the wild-type and mutant tP5abc suggests that site binding of Mg(2+) occurs on submillisecond time scales.
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Affiliation(s)
- Suzette A Pabit
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
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23
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Bianchi C, Zangi R. Base-Flipping Propensities of Unmethylated, Hemimethylated, and Fully Methylated CpG Sites. J Phys Chem B 2013; 117:2348-58. [DOI: 10.1021/jp312145b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Caterina Bianchi
- Department of Organic
Chemistry
I, University of the Basque Country UPV/EHU, Avenida de Tolosa 72, 20018, San Sebastian, Spain
| | - Ronen Zangi
- Department of Organic
Chemistry
I, University of the Basque Country UPV/EHU, Avenida de Tolosa 72, 20018, San Sebastian, Spain
- IKERBASQUE, Basque Foundation for Science, 48011, Bilbao, Spain
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24
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Lacroix-Labonté J, Girard N, Lemieux S, Legault P. Helix-length compensation studies reveal the adaptability of the VS ribozyme architecture. Nucleic Acids Res 2011; 40:2284-93. [PMID: 22086962 PMCID: PMC3299992 DOI: 10.1093/nar/gkr1018] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Compensatory mutations in RNA are generally regarded as those that maintain base pairing, and their identification forms the basis of phylogenetic predictions of RNA secondary structure. However, other types of compensatory mutations can provide higher-order structural and evolutionary information. Here, we present a helix-length compensation study for investigating structure–function relationships in RNA. The approach is demonstrated for stem-loop I and stem-loop V of the Neurospora VS ribozyme, which form a kissing–loop interaction important for substrate recognition. To rapidly characterize the substrate specificity (kcat/KM) of several substrate/ribozyme pairs, a procedure was established for simultaneous kinetic characterization of multiple substrates. Several active substrate/ribozyme pairs were identified, indicating the presence of limited substrate promiscuity for stem Ib variants and helix-length compensation between stems Ib and V. 3D models of the I/V interaction were generated that are compatible with the kinetic data. These models further illustrate the adaptability of the VS ribozyme architecture for substrate cleavage and provide global structural information on the I/V kissing–loop interaction. By exploring higher-order compensatory mutations in RNA our approach brings a deeper understanding of the adaptability of RNA structure, while opening new avenues for RNA research.
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Affiliation(s)
- Julie Lacroix-Labonté
- Département de Biochimie, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, QC, Canada
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25
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Benz-Moy TL, Herschlag D. Structure-function analysis from the outside in: long-range tertiary contacts in RNA exhibit distinct catalytic roles. Biochemistry 2011; 50:8733-55. [PMID: 21815635 PMCID: PMC3186870 DOI: 10.1021/bi2008245] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The conserved catalytic core of the Tetrahymena group I ribozyme is encircled by peripheral elements. We have conducted a detailed structure-function study of the five long-range tertiary contacts that fasten these distal elements together. Mutational ablation of each of the tertiary contacts destabilizes the folded ribozyme, indicating a role of the peripheral elements in overall stability. Once folded, three of the five tertiary contact mutants exhibit defects in overall catalysis that range from 20- to 100-fold. These and the subsequent results indicate that the structural ring of peripheral elements does not act as a unitary element; rather, individual connections have distinct roles as further revealed by kinetic and thermodynamic dissection of the individual reaction steps. Ablation of P14 or the metal ion core/metal ion core receptor (MC/MCR) destabilizes docking of the substrate-containing P1 helix into tertiary interactions with the ribozyme's conserved core. In contrast, ablation of the L9/P5 contact weakens binding of the guanosine nucleophile by slowing its association, without affecting P1 docking. The P13 and tetraloop/tetraloop receptor (TL/TLR) mutations had little functional effect and small, local structural changes, as revealed by hydroxyl radical footprinting, whereas the P14, MC/MCR, and L9/P5 mutants show structural changes distal from the mutation site. These changes extended into regions of the catalytic core involved in docking or guanosine binding. Thus, distinct allosteric pathways couple the long-range tertiary contacts to functional sites within the conserved core. This modular functional specialization may represent a fundamental strategy in RNA structure-function interrelationships.
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Affiliation(s)
- Tara L. Benz-Moy
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - Daniel Herschlag
- Department of Chemistry, Stanford University, Stanford, California 94305
- Department of Biochemistry, Stanford University, Stanford, California 94305
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26
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Use of ribozyme cleavage kinetics to measure salt-induced changes in solution pH. Anal Biochem 2011; 415:12-20. [DOI: 10.1016/j.ab.2011.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Revised: 04/01/2011] [Accepted: 04/05/2011] [Indexed: 11/23/2022]
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27
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Nakano SI, Fujii M, Sugimoto N. Use of nucleic Acid analogs for the study of nucleic Acid interactions. J Nucleic Acids 2011; 2011:967098. [PMID: 21822475 PMCID: PMC3142669 DOI: 10.4061/2011/967098] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Accepted: 05/02/2011] [Indexed: 12/27/2022] Open
Abstract
Unnatural nucleosides have been explored to expand the properties and the applications of oligonucleotides. This paper briefly summarizes nucleic acid analogs in which the base is modified or replaced by an unnatural stacking group for the study of nucleic acid interactions. We also describe the nucleoside analogs of a base pair-mimic structure that we have examined. Although the base pair-mimic nucleosides possess a simplified stacking moiety of a phenyl or naphthyl group, they can be used as a structural analog of Watson-Crick base pairs. Remarkably, they can adopt two different conformations responding to their interaction energies, and one of them is the stacking conformation of the nonpolar aromatic group causing the site-selective flipping of the opposite base in a DNA double helix. The base pair-mimic nucleosides can be used to study the mechanism responsible for the base stacking and the flipping of bases out of a nucleic acid duplex.
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Affiliation(s)
- Shu-Ichi Nakano
- Faculty of Frontiers of Innovative Research in Science and Technology, Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
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28
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DeAbreu DM, Olive JE, Collins RA. Additional roles of a peripheral loop-loop interaction in the Neurospora VS ribozyme. Nucleic Acids Res 2011; 39:6223-8. [PMID: 21507887 PMCID: PMC3152364 DOI: 10.1093/nar/gkr250] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Many RNAs contain tertiary interactions that contribute to folding the RNA into its functional 3D structure. In the VS ribozyme, a tertiary loop-loop kissing interaction involving stem-loops I and V is also required to rearrange the secondary structure of stem-loop I such that nucleotides at the base of stem I, which contains the cleavage-ligation site, can adopt the conformation required for activity. In the current work, we have used mutants that constitutively adopt the catalytically permissive conformation to search for additional roles of the kissing interaction in vitro. Using mutations that disrupt or restore the kissing interaction, we find that the kissing interaction contributes ~1000-fold enhancement to the rates of cleavage and ligation. Large Mg(2+)-dependent effects on equilibrium were also observed: in the presence of the kissing interaction cleavage is favored >10-fold at micromolar concentrations of Mg(2+); whereas ligation is favored >10-fold at millimolar concentrations of Mg(2+). In the absence of the kissing interaction cleavage exceeds ligation at all concentrations of Mg(2+). These data provide evidence that the kissing interaction strongly affects the observed cleavage and ligation rate constants and the cleavage-ligation equilibrium of the ribozyme.
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Affiliation(s)
- Diane M DeAbreu
- Department of Molecular and Medical Genetics, University of Toronto, Toronto, Canada
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29
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Spano MN, Walter NG. Solution structure of an alternate conformation of helix27 from Escherichia coli16S rRNA. Biopolymers 2011; 95:653-68. [PMID: 21442607 DOI: 10.1002/bip.21626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Revised: 03/08/2011] [Accepted: 03/09/2011] [Indexed: 11/09/2022]
Abstract
Helix (H)27 of 16S ribosomal (r)RNA from Escherichia coli was dubbed the "switch helix" when mutagenesis suggested that two alternative base pair registers may have distinct functional roles in the bacterial ribosome. Although more recent genetic analyses suggest that H27 conformational switching is not required for translation, previous solution studies demonstrated that the isolated E. coli H27 can dynamically convert between the 885 and 888 conformations. Here, we have solved the nuclear magnetic resonance solution structure of a locked 888 conformation. NOE and residual dipolar coupling restraints reveal an architecture that markedly differs from that of the 885 conformation found in crystal structures of the bacterial ribosome. In place of the loop E motif that characterizes the 885 conformer and that the 888 conformer cannot adopt, we find evidence for an asymmetrical A-rich internal loop stabilized by stacking interactions among the unpaired A's. Comparison of the isolated H27 888 solution structure with the 885 crystal structure within the context of the ribosome suggests a difference in overall length of H27 that presents one plausible reason for the absence of H27 conformational switching within the sterically confining ribosome.
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30
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Desjardins G, Bonneau E, Girard N, Boisbouvier J, Legault P. NMR structure of the A730 loop of the Neurospora VS ribozyme: insights into the formation of the active site. Nucleic Acids Res 2011; 39:4427-37. [PMID: 21266483 PMCID: PMC3105416 DOI: 10.1093/nar/gkq1244] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Neurospora VS ribozyme is a small nucleolytic ribozyme with unique primary, secondary and global tertiary structures, which displays mechanistic similarities to the hairpin ribozyme. Here, we determined the high-resolution NMR structure of a stem–loop VI fragment containing the A730 internal loop, which forms part of the active site. In the presence of magnesium ions, the A730 loop adopts a structure that is consistent with existing biochemical data and most likely reflects its conformation in the VS ribozyme prior to docking with the cleavage site internal loop. Interestingly, the A730 loop adopts an S-turn motif that is also present in loop B within the hairpin ribozyme active site. The S-turn appears necessary to expose the Watson–Crick edge of a catalytically important residue (A756) so that it can fulfill its role in catalysis. The A730 loop and the cleavage site loop of the VS ribozyme display structural similarities to internal loops found in the active site of the hairpin ribozyme. These similarities provided a rationale to build a model of the VS ribozyme active site based on the crystal structure of the hairpin ribozyme.
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Affiliation(s)
- Geneviève Desjardins
- Département de Biochimie, Université de Montréal, CP 6128, Succursale Centre-Ville, Montréal, Québec H3C 3J7, Canada
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31
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Johnson-Buck AE, McDowell SE, Walter NG. Metal ions: supporting actors in the playbook of small ribozymes. Met Ions Life Sci 2011; 9:175-96. [PMID: 22010272 DOI: 10.1039/9781849732512-00175] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Since the 1980s, several small RNA motifs capable of chemical catalysis have been discovered. These small ribozymes, composed of between approximately 40 and 200 nucleotides, have been found to play vital roles in the replication of subviral and viral pathogens, as well as in gene regulation in prokaryotes, and have recently been discovered in noncoding eukaryotic RNAs. All of the known natural small ribozymes - the hairpin, hammerhead, hepatitis delta virus, Varkud satellite, and glmS ribozymes--catalyze the same self-cleavage reaction as RNase A, resulting in two products, one bearing a 2'-3' cyclic phosphate and the other a 5'-hydroxyl group. Although originally thought to be obligate metalloenzymes like the group I and II self-splicing introns, the small ribozymes are now known to support catalysis in a wide variety of cations that appear to be only indirectly involved in catalysis. Nevertheless, under physiologic conditions, metal ions are essential for the proper folding and function of the small ribozymes, the most effective of these being magnesium. Metal ions contribute to catalysis in the small ribozymes primarily by stabilizing the catalytically active conformation, but in some cases also by activating RNA functional groups for catalysis, directly participating in catalytic acid-base chemistry, and perhaps by neutralizing the developing negative charge of the transition state. Although interactions between the small ribozymes and cations are relatively nonspecific, ribozyme activity is quite sensitive to the types and concentrations of metal ions present in solution, suggesting a close evolutionary relationship between cellular metal ion homeostasis and cation requirements of catalytic RNAs, and perhaps RNA in general.
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Affiliation(s)
- Alexander E Johnson-Buck
- Department of Chemistry, University of Michigan, 930 N. University, Ann Arbor, MI 48109-1055, USA.
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32
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Reymond C, Beaudoin JD, Perreault JP. Modulating RNA structure and catalysis: lessons from small cleaving ribozymes. Cell Mol Life Sci 2009; 66:3937-50. [PMID: 19718544 PMCID: PMC2777235 DOI: 10.1007/s00018-009-0124-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2009] [Revised: 07/30/2009] [Accepted: 07/31/2009] [Indexed: 01/12/2023]
Abstract
RNA is a key molecule in life, and comprehending its structure/function relationships is a crucial step towards a more complete understanding of molecular biology. Even though most of the information required for their correct folding is contained in their primary sequences, we are as yet unable to accurately predict both the folding pathways and active tertiary structures of RNA species. Ribozymes are interesting molecules to study when addressing these questions because any modifications in their structures are often reflected in their catalytic properties. The recent progress in the study of the structures, the folding pathways and the modulation of the small ribozymes derived from natural, self-cleaving, RNA motifs have significantly contributed to today's knowledge in the field.
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Affiliation(s)
- Cedric Reymond
- RNA Group/Groupe ARN, Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1H 5N4 Canada
| | - Jean-Denis Beaudoin
- RNA Group/Groupe ARN, Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1H 5N4 Canada
| | - Jean-Pierre Perreault
- RNA Group/Groupe ARN, Département de biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1H 5N4 Canada
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33
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Nakano SI, Oka H, Uotani Y, Uenishi K, Fujii M, Sugimoto N. Dynamics and Energetics of the Base Flipping Conformation Studied with Base Pair-Mimic Nucleosides. Biochemistry 2009; 48:11304-11. [DOI: 10.1021/bi901496q] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Shu-ichi Nakano
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST)
- Frontier Institute for Biomolecular Engineering Research (FIBER)
| | - Hirohito Oka
- Department of Chemistry, Faculty of Science and Engineering
| | - Yuuki Uotani
- Department of Chemistry, Faculty of Science and Engineering
| | | | - Masayuki Fujii
- Molecular Engineering Institute (MEI)
- Department of Environmental and Biological Chemistry
| | - Naoki Sugimoto
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST)
- Frontier Institute for Biomolecular Engineering Research (FIBER)
- Department of Chemistry, Faculty of Science and Engineering
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34
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The structure and function of catalytic RNAs. ACTA ACUST UNITED AC 2009; 52:232-44. [DOI: 10.1007/s11427-009-0038-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2008] [Accepted: 12/25/2008] [Indexed: 11/26/2022]
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Walter NG, Perumal S. The Small Ribozymes: Common and Diverse Features Observed through the FRET Lens. SPRINGER SERIES IN BIOPHYSICS 2009; 13:103-127. [PMID: 21796234 DOI: 10.1007/978-3-540-70840-7_5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The hammerhead, hairpin, HDV, VS and glmS ribozymes are the five known, naturally occurring catalytic RNAs classified as the "small ribozymes". They share common reaction chemistry in cleaving their own backbone by phosphodiester transfer, but are diverse in their secondary and tertiary structures, indicating that Nature has found at least five independent solutions to a common chemical task. Fluorescence resonance energy transfer (FRET) has been extensively used to detect conformational changes in these ribozymes and dissect their reaction pathways. Common and diverse features are beginning to emerge that, by extension, highlight general biophysical properties of non-protein coding RNAs.
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Affiliation(s)
- Nils G Walter
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, Ann Arbor, MI 48109
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36
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Smith MD, Mehdizadeh R, Olive JE, Collins RA. The ionic environment determines ribozyme cleavage rate by modulation of nucleobase pK a. RNA (NEW YORK, N.Y.) 2008; 14:1942-9. [PMID: 18697921 PMCID: PMC2525962 DOI: 10.1261/rna.1102308] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2008] [Accepted: 06/02/2008] [Indexed: 05/20/2023]
Abstract
Several small ribozymes employ general acid-base catalysis as a mechanism to enhance site-specific RNA cleavage, even though the functional groups on the ribonucleoside building blocks of RNA have pK (a) values far removed from physiological pH. The rate of the cleavage reaction is strongly affected by the identity of the metal cation present in the reaction solution; however, the mechanism(s) by which different cations contribute to rate enhancement has not been determined. Using the Neurospora VS ribozyme, we provide evidence that different cations confer particular shifts in the apparent pK (a) values of the catalytic nucleobases, which in turn determines the fraction of RNA in the protonation state competent for general acid-base catalysis at a given pH, which determines the observed rate of the cleavage reaction. Despite large differences in observed rates of cleavage in different cations, mathematical models of general acid-base catalysis indicate that k (1), the intrinsic rate of the bond-breaking step, is essentially constant irrespective of the identity of the cation(s) in the reaction solution. Thus, in contrast to models that invoke unique roles for metal ions in ribozyme chemical mechanisms, we find that most, and possibly all, of the ion-specific rate enhancement in the VS ribozyme can be explained solely by the effect of the ions on nucleobase pK (a). The inference that k (1) is essentially constant suggests a resolution of the problem of kinetic ambiguity in favor of a model in which the lower pK (a) is that of the general acid and the higher pK (a) is that of the general base.
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Affiliation(s)
- M Duane Smith
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
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37
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Abstract
[Structure: see text]. Five naturally occurring nucleolytic ribozymes have been identified: the hammerhead, hairpin, glmS, hepatitis delta virus (HDV), and Varkud satellite (VS) ribozymes. All of these RNA enzymes catalyze self-scission of the RNA backbone using a chemical mechanism equivalent to that of RNase A. RNase A uses four basic strategies to promote this reaction: geometric constraints, activation of the nucleophile, transition-state stabilization, and leaving group protonation. In this Account, we discuss the current thinking on how nucleolytic ribozymes harness RNase A's four sources of catalytic power. The geometry of the phosphodiester cleavage reaction constrains the nucleotides flanking the scissile phosphate so that they are unstacked from a canonical A-form helix and thus require alternative stabilization. Crystal structures and mutational analysis reveal that cross-strand base pairing, along with unconventional stacking and tertiary hydrogen-bonding interactions, work to stabilize the splayed conformation in nucleolytic ribozymes. Deprotonation of the 2'-OH nucleophile greatly increases its nucleophilicity in the strand scission reaction. Crystal structures of the hammerhead, hairpin, and glmS ribozymes reveal the N1 of a G residue within hydrogen-bonding distance of the 2'-OH. In each case, this residue has also been shown to be important for catalysis. In the HDV ribozyme, a hydrated magnesium has been implicated as the general base. Catalysis by the VS ribozyme requires both an A and a G, but the precise role of either has not been elucidated. Enzymes can lower the energy of a chemical reaction by binding more tightly to the transition state than to the ground states. Comparison of the hairpin ground- and transition-state mimic structures reveal greater hydrogen bonding to the transition-state mimic structure, suggesting transition-state stabilization as a possible catalytic strategy. However, the hydrogen-bonding pattern in the glmS ribozyme transition-state mimic structure and the ground-state structures are equivalent. Protonation of the 5'-O leaving group by a variety of functional groups can promote the cleavage reaction. In the HDV ribozyme, the general acid is a conserved C residue. In the hairpin ribozyme, a G residue has been implicated in protonation of the leaving group. An A in the hammerhead ribozyme probably plays a similar role. In the glmS ribozyme, an exogenous cofactor may provide the general acid. This diversity is in contrast to the relatively small number of functional groups that serve as a general base, where at least three of the nucleolytic ribozymes may use the N1 of a G.
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Affiliation(s)
- Jesse C. Cochrane
- Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520
| | - Scott A. Strobel
- Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520
- Department of Chemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520
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Jaikaran D, Smith MD, Mehdizadeh R, Olive J, Collins RA. An important role of G638 in the cis-cleavage reaction of the Neurospora VS ribozyme revealed by a novel nucleotide analog incorporation method. RNA (NEW YORK, N.Y.) 2008; 14:938-49. [PMID: 18356538 PMCID: PMC2327350 DOI: 10.1261/rna.936508] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We describe a chemical coupling procedure that allows joining of two RNAs, one of which contains a site-specific base analog substitution, in the absence of divalent ions. This method allows incorporation of nucleotide analogs at specific positions even into large, cis-cleaving ribozymes. Using this method we have studied the effects of substitution of G638 in the cleavage site loop of the VS ribozyme with a variety of purine analogs having different functional groups and pK(a) values. Cleavage rate versus pH profiles combined with kinetic solvent isotope experiments indicate an important role for G638 in proton transfer during the rate-limiting step of the cis-cleavage reaction.
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Affiliation(s)
- Dominic Jaikaran
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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39
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Bouchard P, Lacroix-Labonté J, Desjardins G, Lampron P, Lisi V, Lemieux S, Major F, Legault P. Role of SLV in SLI substrate recognition by the Neurospora VS ribozyme. RNA (NEW YORK, N.Y.) 2008; 14:736-48. [PMID: 18314503 PMCID: PMC2271362 DOI: 10.1261/rna.824308] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Substrate recognition by the VS ribozyme involves a magnesium-dependent loop/loop interaction between the SLI substrate and the SLV hairpin from the catalytic domain. Recent NMR studies of SLV demonstrated that magnesium ions stabilize a U-turn loop structure and trigger a conformational change for the extruded loop residue U700, suggesting a role for U700 in SLI recognition. Here, we kinetically characterized VS ribozyme mutants to evaluate the contribution of U700 and other SLV loop residues to SLI recognition. To help interpret the kinetic data, we structurally characterized the SLV mutants by NMR spectroscopy and generated a three-dimensional model of the SLI/SLV complex by homology modeling with MC-Sym. We demonstrated that the mutation of U700 by A, C, or G does not significantly affect ribozyme activity, whereas deletion of U700 dramatically impairs this activity. The U700 backbone is likely important for SLI recognition, but does not appear to be required for either the structural integrity of the SLV loop or for direct interactions with SLI. Thus, deletion of U700 may affect other aspects of SLI recognition, such as magnesium ion binding and SLV loop dynamics. As part of our NMR studies, we developed a convenient assay based on detection of unusual (31)P and (15)N N7 chemical shifts to probe the formation of U-turn structures in RNAs. Our model of the SLI/SLV complex, which is compatible with biochemical data, leads us to propose novel interactions at the loop I/loop V interface.
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Affiliation(s)
- Patricia Bouchard
- Département de Biochimie, Université de Montréal, Montréal, H3C 3J7 Canada
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40
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Wilson TJ, McLeod AC, Lilley DMJ. A guanine nucleobase important for catalysis by the VS ribozyme. EMBO J 2007; 26:2489-500. [PMID: 17464286 PMCID: PMC1868910 DOI: 10.1038/sj.emboj.7601698] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2006] [Accepted: 04/02/2007] [Indexed: 11/08/2022] Open
Abstract
A guanine (G638) within the substrate loop of the VS ribozyme plays a critical role in the cleavage reaction. Replacement by any other nucleotide results in severe impairment of cleavage, yet folding of the substrate is not perturbed, and the variant substrates bind the ribozyme with similar affinity, acting as competitive inhibitors. Functional group substitution shows that the imino proton on the N1 is critical, suggesting a possible role in general acid-base catalysis, and this in accord with the pH dependence of the reaction rate for the natural and modified substrates. We propose a chemical mechanism for the ribozyme that involves general acid-base catalysis by the combination of the nucleobases of guanine 638 and adenine 756. This is closely similar to the probable mechanism of the hairpin ribozyme, and the active site arrangements for the two ribozymes appear topologically equivalent. This has probably arisen by convergent evolution.
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Affiliation(s)
- Timothy J Wilson
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, UK
| | - Aileen C McLeod
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, UK
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, UK
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK. Tel.: +44 1382 384243; Fax: +44 1382 385893; E-mail:
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41
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Smith MD, Collins RA. Evidence for proton transfer in the rate-limiting step of a fast-cleaving Varkud satellite ribozyme. Proc Natl Acad Sci U S A 2007; 104:5818-23. [PMID: 17389378 PMCID: PMC1851575 DOI: 10.1073/pnas.0608864104] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2006] [Indexed: 11/18/2022] Open
Abstract
A fast-cleaving version of the Varkud satellite ribozyme, called RG, shows an apparent cis-cleavage rate constant of 5 sec(-1), similar to the rates of protein enzymes that catalyze similar reactions. Here, we describe mutational, pH-rate, and kinetic solvent isotope experiments that investigate the identity and rate constant of the rate-limiting step in this reaction. Self-cleavage of RG exhibits a bell-shaped rate vs. pH profile with apparent pK(a)s of 5.8 and 8.3, consistent with the protonation state of two nucleotides being important for the rate of cleavage. Cleavage experiments in heavy water (D(2)O) revealed a kinetic solvent isotope effect consistent with proton transfer in the rate-limiting step. A mutant RNA that disrupts a peripheral loop-loop interaction involved in RNA folding exhibits pH- and D(2)O-independent cleavage approximately 10(3)-fold slower than wild type, suggesting that this mutant is limited by a different step than wild type. Substitution of adenosine 756 in the putative active-site loop with cytosine also decreases the cleavage rate approximately 10(3)-fold, but the A756C mutant retains pH- and D(2)O-sensitivity similar to wild type, consistent with this mutant and wild type being limited by the chemical step of the reaction. These results suggest that the RG ribozyme provides a good experimental system to investigate the nature of fast, rate-limiting steps in a ribozyme cleavage reaction.
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Affiliation(s)
- M. Duane Smith
- Department of Molecular and Medical Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8
| | - Richard A. Collins
- Department of Molecular and Medical Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8
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42
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Kovacheva YS, Tzokov SB, Murray IA, Grasby JA. The role of phosphate groups in the VS ribozyme-substrate interaction. Nucleic Acids Res 2004; 32:6240-50. [PMID: 15576350 PMCID: PMC535666 DOI: 10.1093/nar/gkh957] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The VS ribozyme trans-cleavage substrate interacts with the catalytic RNA via tertiary interactions. To study the role of phosphate groups in the ribozyme-substrate interaction, 18 modified substrates were synthesized, where an epimeric phosphorothioate replaces one of the phosphate diester linkages. Sites in the stem-loop substrate where phosphorothioate substitution impaired reaction cluster in two regions. The first site is the scissile phosphate diester linkage and nucleotides downstream of this and the second site is within the loop region. The addition of manganese ions caused recovery of the rate of reaction for phosphorothioate substitutions between A621 and A622 and U631 and C632, suggesting that these two phosphate groups may serve as ligands for two metal ions. In contrast, significant manganese rescue was not observed for the scissile phosphate diester linkage implying that electrophilic catalysis by metal ions is unlikely to contribute to VS ribozyme catalysis. In addition, an increase in the reaction rate of the unmodified VS ribozyme was observed when a mixture of magnesium and manganese ions acted as the cofactor. One possible explanation for this effect is that the cleavage reaction of the VS ribozyme is rate limited by a metal dependent docking of the substrate on the ribozyme.
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Affiliation(s)
- Yana S Kovacheva
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute, University of Sheffield, Sheffield S3 7HF, UK
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43
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Flinders J, Dieckmann T. The solution structure of the VS ribozyme active site loop reveals a dynamic "hot-spot". J Mol Biol 2004; 341:935-49. [PMID: 15328609 DOI: 10.1016/j.jmb.2004.06.084] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2004] [Revised: 06/14/2004] [Accepted: 06/15/2004] [Indexed: 11/19/2022]
Abstract
The VS ribozyme is the largest ribozyme in its class and is also the least structurally characterized thus far. The current working model of the VS ribozyme locates the active site in stem-loop VI. The solution structure of this active site loop was determined using high resolution NMR spectroscopy. The structure reveals that the ground-state conformation of the active site differs significantly from that determined previously from chemical structure probing and mutational analysis of the ribozyme in its active conformation, which contains several looped out bases. In contrast, the base-pairing scheme found for the isolated loop contains three mismatched base-pairs: an A+-C, a G-U wobble, and a sheared G-A base-pair and no looped out bases. Dynamics observed within the active site loop provide insight into the mechanism by which the RNA can rearrange its secondary structure into an "activated" conformation prior to cleavage. These findings lend support to the idea that RNA secondary structure is more fluid than once believed and that a better understanding of structure and dynamic features of ribozymes is required to unravel the intricacies of their catalytic abilities.
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Affiliation(s)
- Jeremy Flinders
- Department of Chemistry, University of California at Davis, 95616, USA
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44
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Abstract
The VS ribozyme is the largest nucleolytic ribozyme, for which there is no crystal structure to date. The ribozyme consists of five helical sections, organized by two three-way junctions. The global structure has been determined by solution methods, particularly FRET. The substrate stem-loop binds into a cleft formed between two helices, while making a loop-loop contact with another section of the ribozyme. The scissile phosphate makes a close contact with an internal loop (the A730 loop), the probable active site of the ribozyme. This loop contains a particularly critical nucleotide A756. Most changes to this nucleotide lead to three-orders of magnitude slower cleavage, and the Watson-Crick edge is especially important. NAIM experiments indicate that a protonated base is required at this position for the ligation reaction. A756 is thus a strong candidate for nucleobase participation in the catalytic chemistry.
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Affiliation(s)
- David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, Department of Biochemistry, The University of Dundee, Dundee DD1 5EH, UK.
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45
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Zamel R, Poon A, Jaikaran D, Andersen A, Olive J, De Abreu D, Collins RA. Exceptionally fast self-cleavage by a Neurospora Varkud satellite ribozyme. Proc Natl Acad Sci U S A 2004; 101:1467-72. [PMID: 14755053 PMCID: PMC341743 DOI: 10.1073/pnas.0305753101] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Most of the small ribozymes, including those that have been investigated as potential therapeutic agents, appear to be rather poor catalysts. These RNAs use an internal phosphoester transfer mechanism to catalyze site-specific RNA cleavage with apparent cleavage rate constants typically <2 min(-1). We have identified variants of one of these, the Neurospora Varkud satellite ribozyme, that self-cleaves with experimentally measured apparent rate constants of up to 10 s(-1) (600 min(-1)), approximately 2 orders of magnitude faster than any previously characterized self-cleaving RNA. We describe structural features of the cleavage site loop and an adjacent helix that affect the apparent rate constants for cleavage and ligation and the equilibrium between them. These data show that the phosphoester transfer ribozymes can catalyze reactions with rate constants much larger than previously appreciated and in the range of those of protein enzymes that perform similar reactions.
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Affiliation(s)
- Ricardo Zamel
- Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
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46
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Lescrinier EMHP, Tessari M, van Kuppeveld FJM, Melchers WJG, Hilbers CW, Heus HA. Structure of the pyrimidine-rich internal loop in the poliovirus 3'-UTR: the importance of maintaining pseudo-2-fold symmetry in RNA helices containing two adjacent non-canonical base-pairs. J Mol Biol 2003; 331:759-69. [PMID: 12909008 DOI: 10.1016/s0022-2836(03)00787-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Formation of non-canonical base-pairs in RNA often plays a very important functional role. In addition they frequently serve as factors in stabilizing the secondary structure elements that provide the frame of large compact RNA structures. Here we describe the structure of an internal loop containing a 5'CU3'/5'UU3' non-canonical tandem base-pair motif, which is conserved within the 3'-UTR of poliovirus-like enteroviruses. Structural details reveal striking regularities of the local helix geometry, resulting from alternating geometrical adjustments, which are important for understanding and predicting stabilities and configurations of tandem non-canonical base-pairs. The C-U and U-U base-pairs severely contract the minor groove of the sugar-phosphate backbone, which might be important for protein recognition or binding to other RNA elements.
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Affiliation(s)
- Eveline M H P Lescrinier
- NSR Center for Molecular Structure, Design and Synthesis, Laboratory of Biophysical Chemistry, University of Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands
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47
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Hoffmann B, Mitchell GT, Gendron P, Major F, Andersen AA, Collins RA, Legault P. NMR structure of the active conformation of the Varkud satellite ribozyme cleavage site. Proc Natl Acad Sci U S A 2003; 100:7003-8. [PMID: 12782785 PMCID: PMC165820 DOI: 10.1073/pnas.0832440100] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2003] [Indexed: 11/18/2022] Open
Abstract
Substrate cleavage by the Neurospora Varkud satellite (VS) ribozyme involves a structural change in the stem-loop I substrate from an inactive to an active conformation. We have determined the NMR solution structure of a mutant stem-loop I that mimics the active conformation of the cleavage site internal loop. This structure shares many similarities, but also significant differences, with the previously determined structures of the inactive internal loop. The active internal loop displays different base-pairing interactions and forms a novel RNA fold composed exclusively of sheared G-A base pairs. From chemical-shift mapping we identified two Mg2+ binding sites in the active internal loop. One of the Mg2+ binding sites forms in the active but not the inactive conformation of the internal loop and is likely important for catalysis. Using the structure comparison program mc-search, we identified the active internal loop fold in other RNA structures. In Thermus thermophilus 16S rRNA, this RNA fold is directly involved in a long-range tertiary interaction. An analogous tertiary interaction may form between the active internal loop of the substrate and the catalytic domain of the VS ribozyme. The combination of NMR and bioinformatic approaches presented here has identified a novel RNA fold and provides insights into the structural basis of catalytic function in the Neurospora VS ribozyme.
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Affiliation(s)
- Bernd Hoffmann
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
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48
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Puerta-Fernández E, Romero-López C, Barroso-delJesus A, Berzal-Herranz A. Ribozymes: recent advances in the development of RNA tools. FEMS Microbiol Rev 2003; 27:75-97. [PMID: 12697343 DOI: 10.1016/s0168-6445(03)00020-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The discovery 20 years ago that some RNA molecules, called ribozymes, are able to catalyze chemical reactions was a breakthrough in biology. Over the last two decades numerous natural RNA motifs endowed with catalytic activity have been described. They all fit within a few well-defined types that respond to a specific RNA structure. The prototype catalytic domain of each one has been engineered to generate trans-acting ribozymes that catalyze the site-specific cleavage of other RNA molecules. On the 20th anniversary of ribozyme discovery we briefly summarize the main features of the different natural catalytic RNAs. We also describe progress towards developing strategies to ensure an efficient ribozyme-based technology, dedicating special attention to the ones aimed to achieve a new generation of therapeutic agents.
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Affiliation(s)
- Elena Puerta-Fernández
- Instituto de Parasitología y Biomedicina López-Neyra, CSIC, Ventanilla 11, 18001 Granada, Spain
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49
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Zamel R, Collins RA. Rearrangement of substrate secondary structure facilitates binding to the Neurospora VS ribozyme. J Mol Biol 2002; 324:903-15. [PMID: 12470948 DOI: 10.1016/s0022-2836(02)01151-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The Neurospora VS ribozyme differs from other small, naturally occurring ribozymes in that it recognizes for trans cleavage or ligation a substrate that consists largely of a stem-loop structure. We have previously found that cleavage or ligation by the VS ribozyme requires substantial rearrangement of the secondary structure of stem-loop I, which contains the cleavage/ligation site. This rearrangement includes breaking the top base-pair of stem-loop I, allowing formation of a kissing interaction with loop V, and changing the partners of at least three other base-pairs within stem-loop I to adopt a conformation termed shifted. In the work presented, we have designed a binding assay and used mutational analysis to investigate the contribution of each of these structural changes to binding and ligation. We find that the loop I-V kissing interaction is necessary but not sufficient for binding and ligation. Constitutive opening of the top base-pair of stem-loop I has little, if any, effect on either activity. In contrast, the ability to adopt the shifted conformation of stem-loop I is a major determinant of binding: mutants that cannot adopt this conformation bind much more weakly than wild-type and mutants with a constitutively shifted stem-loop I bind much more strongly. These results implicate the adoption of the shifted structure of stem-loop I as an important process at the binding step in the VS ribozyme reaction pathway. Further investigation of features near the cleavage/ligation site revealed that sulphur substitution of the non-bridging phosphate oxygen atoms immediately downstream of the cleavage/ligation site, implicated in a putative metal ion binding site, significantly altered the cleavage/ligation equilibrium but did not perturb substrate binding significantly. This indicates that the substituted oxygen atoms, or an associated metal ion, affect a step that occurs after binding and that they influence the rates of cleavage and ligation differently.
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Affiliation(s)
- Ricardo Zamel
- Department of Molecular and Medical Genetics #4280, University of Toronto, 1 King's College Circle, M5S 1A8, Toronto, Ont., Canada
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Tzokov SB, Murray IA, Grasby JA. The role of magnesium ions and 2'-hydroxyl groups in the VS ribozyme-substrate interaction. J Mol Biol 2002; 324:215-26. [PMID: 12441101 DOI: 10.1016/s0022-2836(02)01063-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The minimal substrate of the trans-cleaving Neurospora VS ribozyme has a stem-loop structure and interacts with the ribozyme by RNA tertiary interactions that remain only partially defined. The magnesium ion dependence of the catalytic parameters of a trans-cleaving VS-derived ribozyme were studied. The turnover number of the catalytic RNA was found to depend on the binding of at least three magnesium ions, with an apparent magnesium ion dissociation constant of 16mM, but K(M) was observed to be metal ion independent in the millimolar range. To address the role of 2'-hydroxyl groups of the VS substrate RNA in interactions with the ribozyme, 23 altered substrates, each with a single 2'-deoxyribonucleoside substitution, were synthesised and their kinetic properties in the VS ribozyme reaction were analysed. The removal of five 2'-hydroxyl groups, at positions G620, A621, U628, C629 and G630 inhibited the reaction, whereas at two sites, G623 and A639, reaction was stimulated by the modification. Substitution of G620 with a 2'-deoxynucleoside was expected to inhibit the reaction, in line with the critical role of this 2'-hydroxyl group in the transesterification reaction. Altered substrates in which a 2'-O-methyl nucleoside replaced A621, U628, C629 and G630 were prepared and characterised. Although removal of the hydroxyl group of A621 inhibited the turnover number of the ribozyme significantly, this activity was recovered upon 2'-O-methyl adenosine substitution, suggesting that the 2'-oxygen atom of this nucleoside forms an important contact within the ribozyme active site. A cluster of residues within the loop region of the substrate, were more modestly affected by 2'-deoxynucleoside substitution. In two cases, magnesium binding was impaired, suggesting that stem-loop I is a possible magnesium ion binding site.
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Affiliation(s)
- Svetomir B Tzokov
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute, University of Sheffield, Dainton Building, Brook Hill, S3 7HF, Sheffield, UK
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