1
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Ortolá B, Daròs JA. Viroids: Non-Coding Circular RNAs Able to Autonomously Replicate and Infect Higher Plants. BIOLOGY 2023; 12:biology12020172. [PMID: 36829451 PMCID: PMC9952643 DOI: 10.3390/biology12020172] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 01/24/2023]
Abstract
Viroids are a unique type of infectious agent, exclusively composed of a relatively small (246-430 nt), highly base-paired, circular, non-coding RNA. Despite the small size and non-coding nature, the more-than-thirty currently known viroid species infectious of higher plants are able to autonomously replicate and move systemically through the host, thereby inducing disease in some plants. After recalling viroid discovery back in the late 60s and early 70s of last century and discussing current hypotheses about their evolutionary origin, this article reviews our current knowledge about these peculiar infectious agents. We describe the highly base-paired viroid molecules that fold in rod-like or branched structures and viroid taxonomic classification in two families, Pospiviroidae and Avsunviroidae, likely gathering nuclear and chloroplastic viroids, respectively. We review current knowledge about viroid replication through RNA-to-RNA rolling-circle mechanisms in which host factors, notably RNA transporters, RNA polymerases, RNases, and RNA ligases, are involved. Systemic movement through the infected plant, plant-to-plant transmission and host range are also discussed. Finally, we focus on the mechanisms of viroid pathogenesis, in which RNA silencing has acquired remarkable importance, and also for the initiation of potential biotechnological applications of viroid molecules.
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2
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Vicino MF, Wuebben C, Kerzhner M, Famulok M, Schiemann O. Spin Labeling of Long RNAs Via Click Reaction and Enzymatic Ligation. Methods Mol Biol 2022; 2439:205-221. [PMID: 35226324 DOI: 10.1007/978-1-0716-2047-2_14] [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: 06/14/2023]
Abstract
Electron paramagnetic resonance (EPR) is a spectroscopic method for investigating structures, conformational changes, and dynamics of biomacromolecules, for example, oligonucleotides. In order to be applicable, the oligonucleotide has to be labeled site-specifically with paramagnetic tags, the so-called spin labels. Here, we provide a protocol for spin labeling of long oligonucleotides with nitroxides. In the first step, a short and commercially available RNA strand is labeled with a nitroxide via a copper-(I)-catalyzed azide-alkyne cycloaddition (CuAAC), also referred to as "click" reaction. In the second step, the labeled RNA strand is fused to another RNA sequence by means of enzymatic ligation to obtain the labeled full-length construct. The protocol is robust and has been shown experimentally to deliver high yields for RNA sequences up to 81 nucleotides, but longer strands are in principle also feasible. Moreover, it sets the path to label, for example, long riboswitches, ribozymes, and DNAzymes for coarse-grained structure determination and enables to investigate mechanistical features of these systems.
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Affiliation(s)
- Maria Francesca Vicino
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich Wilhelms University, Bonn, Germany
| | - Christine Wuebben
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich Wilhelms University, Bonn, Germany
| | - Mark Kerzhner
- Life & Medical Sciences Institute (LIMES), Chemische Biologie, c/o Kekulé-Institut für organische Chemie, Bonn, Germany
| | - Michael Famulok
- Life & Medical Sciences Institute (LIMES), Chemische Biologie, c/o Kekulé-Institut für organische Chemie, Bonn, Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich Wilhelms University, Bonn, Germany.
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3
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Genome Evolution from Random Ligation of RNAs of Autocatalytic Sets. Int J Mol Sci 2021; 22:ijms222413526. [PMID: 34948321 PMCID: PMC8707343 DOI: 10.3390/ijms222413526] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/08/2021] [Accepted: 12/15/2021] [Indexed: 11/16/2022] Open
Abstract
The evolutionary origin of the genome remains elusive. Here, I hypothesize that its first iteration, the protogenome, was a multi-ribozyme RNA. It evolved, likely within liposomes (the protocells) forming in dry-wet cycling environments, through the random fusion of ribozymes by a ligase and was amplified by a polymerase. The protogenome thereby linked, in one molecule, the information required to seed the protometabolism (a combination of RNA-based autocatalytic sets) in newly forming protocells. If this combination of autocatalytic sets was evolutionarily advantageous, the protogenome would have amplified in a population of multiplying protocells. It likely was a quasispecies with redundant information, e.g., multiple copies of one ribozyme. As such, new functionalities could evolve, including a genetic code. Once one or more components of the protometabolism were templated by the protogenome (e.g., when a ribozyme was replaced by a protein enzyme), and/or addiction modules evolved, the protometabolism became dependent on the protogenome. Along with increasing fidelity of the RNA polymerase, the protogenome could grow, e.g., by incorporating additional ribozyme domains. Finally, the protogenome could have evolved into a DNA genome with increased stability and storage capacity. I will provide suggestions for experiments to test some aspects of this hypothesis, such as evaluating the ability of ribozyme RNA polymerases to generate random ligation products and testing the catalytic activity of linked ribozyme domains.
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Lihanova Y, Weinberg CE. Biochemical analysis of cleavage and ligation activities of the pistol ribozyme from Paenibacillus polymyxa. RNA Biol 2021; 18:1858-1866. [PMID: 33622172 DOI: 10.1080/15476286.2021.1874706] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Nine distinct classes of self-cleaving ribozymes are known to date, of which the pistol ribozyme class was discovered only 5 years ago. Self-cleaving ribozymes are able to cleave their own phosphodiester backbone at a specific site with rates much higher than those of spontaneous RNA degradation. Our study focuses on a bioinformatically predicted pistol ribozyme from the bacterium Paenibacillus polymyxa. We provide a biochemical characterization of this ribozyme, which includes an investigation of the effect of various metal ions on ribozyme cleavage and a kinetic analysis of ribozyme activity under increasing Mg2+ concentrations and pH. Based on the obtained results, we discuss a possible catalytic role of divalent metal ions. Moreover, we investigated the ligation activity of the P. polymyxa pistol ribozyme - an aspect that has not been previously analysed for this ribozyme class. We determined that the P. polymyxa pistol ribozyme is almost fully cleaved at equilibrium with the ligation rate constant being nearly 30-fold lower than the cleavage rate constant. In summary, we have characterized an additional representative of this recently discovered ribozyme class isolated from P. polymyxa. We expect that our biochemical characterization of a pistol representative in a cultivatable, genetically tractable organism will support our future investigation of the biological roles of this ribozyme class in bacteria.
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Affiliation(s)
- Yuliia Lihanova
- Institute for Biochemistry, Leipzig University, Leipzig, Germany
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5
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Cervera A, de la Peña M. Small circRNAs with self-cleaving ribozymes are highly expressed in diverse metazoan transcriptomes. Nucleic Acids Res 2020; 48:5054-5064. [PMID: 32198887 PMCID: PMC7229834 DOI: 10.1093/nar/gkaa187] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 03/09/2020] [Accepted: 03/11/2020] [Indexed: 12/13/2022] Open
Abstract
Ribozymes are catalytic RNAs present in modern genomes but regarded as remnants of a prebiotic RNA world. The paradigmatic hammerhead ribozyme (HHR) is a small self-cleaving motif widespread from bacterial to human genomes. Here, we report that most of the classical type I HHRs frequently found in the genomes of animals are contained within a novel family of non-autonomous non-LTR retrotransposons of the retrozyme class. These retroelements are expressed as abundant linear and circular RNAs of ∼170-400 nt in different animal tissues. Bioinformatic and in vitro analyses indicate an efficient self-cleavage of the HHRs harboured in most invertebrate retrozymes, whereas HHRs in retrozymes of vertebrates, such as the axolotl and other amphibians, require to act as dimeric motifs to reach higher self-cleavage rates. Ligation assays of retrozyme RNAs with a protein ligase versus HHR self-ligation indicate that, most likely, tRNA ligases and not the ribozymes are involved in the step of RNA circularization. Altogether, these results confirm the existence of a new and conserved pathway in animals and, likely, eukaryotes in general, for the efficient biosynthesis of RNA circles through small ribozymes, which opens the door for the development of new tools in the emerging field of study of circRNAs.
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Affiliation(s)
- Amelia Cervera
- IBMCP (CSIC-UPV). C/ Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
| | - Marcos de la Peña
- IBMCP (CSIC-UPV). C/ Ingeniero Fausto Elio s/n, 46022 Valencia, Spain
- To whom correspondence should be addressed. Tel: +34 963 877 915; Fax: +34 963 877 859;
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6
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Abstract
The nucleolytic ribozymes carry out site-specific RNA cleavage reactions by nucleophilic attack of the 2'-oxygen atom on the adjacent phosphorus with an acceleration of a million-fold or greater. A major part of this arises from concerted general acid-base catalysis. Recent identification of new ribozymes has expanded the group to a total of nine and this provides a new opportunity to identify sub-groupings according to the nature of the general base and acid. These include nucleobases, hydrated metal ions, and 2'-hydroxyl groups. Evolution has selected a number of different combinations of these elements that lead to efficient catalysis. These differences provide a new mechanistic basis for classifying these ribozymes.
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Affiliation(s)
- David M.J. Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, UK
- School of Life Sciences, Xiamen University, Xiamen, China
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7
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Maurel MC, Leclerc F, Vergne J, Zaccai G. RNA Back and Forth: Looking through Ribozyme and Viroid Motifs. Viruses 2019; 11:E283. [PMID: 30901893 PMCID: PMC6466107 DOI: 10.3390/v11030283] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 03/14/2019] [Accepted: 03/18/2019] [Indexed: 12/28/2022] Open
Abstract
Current cellular facts allow us to follow the link from chemical to biochemical metabolites, from the ancient to the modern world. In this context, the "RNA world" hypothesis proposes that early in the evolution of life, the ribozyme was responsible for the storage and transfer of genetic information and for the catalysis of biochemical reactions. Accordingly, the hammerhead ribozyme (HHR) and the hairpin ribozyme belong to a family of endonucleolytic RNAs performing self-cleavage that might occur during replication. Furthermore, regarding the widespread occurrence of HHRs in several genomes of modern organisms (from mammals to small parasites and elsewhere), these small ribozymes have been regarded as living fossils of a primitive RNA world. They fold into 3D structures that generally require long-range intramolecular interactions to adopt the catalytically active conformation under specific physicochemical conditions. By studying viroids as plausible remains of ancient RNA, we recently demonstrated that they replicate in non-specific hosts, emphasizing their adaptability to different environments, which enhanced their survival probability over the ages. All these results exemplify ubiquitous features of life. Those are the structural and functional versatility of small RNAs, ribozymes, and viroids, as well as their diversity and adaptability to various extreme conditions. All these traits must have originated in early life to generate novel RNA populations.
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Affiliation(s)
- Marie-Christine Maurel
- Sorbonne Université, Museum National d'Histoire Naturelle, CNRS MNHN UMR 7205, Institut de Systématique, Evolution, Biodiversité, ISYEB, F-75005 Paris, France.
| | - Fabrice Leclerc
- Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Université Paris Sud, F-91198 Gif-sur-Yvette, France.
| | - Jacques Vergne
- Sorbonne Université, Museum National d'Histoire Naturelle, CNRS MNHN UMR 7205, Institut de Systématique, Evolution, Biodiversité, ISYEB, F-75005 Paris, France.
| | - Giuseppe Zaccai
- Institut de Biologie Structurale CNRS-CEA-UGA, F-380447 Grenoble, France, and Institut Laue Langevin, 71 Avenue des Martyrs, F-38042 Grenoble, France.
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8
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O'Rourke SM, Scott WG. Structural Simplicity and Mechanistic Complexity in the Hammerhead Ribozyme. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2018; 159:177-202. [PMID: 30340787 DOI: 10.1016/bs.pmbts.2018.07.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Natural or full-length hammerhead ribozymes are up to 1000-fold more active than their minimal counterparts that lack a complex tertiary interaction that pre-organizes and stabilizes the ribozyme active site, positioning RNA functional groups to facilitate acid-base catalysis. The recent discovery that a single tertiary contact (an AU Hoogsteen pair) between Stems I and II confers essentially all of the enhanced activity greatly simplifies our understanding of the structural requirements for hammerhead ribozyme activity. In contrast, the simplest mechanistic interpretations are challenged with the presentation of more complex alternatives. These alternatives are elucidated and critically analyzed in the context of several of the active hammerhead ribozyme structures now available.
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Affiliation(s)
- Sara M O'Rourke
- The Center for the Molecular Biology of RNA, University of California at Santa Cruz, Santa Cruz, CA, United States
| | - William G Scott
- The Center for the Molecular Biology of RNA, University of California at Santa Cruz, Santa Cruz, CA, United States.
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9
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Cordero T, Ortolá B, Daròs JA. Mutational Analysis of Eggplant Latent Viroid RNA Circularization by the Eggplant tRNA Ligase in Escherichia coli. Front Microbiol 2018; 9:635. [PMID: 29675002 PMCID: PMC5895719 DOI: 10.3389/fmicb.2018.00635] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 03/19/2018] [Indexed: 11/13/2022] Open
Abstract
Eggplant latent viroid (ELVd) is a relatively small non-coding circular RNA that induces asymptomatic infections in eggplants (Solanum melongena L.). Like other viroid species that belong to the family Avsunviroidae, ELVd contains hammerhead ribozymes in the strands of both polarities that self-cleave RNAs producing terminal 5'-hydroxyl and 2',3'-cyclic phosphodiester groups. Available experimental data indicate that ELVd replicates in the chloroplasts of infected cells through a symmetric rolling-circle mechanism, in which RNA circularization is catalyzed by the chloroplastic isoform of the tRNA ligase. In this work, a mutational analysis was performed to gain insight into the sequence and structural requirements of the tRNA ligase-mediated circularization of ELVd RNAs. In the predicted minimum free energy conformation of the monomeric linear ELVd RNA intermediate of plus (+) polarity, the ligation site is located in the lower part of an opened internal loop, which is present in a quasi-rod-like structure that occupies the center of the molecule. The mutations analyzed herein consisted of punctual nucleotide substitutions and deletions surrounding the ligation site on the upper and lower strands of the ELVd quasi-double-stranded structure. Computational predictions of the mutated ELVd conformations indicated different degrees of distortions compared to the minimum free energy conformation of the wild-type ELVd linear monomer of + polarity. When these mutant RNAs were expressed in Escherichia coli, they were all circularized by the eggplant tRNA ligase with approximately the same efficiency as the wild-type ELVd, except for those that directly affected the ribozyme domain. These results suggest that the viroid ribozyme domains, in addition to self-cleavage, are also involved in the tRNA ligase-mediated circularization of the monomeric linear replication intermediates.
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Affiliation(s)
- Teresa Cordero
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas - Universitat Politècnica de València), Valencia, Spain
| | - Beltrán Ortolá
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas - Universitat Politècnica de València), Valencia, Spain
| | - José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas - Universitat Politècnica de València), Valencia, Spain
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10
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Lilley DMJ. How RNA acts as a nuclease: some mechanistic comparisons in the nucleolytic ribozymes. Biochem Soc Trans 2017; 45:683-691. [PMID: 28620029 DOI: 10.1042/bst20160158] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 02/28/2017] [Accepted: 03/02/2017] [Indexed: 02/11/2024]
Abstract
Recent structural and mechanistic studies have shed considerable light on the catalytic mechanisms of nucleolytic ribozymes. The discovery of several new ribozymes in this class has now allowed comparisons to be made, and the beginnings of mechanistic groupings to emerge.
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Affiliation(s)
- David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, U.K.
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11
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Liu Y, Wilson TJ, Lilley DM. The structure of a nucleolytic ribozyme that employs a catalytic metal ion. Nat Chem Biol 2017; 13:508-513. [PMID: 28263963 PMCID: PMC5392355 DOI: 10.1038/nchembio.2333] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 12/21/2016] [Indexed: 01/05/2023]
Abstract
The TS ribozyme (originally called "twister sister") is a catalytic RNA. We present a crystal structure of the ribozyme in a pre-reactive conformation. Two co-axial helical stacks are organized by a three-way junction and two tertiary contacts. Five divalent metal ions are directly coordinated to RNA ligands, making important contributions to the RNA architecture. The scissile phosphate lies in a quasihelical loop region that is organized by a network of hydrogen bonding. A divalent metal ion is directly bound to the nucleobase 5' to the scissile phosphate, with an inner-sphere water molecule positioned to interact with the O2' nucleophile. The rate of ribozyme cleavage correlated in a log-linear manner with divalent metal ion pKa, consistent with proton transfer in the transition state, and we propose that the bound metal ion is a likely general base for the cleavage reaction. Our data indicate that the TS ribozyme functions predominantly as a metalloenzyme.
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Affiliation(s)
- Yijin Liu
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Timothy J. Wilson
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - David M.J. Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, U.K
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12
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de la Peña M, García-Robles I, Cervera A. The Hammerhead Ribozyme: A Long History for a Short RNA. Molecules 2017; 22:molecules22010078. [PMID: 28054987 PMCID: PMC6155905 DOI: 10.3390/molecules22010078] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 12/28/2016] [Accepted: 12/29/2016] [Indexed: 01/22/2023] Open
Abstract
Small nucleolytic ribozymes are a family of naturally occurring RNA motifs that catalyse a self-transesterification reaction in a highly sequence-specific manner. The hammerhead ribozyme was the first reported and the most extensively studied member of this family. However, and despite intense biochemical and structural research for three decades since its discovery, the history of this model ribozyme seems to be far from finished. The hammerhead ribozyme has been regarded as a biological oddity typical of small circular RNA pathogens of plants. More recently, numerous and new variations of this ribozyme have been found to inhabit the genomes of organisms from all life kingdoms, although their precise biological functions are not yet well understood.
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Affiliation(s)
- Marcos de la Peña
- Instituto de Biología Molecular y Celular de Plantas (IBMCP) (CSIC-UPV), C/Ingeniero Fausto Elio s/n, 46022 Valencia, Spain.
| | - Inmaculada García-Robles
- Department of Genetics, University of Valencia, C/Dr. Moliner 50, Burjassot, 46100 Valencia, Spain.
| | - Amelia Cervera
- Instituto de Biología Molecular y Celular de Plantas (IBMCP) (CSIC-UPV), C/Ingeniero Fausto Elio s/n, 46022 Valencia, Spain.
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13
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Daròs JA. Eggplant latent viroid: a friendly experimental system in the family Avsunviroidae. MOLECULAR PLANT PATHOLOGY 2016; 17:1170-7. [PMID: 26696449 PMCID: PMC6638527 DOI: 10.1111/mpp.12358] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 11/24/2015] [Accepted: 12/10/2015] [Indexed: 05/22/2023]
Abstract
TAXONOMY Eggplant latent viroid (ELVd) is the only species of the genus Elaviroid (family Avsunviroidae). All the viroids in the family Avsunviroidae contain hammerhead ribozymes in the strands of both polarities, and are considered to replicate in the chloroplasts of infected cells. This family includes two other genera: Avsunviroid and Pelamoviroid. PHYSICAL PROPERTIES ELVd consists of a single-stranded, circular, non-coding RNA of 332-335 nucleotides that folds in a branched quasi-rod-like minimum free-energy conformation. RNAs of complementary polarity exist in infected cells and are considered to be replication intermediates. Plus (+) polarity is assigned arbitrarily to the strand that accumulates at a higher concentration in infected tissues. HOST: To date, ELVd has only been shown to infect eggplant (Solanum melongena L.), the species in which it was discovered. A very narrow host range seems to be a common property in members of the family Avsunviroidae. SYMPTOMS ELVd infections of eggplants are apparently symptomless. TRANSMISSION ELVd is transmitted mechanically and by seed. USEFUL WEBSITE http://subviral.med.uottawa.ca.
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Affiliation(s)
- José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas - Universidad Politécnica de Valencia), Avenida de los Naranjos s/n, 46022, Valencia, Spain.
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14
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Gourbal B, Théron A, Grunau C, Duval D, Mitta G. Polymorphic Mucin-Like Proteins in Schistosoma mansoni, a Variable Antigen and a Key Component of the Compatibility Between the Schistosome and Its Snail Host. Results Probl Cell Differ 2016; 57:91-108. [PMID: 26537378 DOI: 10.1007/978-3-319-20819-0_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The arms race between vertebrate hosts and parasites has led to diversification systems able to generate huge repertoires of immune recognition receptors and antigenic variants. Until recently, the invertebrate immunity was considered to be poorly specific, and consequently, antigenic variability was not expected to be high for their respective parasites. In the present chapter, we show how the study of the interaction between the snail Biomphalaria glabrata and its parasite Schistosome mansoni has shaken this paradigm. We show that the fate of the interaction between the snail and its parasite is at least partly the result of the concordance of highly variable repertoires of immune recognition receptors in the snail and corresponding antigenic variants in the parasite. We call these antigenic variants of the schistosome Schistosoma mansoni polymorphic mucins (SmPoMucs). We show that their high level of diversification is the result of a complex cascade of mechanisms, thus presenting evidence for antigenic variation in a parasite infecting an invertebrate species.
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Affiliation(s)
- Benjamin Gourbal
- CNRS, Ecologie et Evolution des Interactions, UMR 5244, Université de Perpignan Via Domitia, 58 avenue Paul Alduy, Perpignan, 66860, France.
| | - André Théron
- CNRS, Ecologie et Evolution des Interactions, UMR 5244, Université de Perpignan Via Domitia, 58 avenue Paul Alduy, Perpignan, 66860, France.
| | - Christoph Grunau
- CNRS, Ecologie et Evolution des Interactions, UMR 5244, Université de Perpignan Via Domitia, 58 avenue Paul Alduy, Perpignan, 66860, France.
| | - David Duval
- CNRS, Ecologie et Evolution des Interactions, UMR 5244, Université de Perpignan Via Domitia, 58 avenue Paul Alduy, Perpignan, 66860, France.
| | - Guillaume Mitta
- CNRS, Ecologie et Evolution des Interactions, UMR 5244, Université de Perpignan Via Domitia, 58 avenue Paul Alduy, Perpignan, 66860, France.
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15
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Ligation of RNA Oligomers by the Schistosoma mansoni Hammerhead Ribozyme in Frozen Solution. J Mol Evol 2016; 82:81-92. [PMID: 26897022 DOI: 10.1007/s00239-016-9729-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 02/10/2016] [Indexed: 01/29/2023]
Abstract
The interstitial liquid phase within frozen aqueous solutions is an environment that minimizes RNA degradation and facilitates reactions that may have relevance to the RNA World hypothesis. Previous work has shown that frozen solutions support condensation of activated nucleotides into RNA oligomers, RNA ligation by the hairpin ribozyme, and RNA synthesis by a RNA polymerase ribozyme. In the current study, we examined the activity of a hammerhead ribozyme (HHR) in frozen solution. The Schistosoma mansoni hammerhead ribozyme, which predominantly cleaves RNA, can ligate its cleaved products (P1 and P2) with yields up to ~23 % in single turnover experiments at 25 °C in the presence of Mg(2+). Our studies show that this HHR ligates RNA oligomers in frozen solution in the absence of divalent cations. Citrate and other anions that exhibit strong ion-water affinity enhanced ligation. Yields up to 43 % were observed in one freeze-thaw cycle and a maximum of 60 % was obtained after several freeze-thaw cycles using wild-type P1 and P2. Truncated and mutated P1 substrates were ligated to P2 with yields of 14-24 % in one freeze-thaw cycle. A pool of P2 substrates with mixtures of all four bases at five positions were ligated with P1 in frozen solution. High-throughput sequencing indicated that 70 of the 1024 possible P2 sequences were represented in ligated products at 1000 or more read counts per million reads. The results indicate that the HHR can ligate a range of short RNA oligomers into an ensemble of diverse sequences in ice.
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16
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Scott WG, Horan LH, Martick M. The hammerhead ribozyme: structure, catalysis, and gene regulation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 120:1-23. [PMID: 24156940 DOI: 10.1016/b978-0-12-381286-5.00001-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The hammerhead ribozyme has long been considered a prototype for understanding RNA catalysis, but discrepancies between the earlier crystal structures of a minimal hammerhead self-cleaving motif and various biochemical investigations frustrated attempt to understand hammerhead ribozyme catalysis in terms of structure. With the discovery that a tertiary contact distal from the ribozyme's active site greatly enhances its catalytic prowess, and the emergence of new corresponding crystal structures of full-length hammerhead ribozymes, a unified understanding of catalysis in terms of the structure is now possible. A mechanism in which the invariant residue G12 functions as a general base, and the 2'-OH moiety of the invariant G8, itself forming a tertiary base pair with the invariant C3, is the general acid, appears consistent with both the crystal structure and biochemical experimental results. Originally discovered in the context of plant satellite RNA viruses, the hammerhead more recently has been found embedded in the 3'-untranslated region of mature mammalian mRNAs, suggesting additional biological roles in genetic regulation.
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Affiliation(s)
- William G Scott
- The Center for the Molecular Biology of RNA, Sinsheimer Laboratories, University of California at Santa Cruz, Santa Cruz, California, USA
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Lee TS, Wong KY, Giambasu GM, York DM. Bridging the gap between theory and experiment to derive a detailed understanding of hammerhead ribozyme catalysis. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 120:25-91. [PMID: 24156941 PMCID: PMC4747252 DOI: 10.1016/b978-0-12-381286-5.00002-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Herein we summarize our progress toward the understanding of hammerhead ribozyme (HHR) catalysis through a multiscale simulation strategy. Simulation results collectively paint a picture of HHR catalysis: HHR first folds to form an electronegative active site pocket to recruit a threshold occupation of cationic charges, either a Mg(2+) ion or multiple monovalent cations. Catalytically active conformations that have good in-line fitness are supported by specific metal ion coordination patterns that involve either a bridging Mg(2+) ion or multiple Na(+) ions, one of which is also in a bridging coordination pattern. In the case of a single Mg(2+) ion bound in the active site, the Mg(2+) ion undergoes a migration that is coupled with deprotonation of the nucleophile (C17:O2'). As the reaction proceeds, the Mg(2+) ion stabilizes the accumulating charge of the leaving group and significantly increases the general acid ability of G8:O2'. Further computational mutagenesis simulations suggest that the disruptions due to mutations may severely impact HHR catalysis at different stages of the reaction. Catalytic mechanisms supported by the simulation results are consistent with available structural and biochemical experiments, and together they advance our understanding of HHR catalysis.
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Affiliation(s)
- Tai-Sung Lee
- Center for Integrative Proteomics Research and BioMaPS Institute for Quantitative Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA,Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Kin-Yiu Wong
- Center for Integrative Proteomics Research and BioMaPS Institute for Quantitative Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA,Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - George M. Giambasu
- Center for Integrative Proteomics Research and BioMaPS Institute for Quantitative Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA,Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Darrin M. York
- Center for Integrative Proteomics Research and BioMaPS Institute for Quantitative Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA,Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
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Kennedy AB, Liang JC, Smolke CD. A versatile cis-blocking and trans-activation strategy for ribozyme characterization. Nucleic Acids Res 2012; 41:e41. [PMID: 23155065 PMCID: PMC3553993 DOI: 10.1093/nar/gks1036] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Synthetic RNA control devices that use ribozymes as gene-regulatory components have been applied to controlling cellular behaviors in response to environmental signals. Quantitative measurement of the in vitro cleavage rate constants associated with ribozyme-based devices is essential for advancing the molecular design and optimization of this class of gene-regulatory devices. One of the key challenges encountered in ribozyme characterization is the efficient generation of full-length RNA from in vitro transcription reactions, where conditions generally lead to significant ribozyme cleavage. Current methods for generating full-length ribozyme-encoding RNA rely on a trans-blocking strategy, which requires a laborious gel separation and extraction step. Here, we develop a simple two-step gel-free process including cis-blocking and trans-activation steps to support scalable generation of functional full-length ribozyme-encoding RNA. We demonstrate our strategy on various types of natural ribozymes and synthetic ribozyme devices, and the cleavage rate constants obtained for the RNA generated from our strategy are comparable with those generated through traditional methods. We further develop a rapid, label-free ribozyme cleavage assay based on surface plasmon resonance, which allows continuous, real-time monitoring of ribozyme cleavage. The surface plasmon resonance-based characterization assay will complement the versatile cis-blocking and trans-activation strategy to broadly advance our ability to characterize and engineer ribozyme-based devices.
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Affiliation(s)
- Andrew B. Kennedy
- Department of Bioengineering, Stanford University, 473 Via Ortega, MC 4201, Stanford, CA 94305 and Division of Chemistry and Chemical Engineering, 1200 E. California Blvd., MC 210-41, California Institute of Technology, Pasadena, CA 91125, USA
| | - Joe C. Liang
- Department of Bioengineering, Stanford University, 473 Via Ortega, MC 4201, Stanford, CA 94305 and Division of Chemistry and Chemical Engineering, 1200 E. California Blvd., MC 210-41, California Institute of Technology, Pasadena, CA 91125, USA
| | - Christina D. Smolke
- Department of Bioengineering, Stanford University, 473 Via Ortega, MC 4201, Stanford, CA 94305 and Division of Chemistry and Chemical Engineering, 1200 E. California Blvd., MC 210-41, California Institute of Technology, Pasadena, CA 91125, USA
- *To whom correspondence should be addressed. Tel: +1 650 721 6371; Fax: +1 650 721 6602;
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Nohales MÁ, Molina-Serrano D, Flores R, Daròs JA. Involvement of the chloroplastic isoform of tRNA ligase in the replication of viroids belonging to the family Avsunviroidae. J Virol 2012; 86:8269-76. [PMID: 22623792 PMCID: PMC3421689 DOI: 10.1128/jvi.00629-12] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 05/15/2012] [Indexed: 11/20/2022] Open
Abstract
Avocado sunblotch viroid, peach latent mosaic viroid, chrysanthemum chlorotic mottle viroid, and eggplant latent viroid (ELVd), the four recognized members of the family Avsunviroidae, replicate through the symmetric pathway of an RNA-to-RNA rolling-circle mechanism in chloroplasts of infected cells. Viroid oligomeric transcripts of both polarities contain embedded hammerhead ribozymes that, during replication, mediate their self-cleavage to monomeric-length RNAs with 5'-hydroxyl and 2',3'-phosphodiester termini that are subsequently circularized. We report that a recombinant version of the chloroplastic isoform of the tRNA ligase from eggplant (Solanum melongena L.) efficiently catalyzes in vitro circularization of the plus [(+)] and minus [(-)] monomeric linear replication intermediates from the four Avsunviroidae. We also show that while this RNA ligase specifically recognizes the genuine monomeric linear (+) ELVd replication intermediate, it does not do so with five other monomeric linear (+) ELVd RNAs with their ends mapping at different sites along the molecule, despite containing the same 5'-hydroxyl and 2',3'-phosphodiester terminal groups. Moreover, experiments involving transient expression of a dimeric (+) ELVd transcript in Nicotiana benthamiana Domin plants preinoculated with a tobacco rattle virus-derived vector to induce silencing of the plant endogenous tRNA ligase show a significant reduction of ELVd circularization. In contrast, circularization of a viroid replicating in the nucleus occurring through a different pathway is unaffected. Together, these results support the conclusion that the chloroplastic isoform of the plant tRNA ligase is the host enzyme mediating circularization of both (+) and (-) monomeric linear intermediates during replication of the viroids belonging to the family Avsunviroidae.
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Affiliation(s)
- María-Ángeles Nohales
- Instituto de Biología Molecular y Celular de Plantas (Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia), Valencia, Spain
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Kaddour H, Vergne J, Hervé G, Maurel MC. High-pressure analysis of a hammerhead ribozyme from Chrysanthemum chlorotic mottle viroid reveals two different populations of self-cleaving molecule. FEBS J 2011; 278:3739-47. [PMID: 21824288 DOI: 10.1111/j.1742-4658.2011.08291.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The activity of the full-length hammerhead ribozyme requires a tertiary interaction between its distal loops leading to the closure of the molecule and its stabilization in the active conformation. In this study, the conformational changes accompanying the cis-cleavage reaction of Chrysanthemum chlorotic mottle viroid hammerhead ribozyme were investigated by high-pressure experiments on the complete cleavage reaction. Two activation volumes (ΔV(≠)) were measured, pointing to the presence of two different populations of molecules corresponding to fast-cleaving and slow-cleaving ribozymes in the reaction mixture. The fast population, with a small ΔV(≠) of 2.6 mL·mol(-1), most likely represents molecules in the near-active conformation, whereas the slow population, with a larger ΔV(≠) of 11.6 mL·mol(-1 , represents molecules that need a larger conformational change to induce activity. In addition, pH-dependence experiments suggest that the group whose deprotonation is required for activity intervenes in the formation of the transition state or in the chemistry of the reaction, but not in the conformational change that precedes it.
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Affiliation(s)
- Hussein Kaddour
- Acides Nucléiques et Biophotonique, CNRS FRE 3207, UPMC Université Paris 06, France
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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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Jimenez RM, Delwart E, Lupták A. Structure-based search reveals hammerhead ribozymes in the human microbiome. J Biol Chem 2011; 286:7737-7743. [PMID: 21257745 DOI: 10.1074/jbc.c110.209288] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Deep sequencing of viral or bacterial nucleic acids monitors the presence and diversity of microbes in select populations and locations. Metagenomic study of mammalian viromes can help trace paths of viral transmissions within or between species. High throughput sequencing of patient and untreated sewage microbiomes showed many sequences with no similarity to genomic sequences of known function or origin. To estimate the distribution of functional RNAs in these microbiomes, we used the hammerhead ribozyme (HHR) motif to search for sequences capable of assuming its three-way junction fold. Although only two of the three possible natural HHR topologies had been known, our analysis revealed highly active ribozymes that terminated in any of the three stems. The most abundant of these are type II HHRs, one of which is the fastest natural cis-acting HHR yet discovered. Altogether, 13 ribozymes were confirmed in vitro, but only one showed sequence similarity to previously described HHRs. Sequences surrounding the ribozymes do not generally show similarity to known genes, except in one case, where a ribozyme is immediately preceded by a bacterial RadC gene. We demonstrate that a structure-based search for a known functional RNA is a powerful tool for analysis of metagenomic datasets, complementing sequence alignments.
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Affiliation(s)
| | - Eric Delwart
- the Blood Systems Research Institute and; Department of Laboratory Medicine, University of California, San Francisco, California 94118
| | - Andrej Lupták
- From the Departments of Pharmaceutical Sciences,; Chemistry, and; Molecular Biology and Biochemistry, University of California, Irvine, California 92697 and.
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Lee TS, York DM. Computational mutagenesis studies of hammerhead ribozyme catalysis. J Am Chem Soc 2010; 132:13505-18. [PMID: 20812715 DOI: 10.1021/ja105956u] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Computational studies of the mutational effects at the C3, G8, and G5 positions of the hammerhead ribozyme (HHR) are reported, based on a series of twenty-four 100-ns molecular dynamics simulations of the native and mutated HHR in the reactant state and in an activated precursor state (G8:2'OH deprotonated). Invoking the assumptions that G12 acts as the general base while the 2'OH of G8 acts as a general acid, the simulations are able to explain the origins of experimentally observed mutational effects, including several that are not easily inferred from the crystal structure. Simulations suggest that the Watson-Crick base-pairing between G8 and C3, the hydrogen bond network between C17 and G5, and the base stacking interactions between G8 and C1.1, collectively, are key to maintaining an active site structure conducive for catalytic activity. Mutation-induced disruption of any of these interactions will adversely affect activity. The simulation results predict that the C3U/G8D double mutant, where D is 2,6-diaminopurine, will have a rescue effect relative to the corresponding single mutations. Two general conclusions about the simulations emerge from this work. First, mutation simulations may require 30 ns or more to suitably relax such that the mutational effects become apparent. Second, in some cases, it is necessary to look beyond the reactant state in order to interpret mutational effects in terms of catalytically active structure. The present simulation results lead to better understanding of the origin of experimental mutational effects and provide insight into the key conserved features necessary to maintain the integrity of the active site architecture.
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Affiliation(s)
- Tai-Sung Lee
- BioMaPS Institute for Quantitative Biology and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA
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Abstract
The hammerhead, hairpin, hepatitis delta virus (HDV), Varkud Satellite (VS), and glmS ribozymes catalyze sequence-specific intramolecular cleavage of RNA. They range between 50 and 150 nucleotides in length, and are known as the "small self-cleaving ribozymes." Except for the glmS ribozyme that functions as a riboswitch in Gram-positive bacteria, they were originally discovered as domains of satellite RNAs. However, recent studies show that several of them are broadly distributed in genomes of organisms from many phyla. Each of these ribozymes has a unique overall architecture and active site organization. Crystal structures have revealed how RNA active sites can bind preferentially to the transition state of a reaction, whereas mechanistic studies have shown that nucleobases can efficiently perform general acid-base and electrostatic catalysis. This versatility explains the abundance of ribozymes in contemporary organisms and also supports a role for catalytic RNAs early in evolution.
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Affiliation(s)
- Adrian R Ferré-D'Amaré
- Howard Hughes Medical Institute and Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 8109-1024, USA.
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Shepotinovskaya I, Uhlenbeck OC. Enhanced product stability in the hammerhead ribozyme. Biochemistry 2010; 49:4494-500. [PMID: 20423112 DOI: 10.1021/bi902025m] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The rate of dissociation of P1, the 5' product of hammerhead cleavage, is 100-300-fold slower in full-length hammerheads than in hammerheads that either lack or have disrupting mutations in the loop-loop tertiary interaction. The added stability requires the presence of residue 17 at the 3' terminus of P1 but not the 2', 3' terminal phosphate. Since residue 17 is buried within the catalytic core of the hammerhead in the X-ray structure, we propose that the enhanced P1 stability is a result of the cooperative folding of the hammerhead around this residue. However, since P1 is fully stabilized at >2.5 mM MgCl(2) while hammerhead activity continues to increase with an increase in MgCl(2) concentration, it is clear that the hammerhead structure in the transition state must differ from that of the product complex. The product stabilization assay is used to test our earlier proposal that different tertiary interactions modulate the cleavage rate by differentially stabilizing the core.
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Affiliation(s)
- Irina Shepotinovskaya
- Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, Evanston, Illinois 60208, USA
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Martinsen L, Johnsen A, Venanzetti F, Bachmann L. Phylogenetic footprinting of non-coding RNA: hammerhead ribozyme sequences in a satellite DNA family of Dolichopoda cave crickets (Orthoptera, Rhaphidophoridae). BMC Evol Biol 2010; 10:3. [PMID: 20047671 PMCID: PMC2837043 DOI: 10.1186/1471-2148-10-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2009] [Accepted: 01/04/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The great variety in sequence, length, complexity, and abundance of satellite DNA has made it difficult to ascribe any function to this genome component. Recent studies have shown that satellite DNA can be transcribed and be involved in regulation of chromatin structure and gene expression. Some satellite DNAs, such as the pDo500 sequence family in Dolichopoda cave crickets, have a catalytic hammerhead (HH) ribozyme structure and activity embedded within each repeat. RESULTS We assessed the phylogenetic footprints of the HH ribozyme within the pDo500 sequences from 38 different populations representing 12 species of Dolichopoda. The HH region was significantly more conserved than the non-hammerhead (NHH) region of the pDo500 repeat. In addition, stems were more conserved than loops. In stems, several compensatory mutations were detected that maintain base pairing. The core region of the HH ribozyme was affected by very few nucleotide substitutions and the cleavage position was altered only once among 198 sequences. RNA folding of the HH sequences revealed that a potentially active HH ribozyme can be found in most of the Dolichopoda populations and species. CONCLUSIONS The phylogenetic footprints suggest that the HH region of the pDo500 sequence family is selected for function in Dolichopoda cave crickets. However, the functional role of HH ribozymes in eukaryotic organisms is unclear. The possible functions have been related to trans cleavage of an RNA target by a ribonucleoprotein and regulation of gene expression. Whether the HH ribozyme in Dolichopoda is involved in similar functions remains to be investigated. Future studies need to demonstrate how the observed nucleotide changes and evolutionary constraint have affected the catalytic efficiency of the hammerhead.
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Affiliation(s)
- Lene Martinsen
- Natural History Museum, Department for Research and Collections, University of Oslo, 0318 Oslo, Norway
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Scott WG, Martick M, Chi YI. Structure and function of regulatory RNA elements: ribozymes that regulate gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2009; 1789:634-41. [PMID: 19781673 DOI: 10.1016/j.bbagrm.2009.09.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Revised: 09/01/2009] [Accepted: 09/13/2009] [Indexed: 01/14/2023]
Abstract
Since their discovery in the 1980s, it has gradually become apparent that there are several functional classes of naturally occurring ribozymes. These include ribozymes that mediate RNA splicing (the Group I and Group II introns, and possibly the RNA components of the spliceosome), RNA processing ribozymes (RNase P, which cleaves precursor tRNAs and other structural RNA precursors), the peptidyl transferase center of the ribosome, and small, self-cleaving genomic ribozymes (including the hammerhead, hairpin, HDV and VS ribozymes). The most recently discovered functional class of ribozymes include those that are embedded in the untranslated regions of mature mRNAs that regulate the gene's translational expression. These include the prokaryotic glmS ribozyme, a bacterial riboswitch, and a variant of the hammerhead ribozyme, which has been found embedded in mammalian mRNAs. With the discovery of a mammalian riboswitch ribozyme, the question of how an embedded hammerhead ribozyme's switching mechanism works becomes a compelling question. Recent structural results suggest several possibilities.
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Affiliation(s)
- William G Scott
- Center for the Molecular Biology of RNA, Sinsheimer Laboratory, University of California at Santa Cruz, Santa Cruz, CA, USA.
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28
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Martínez F, Marqués J, Salvador ML, Daròs JA. Mutational analysis of eggplant latent viroid RNA processing in Chlamydomonas reinhardtii chloroplast. J Gen Virol 2009; 90:3057-3065. [PMID: 19675190 DOI: 10.1099/vir.0.013425-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Viroids of the family Avsunviroidae, such as eggplant latent viroid (ELVd), contain hammerhead ribozymes and replicate in the chloroplasts of the host plant through an RNA-based symmetrical rolling-circle mechanism in which oligomeric RNAs of both polarity are processed to monomeric linear RNAs (by cleavage) and to monomeric circular RNAs (by ligation). Using an experimental system consisting of transplastomic lines of the alga Chlamydomonas reinhardtii, a mutational analysis of sequence and structural elements in the ELVd molecule that are involved in transcript processing in vivo in a chloroplastic context was carried out. A collection of six insertion and three deletion ELVd mutants was created and expressed in C. reinhardtii chloroplast. All mutants cleaved efficiently except for the control with an insertion inside the hammerhead ribozyme domain, supporting the prediction that this domain is necessary and sufficient to mediate transcript cleavage in vivo. However, two deletion mutants that cleaved efficiently showed ligation defects, indicating that during RNA circularization, other parts of the molecule are involved in addition to the hammerhead ribozyme domain. This is probably a quasi double-stranded structure present in the central part of the molecule which contains the ligation site in an internal loop. However, the mutations prevented the viroid from infecting its natural host, eggplant, indicating that they affected other essential functions in ELVd infectious cycle. The insertion in the terminal loop of the right upper hairpin of ELVd did not have this effect; it was tolerated and partially maintained in the progeny.
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Affiliation(s)
- Fernando Martínez
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Avenida de los Naranjos, 46022 Valencia, Spain
| | - Jorge Marqués
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Avenida de los Naranjos, 46022 Valencia, Spain
| | - María L Salvador
- Departamento de Bioquímica y Biología Molecular, Universitat de València, Avenida Dr Moliner, 46100 Burjassot, Spain
| | - José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Avenida de los Naranjos, 46022 Valencia, Spain
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29
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Abstract
Self-cleaving hammerhead, hairpin, hepatitis delta virus, and glmS ribozymes comprise a family of small catalytic RNA motifs that catalyze the same reversible phosphodiester cleavage reaction, but each motif adopts a unique structure and displays a unique array of biochemical properties. Recent structural, biochemical, and biophysical studies of these self-cleaving RNAs have begun to reveal how active site nucleotides exploit general acid-base catalysis, electrostatic stabilization, substrate destabilization, and positioning and orientation to reduce the free energy barrier to catalysis. Insights into the variety of catalytic strategies available to these model RNA enzymes are likely to have important implications for understanding more complex RNA-catalyzed reactions fundamental to RNA processing and protein synthesis.
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Affiliation(s)
- Martha J Fedor
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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30
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Thomas JM, Perrin DM. Probing general acid catalysis in the hammerhead ribozyme. J Am Chem Soc 2009; 131:1135-43. [PMID: 19154176 DOI: 10.1021/ja807790e] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recent crystallographic and computational studies have provided fresh insights into the catalytic mechanism of the RNA-cleaving hammerhead ribozyme. Based on these findings, specific ribozyme functional groups have been hypothesized to act directly as the general acid and base catalysts, although the catalytic role of divalent metal cations (M(2+)) remains uncertain. We now report a functional characterization of the general acid catalysis mechanism and the role of an M(2+) cofactor therein, for the S. mansoni hammerhead (an "extended" hammerhead ribozyme). We have compared hammerhead cleavage of substrates with natural (ribo-phosphodiester) versus bridging-5'-phosphorothioate scissile linkages, in the contexts of active site mutations and M(2+) substitution. Cleavage of the natural substrate is inhibited by modification of the G8 2'-OH ribozyme residue and depends strongly upon the presence and identity of an M(2+) cofactor; in contrast, cleavage of the bridging-phosphorothioate substrate is conspicuously insensitive to any of these factors. These results imply that (1) both an M(2+) cofactor and the G8 2'-OH play crucial roles in hammerhead general acid catalysis and (2) the M(2+) cofactor does not contribute to general acid catalysis via Lewis acid stabilization of the leaving group. General acid pK(a) perturbation was also demonstrated for both M(2+) substitution and G8 2'-OH modification, which suggests transition state M(2+) coordination of the G8 2'-OH, to lower its pK(a) and improve its ability to transfer a proton to the leaving group. We also report a simple method for synthesizing radiolabeled bridging-5'-phosphorothioate substrates.
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Affiliation(s)
- Jason M Thomas
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, B.C., Canada, V6T 1Z1
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Roger E, Grunau C, Pierce RJ, Hirai H, Gourbal B, Galinier R, Emans R, Cesari IM, Cosseau C, Mitta G. Controlled chaos of polymorphic mucins in a metazoan parasite (Schistosoma mansoni) interacting with its invertebrate host (Biomphalaria glabrata). PLoS Negl Trop Dis 2008; 2:e330. [PMID: 19002242 PMCID: PMC2576457 DOI: 10.1371/journal.pntd.0000330] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2008] [Accepted: 10/10/2008] [Indexed: 01/21/2023] Open
Abstract
Invertebrates were long thought to possess only a simple, effective and hence non-adaptive defence system against microbial and parasitic attacks. However, recent studies have shown that invertebrate immunity also relies on immune receptors that diversify (e.g. in echinoderms, insects and mollusks (Biomphalaria glabrata)). Apparently, individual or population-based polymorphism-generating mechanisms exists that permit the survival of invertebrate species exposed to parasites. Consequently, the generally accepted arms race hypothesis predicts that molecular diversity and polymorphism also exist in parasites of invertebrates. We investigated the diversity and polymorphism of parasite molecules (Schistosoma mansoni Polymorphic Mucins, SmPoMucs) that are key factors for the compatibility of schistosomes interacting with their host, the mollusc Biomphalaria glabrata. We have elucidated the complex cascade of mechanisms acting both at the genomic level and during expression that confer polymorphism to SmPoMuc. We show that SmPoMuc is coded by a multi-gene family whose members frequently recombine. We show that these genes are transcribed in an individual-specific manner, and that for each gene, multiple splice variants exist. Finally, we reveal the impact of this polymorphism on the SmPoMuc glycosylation status. Our data support the view that S. mansoni has evolved a complex hierarchical system that efficiently generates a high degree of polymorphism—a “controlled chaos”—based on a relatively low number of genes. This contrasts with protozoan parasites that generate antigenic variation from large sets of genes such as Trypanosoma cruzi, Trypanosoma brucei and Plasmodium falciparum. Our data support the view that the interaction between parasites and their invertebrate hosts are far more complex than previously thought. While most studies in this matter have focused on invertebrate host diversification, we clearly show that diversifying mechanisms also exist on the parasite side of the interaction. Our findings shed new light on how and why invertebrate immunity develops. Contrary to the traditional view that immunity in invertebrates is limited to non-specific mechanisms, recent studies have shown that they have diverse, specific immune receptors. An example is provided by the FREPs of the mollusk Biomphalaria glabrata, polymorphic members of the immunoglobulin superfamily. This capacity for an individual or population-based polymorphic immune response raises the question of whether a corresponding polymorphism exists in parasites of invertebrates, as would be expected in an “arms race” between host and parasite. We have indeed identified such polymorphic molecules in Schistosoma mansoni, a flatworm parasite of B. glabrata, by comparing two strains of schistosome that are respectively compatible and incompatible with the same mollusk host strain. However, in contrast to antigenic variation in protozoan parasites that is based on an extensive gene repertoire, we show here that a high level of polymorphism in these S. mansoni polymorphic mucins (SmPoMucs) is generated from a low number of genes by a complex cascade of mechanisms, a “controlled chaos”.
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Affiliation(s)
- Emmanuel Roger
- Parasitologie Fonctionnelle et Evolutive, UMR 5244, CNRS Université de Perpignan, Perpignan, France
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Chi YI, Martick M, Lares M, Kim R, Scott WG, Kim SH. Capturing hammerhead ribozyme structures in action by modulating general base catalysis. PLoS Biol 2008; 6:e234. [PMID: 18834200 PMCID: PMC2553840 DOI: 10.1371/journal.pbio.0060234] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2008] [Accepted: 08/18/2008] [Indexed: 11/19/2022] Open
Abstract
We have obtained precatalytic (enzyme–substrate complex) and postcatalytic (enzyme–product complex) crystal structures of an active full-length hammerhead RNA that cleaves in the crystal. Using the natural satellite tobacco ringspot virus hammerhead RNA sequence, the self-cleavage reaction was modulated by substituting the general base of the ribozyme, G12, with A12, a purine variant with a much lower pKa that does not significantly perturb the ribozyme's atomic structure. The active, but slowly cleaving, ribozyme thus permitted isolation of enzyme–substrate and enzyme–product complexes without modifying the nucleophile or leaving group of the cleavage reaction, nor any other aspect of the substrate. The predissociation enzyme-product complex structure reveals RNA and metal ion interactions potentially relevant to transition-state stabilization that are absent in precatalytic structures. Enzymes use variations of a few standard approaches to catalyze reactions. One of these approaches, acid–base catalysis, is of such fundamental importance that it is common to both protein enzymes and RNA-based enzymes, or ribozymes. The hammerhead ribozyme is one such ribozyme that uses an invariant guanine residue as a general base in its catalytic reaction. By changing this to an adenine, we can slow the reaction rate 100,000-fold, permitting us to capture both active, precatalytic, and postcatalytic forms of the ribozyme. We have exploited this approach to obtain near-atomic–resolution three-dimensional structures of the hammerhead ribozyme both before and after catalytic self-cleavage. These structures provide complementary views of the chemical step of hammerhead ribozyme catalysis. The hammerhead ribozyme exploits acid/base catalysis as an enzymatic mechanism. Weakening the general base, G12, by mutating it into an A, greatly slows the reaction. As a result, the before and after cleavage structures could be captured in a crystal lattice.
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Affiliation(s)
- Young-In Chi
- Center for Structural Biology, Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
- * To whom correspondence should be addressed. E-mail: (Y-IC); (WGS); (SHK)
| | - Monika Martick
- Center for the Molecular Biology of RNA, Sinsheimer Laboratory, University of California at Santa Cruz, Santa Cruz, California, United States of America
| | - Monica Lares
- Center for the Molecular Biology of RNA, Sinsheimer Laboratory, University of California at Santa Cruz, Santa Cruz, California, United States of America
| | - Rosalind Kim
- Department of Chemistry, University of California, Berkeley, Berkeley, California, United States of America
| | - William G Scott
- Center for the Molecular Biology of RNA, Sinsheimer Laboratory, University of California at Santa Cruz, Santa Cruz, California, United States of America
- * To whom correspondence should be addressed. E-mail: (Y-IC); (WGS); (SHK)
| | - Sung-Hou Kim
- Department of Chemistry, University of California, Berkeley, Berkeley, California, United States of America
- * To whom correspondence should be addressed. E-mail: (Y-IC); (WGS); (SHK)
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Boots JL, Canny MD, Azimi E, Pardi A. Metal ion specificities for folding and cleavage activity in the Schistosoma hammerhead ribozyme. RNA (NEW YORK, N.Y.) 2008; 14:2212-22. [PMID: 18755844 PMCID: PMC2553736 DOI: 10.1261/rna.1010808] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Accepted: 07/02/2008] [Indexed: 05/20/2023]
Abstract
The effects of various metal ions on cleavage activity and global folding have been studied in the extended Schistosoma hammerhead ribozyme. Fluorescence resonance energy transfer was used to probe global folding as a function of various monovalent and divalent metal ions in this ribozyme. The divalent metals ions Ca(2+), Mg(2+), Mn(2+), and Sr(2+) have a relatively small variation (less than sixfold) in their ability to globally fold the hammerhead ribozyme, which contrasts with the very large difference (>10,000-fold) in apparent rate constants for cleavage for these divalent metal ions in single-turnover kinetic experiments. There is still a very large range (>4600-fold) in the apparent rate constants for cleavage for these divalent metal ions measured in high salt (2 M NaCl) conditions where the ribozyme is globally folded. These results demonstrate that the identity of the divalent metal ion has little effect on global folding of the Schistosoma hammerhead ribozyme, whereas it has a very large effect on the cleavage kinetics. Mechanisms by which the identity of the divalent metal ion can have such a large effect on cleavage activity in the Schistosoma hammerhead ribozyme are discussed.
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Affiliation(s)
- Jennifer L Boots
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309-0215, USA
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Shepotinovskaya IV, Uhlenbeck OC. Catalytic diversity of extended hammerhead ribozymes. Biochemistry 2008; 47:7034-42. [PMID: 18543946 DOI: 10.1021/bi7025358] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chimeras of the well-characterized minimal hammerhead 16 and nine extended hammerheads derived from natural viroids and satellite RNAs were constructed with the goal of assessing whether their very different peripheral tertiary interactions modulate their catalytic properties. For each chimera, three different assays were used to determine the rate of cleavage and the fraction of full-length hammerhead at equilibrium and thereby deduce the elemental cleavage ( k 2) and ligation ( k -2) rate constants. The nine chimeras were all more active than minimal hammerheads and exhibited a very broad range of catalytic properties, with values of k 2 varying by 750-fold and k -2 by 100-fold. At least two of the hammerheads exhibited an altered dependence of k obs on magnesium concentration. Since much less catalytic diversity is observed among minimal hammerheads that lack the tertiary interactions, a possible role for the different tertiary interaction is to modulate the hammerhead cleavage properties in viroids. For example, differing hammerhead cleavage and ligation rates could affect the steady state concentrations of linear, circular, and polymeric genomes in infected cells.
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Affiliation(s)
- Irina V Shepotinovskaya
- Department of Biochemistry, Molecular Biology, and Cellular Biology, Northwestern University, 2205 Tech Drive, Hogan 2-100, Evanston, Illinois 60208, USA
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Kisseleva N, Khvorova A, Westhof E, Schiemann O, Wolfson AD. The Different Role of High-Affinity and Low-Affinity Metal Ions in Cleavage by a Tertiary Stabilized Cis Hammerhead Ribozyme from Tobacco Ringspot Virus. Oligonucleotides 2008. [DOI: 10.1089/oli.2008.0129] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Natalia Kisseleva
- Institute of Physical and Theoretical Chemistry, Center of Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | | | - Eric Westhof
- Institut de Biologie Moléculaire et Cellulaire, Université Louis Pasteur, Strasbourg Cedex, France
| | - Olav Schiemann
- Centre for Biomolecular Sciences, University of St Andrews, St Andrews, UK
| | - Alexey D. Wolfson
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO
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Nelson JA, Uhlenbeck OC. Hammerhead redux: does the new structure fit the old biochemical data? RNA (NEW YORK, N.Y.) 2008; 14:605-615. [PMID: 18287565 PMCID: PMC2271363 DOI: 10.1261/rna.912608] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The cleavage rates of 78 hammerhead ribozymes containing structurally conservative chemical modifications were collected from the literature and compared to the recently determined crystal structure of the Schistosoma mansoni hammerhead. With only a few exceptions, the biochemical data were consistent with the structure, indicating that the new structure closely resembles the transition state of the reaction. Since all the biochemical data were collected on minimal hammerheads that have a very different structure, the minimal hammerhead must be dynamic and occasionally adopt the quite different extended structure in order to cleave.
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Affiliation(s)
- Jennifer A Nelson
- Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, Illinois 60208, USA
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Hoogstraten CG, Sumita M. Structure-function relationships in RNA and RNP enzymes: recent advances. Biopolymers 2008; 87:317-28. [PMID: 17806104 DOI: 10.1002/bip.20836] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The structural biology of ribozymes and ribonucleoprotein (RNP) enzymes is now sufficiently advanced that a true dialogue between structural and functional studies is possible. In this review, we consider three important systems in which an integration of structural and biochemical data has recently led to major advances in mechanistic understanding. In the hammerhead ribozyme, application-driven biochemical studies led to the discovery of a key structural interaction that had been omitted from previously-studied constructs. A new crystal structure of the resulting, tertiary-stabilized hammerhead has resolved a remarkable number of longstanding paradoxes in the structure-function relationship of this ribozyme. In the Group I intron ribozyme, a flurry of high-resolution structures has largely confirmed, but in some cases refined or challenged, a detailed model of a metalloenzyme active site that had previously been derived by meticulous quantitative metal ion rescue experiments. Finally, for the peptidyl transferase center of the ribosome, recent biochemical and chemical results motivated by the pioneering crystal structures have suggested a picture of a catalytic mechanism dominated by proximity and orientation effects and substrate-assisted catalysis. These results refocus attention on catalysis as a property of the integrated RNP machinery as a whole, as opposed to a narrow concern with the RNA functional groups in immediate contact with the reactive center.
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Affiliation(s)
- Charles G Hoogstraten
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.
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Nelson JA, Uhlenbeck OC. Minimal and extended hammerheads utilize a similar dynamic reaction mechanism for catalysis. RNA (NEW YORK, N.Y.) 2008; 14:43-54. [PMID: 17998291 PMCID: PMC2151028 DOI: 10.1261/rna.717908] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2007] [Accepted: 09/21/2007] [Indexed: 05/25/2023]
Abstract
Analysis of the catalytic activity of identical mutations in the catalytic cores of nHH8, a very active "extended" hammerhead, and HH16, a less active "minimal" hammerhead, reveal that the tertiary Watson-Crick base pair between C3 and G8 seen in the recent structure of the Schistosoma mansoni extended hammerhead can be replaced by other base pairs in both backgrounds. This supports the model that both hammerheads utilize a similar catalytic mechanism but HH16 is slower because it infrequently samples the active conformation. The relative effect of different mutations at positions 3 and 8 also depends on the identity of residue 17 in both nHH8 and HH16. This synergistic effect can best be explained by transient pairing between residues 3 and 17 and 8 and 13, which stabilize an inactive conformation. Thus, mutants of nHH8 and possibly nHH8 itself are also in dynamic equilibrium with an inactive conformation that may resemble the X-ray structure of a minimal hammerhead. Therefore, both minimal and extended hammerhead structures must be considered to fully understand hammerhead catalysis.
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Affiliation(s)
- Jennifer A Nelson
- Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, Illinois 60208, USA
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Przybilski R, Hammann C. Idiosyncratic cleavage and ligation activity of individual hammerhead ribozymes and core sequence variants thereof. Biol Chem 2007; 388:737-41. [PMID: 17570826 DOI: 10.1515/bc.2007.065] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The hammerhead ribozyme is a small RNA endonuclease found in sub-viral plant pathogens, in transcripts from certain animal satellite DNAs and encoded at distinct loci of Arabidopsis thaliana. Kinetic analyses of tertiary stabilised ribozymes from peach latent mosaic viroid (PLMVd), Schistosoma mansoni and A. thaliana revealed a ten-fold difference in cleavage rates. Core nucleotide variations affected cleavage reactions least in the A. thaliana ribozyme, and most in the S. mansoni ribozyme. The reverse ligation reaction was catalysed efficiently by the PLMVd and A. thaliana ribozymes. The different behaviour of the individual hammerhead ribozymes is discussed in terms of structure and function.
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Affiliation(s)
- Rita Przybilski
- AG Molecular Interactions, Department of Genetics, University of Kassel, Heinrich-Plett-Str 40, Kassel, Germany
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Cottrell JW, Kuzmin YI, Fedor MJ. Functional Analysis of Hairpin Ribozyme Active Site Architecture. J Biol Chem 2007; 282:13498-507. [PMID: 17351263 DOI: 10.1074/jbc.m700451200] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The hairpin ribozyme is a small catalytic motif found in plant satellite RNAs where it catalyzes a reversible self-cleavage reaction during processing of replication intermediates. Crystallographic studies of hairpin ribozymes have provided high resolution views of the RNA functional groups that comprise the active site and stimulated biochemical studies that probed the contributions of nucleobase functional groups to catalytic chemistry. The dramatic loss of activity that results from perturbation of active site architecture points to the importance of positioning and orientation in catalytic rate acceleration. The current study focuses on the network of noncovalent interactions that align nucleophilic and leaving group oxygens in the orientation required for the S(N)2-type reaction mechanism and orient the active site nucleobases near the reactive phosphate to facilitate catalytic chemistry. Nucleotide modifications that alter or eliminate individual hydrogen bonding partners had different effects on the activation barrier to catalysis, the stability of ribozyme complexes in the ground state, and the internal equilibrium between cleavage and ligation of bound products. Furthermore, substitution of hydrogen bond donors and acceptors with seemingly equivalent pairs sometimes had very different functional consequences. These biochemical analyses augment high resolution structural information to provide insights into the functional significance of active site architecture.
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Affiliation(s)
- Joseph W Cottrell
- Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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