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Harish B, Wang J, Hayden EJ, Grabe B, Hiller W, Winter R, Royer CA. Hidden intermediates in Mango III RNA aptamer folding revealed by pressure perturbation. Biophys J 2022; 121:421-429. [PMID: 34971617 PMCID: PMC8822612 DOI: 10.1016/j.bpj.2021.12.037] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 11/12/2021] [Accepted: 12/23/2021] [Indexed: 02/03/2023] Open
Abstract
Fluorescent RNA aptamers have the potential to enable routine quantitation and localization of RNA molecules and serve as models for understanding biologically active aptamers. In recent years, several fluorescent aptamers have been selected and modified to improve their properties, revealing that small changes to the RNA or the ligands can modify significantly their fluorescent properties. Although structural biology approaches have revealed the bound, ground state of several fluorescent aptamers, characterization of low-abundance, excited states in these systems is crucial to understanding their folding pathways. Here we use pressure as an alternative variable to probe the suboptimal states of the Mango III aptamer with both fluorescence and NMR spectroscopy approaches. At moderate KCl concentrations, increasing pressure disrupted the G-quadruplex structure of the Mango III RNA and led to an intermediate with lower fluorescence. These observations indicate the existence of suboptimal RNA structural states that still bind the TO1-biotin fluorophore and moderately enhance fluorescence. At higher KCl concentration as well, the intermediate fluorescence state was populated at high pressure, but the G-quadruplex remained stable at high pressure, supporting the notion of parallel folding and/or binding pathways. These results demonstrate the usefulness of pressure for characterizing RNA folding intermediates.
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Affiliation(s)
| | - Jinqiu Wang
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy
| | | | - Bastian Grabe
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Wolf Hiller
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Roland Winter
- Physical Chemistry I - Biophysical Chemistry, Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Catherine A. Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy,Corresponding author
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Kaddour H, Lucchi H, Hervé G, Vergne J, Maurel MC. Kinetic Study of the Avocado Sunblotch Viroid Self-Cleavage Reaction Reveals Compensatory Effects between High-Pressure and High-Temperature: Implications for Origins of Life on Earth. BIOLOGY 2021; 10:720. [PMID: 34439952 PMCID: PMC8389264 DOI: 10.3390/biology10080720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/23/2021] [Accepted: 07/25/2021] [Indexed: 11/17/2022]
Abstract
A high pressure apparatus allowing one to study enzyme kinetics under pressure was used to study the self-cleavage activity of the avocado sunblotch viroid. The kinetics of this reaction were determined under pressure over a range up to 300 MPa (1-3000 bar). It appears that the initial rate of this reaction decreases when pressure increases, revealing a positive ΔV≠ of activation, which correlates with the domain closure accompanying the reaction and the decrease of the surface of the viroid exposed to the solvent. Although, as expected, temperature increases the rate of the reaction whose energy of activation was determined, it appeared that it does not significantly influence the ΔV≠ of activation and that pressure does not influence the energy of activation. These results provide information about the structural aspects or this self-cleavage reaction, which is involved in the process of maturation of this viroid. The behavior of ASBVd results from the involvement of the hammerhead ribozyme present at its catalytic domain, indeed a structural motif is very widespread in the ancient and current RNA world.
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Affiliation(s)
- Hussein Kaddour
- Department of pharmacology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA;
| | - Honorine Lucchi
- Société PYMABS, 5 rue Henri Auguste Desbyeres, 91000 Évry-Courcouronnes, France;
| | - Guy Hervé
- Laboratoire BIOSIPE, Institut de biologie Paris-Seine, Sorbonne Université, 7 quai Saint-Bernard, 75005 Paris, France;
| | - Jacques Vergne
- Institut de Systématique, Evolution, Biodiversité, (ISYEB), Sorbonne Université, Museum National d’Histoire Naturelle, CNRS, EPHE, F 75005 Paris, France;
| | - Marie-Christine Maurel
- Institut de Systématique, Evolution, Biodiversité, (ISYEB), Sorbonne Université, Museum National d’Histoire Naturelle, CNRS, EPHE, F 75005 Paris, France;
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Kumar N, Marx D. On the Adaptability of the Chemical Reaction of Hairpin Ribozyme to High Pressures. J Phys Chem Lett 2020; 11:9298-9303. [PMID: 33085887 DOI: 10.1021/acs.jpclett.0c02902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The discovery of RNA enzymes, ribozymes, provided strong support to the RNA world hypothesis suggesting that early life evolved from RNAs able to both store genetic information and catalyze biochemical reactions. Moreover, evidence is accumulating that primitive life might have emerged in deep-sea environments and, thus, at high hydrostatic pressures. If true, ribozymes should be able to function under those pressures. In this work, we ask if and possibly how ribozymes could function at high pressures. To this end, we specifically focus on the chemical reaction steps of the self-cleavage catalysis of hairpin ribozyme by employing extensive QM/MM metadynamics simulations. We find that the reaction scenario at high pressures is vastly different than that at ambient conditions, yet the rate-limiting reaction barrier and, thus, the reaction rate are only marginally affected. Therefore, the results indeed suggest that ribozymes would function at high pressures but by following a vastly different reaction scenario.
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Affiliation(s)
- Narendra Kumar
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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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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5
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Kumar N, Marx D. How do ribozymes accommodate additional water molecules upon hydrostatic compression deep into the kilobar pressure regime? Biophys Chem 2019; 252:106192. [DOI: 10.1016/j.bpc.2019.106192] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/23/2019] [Accepted: 05/23/2019] [Indexed: 12/19/2022]
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Kumar N, Marx D. Mechanistic role of nucleobases in self-cleavage catalysis of hairpin ribozyme at ambient versus high-pressure conditions. Phys Chem Chem Phys 2019; 20:20886-20898. [PMID: 30067263 DOI: 10.1039/c8cp03142h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Ribozymes catalyze the site-specific self-cleavage of intramolecular phosphodiester bonds. Initially thought to act as metalloenzymes, they are now known to be functional even in the absence of divalent metal ions and specific nucleobases directly participate in the self-cleavage reaction. Here, we use extensive replica exchange molecular dynamics simulations to probe the precise mechanistic role of nucleobases by simulating precatalytic reactant and active precursor states of a hairpin ribozyme along its reaction path at ambient as well as high-pressure conditions. The results provide novel key insights into the self-cleavage of ribozymes. We find that deprotonation of the hydroxyl group is crucial and might be the penultimate step to the self-cleavage. The G8 nucleobase is found to stabilize the activated precursor into inline arrangement for facile nucleophilic attack of the scissile phosphate only after deprotonation of the hydroxyl group. The protonated A38 nucleobase, in contrast, mainly acts a proton donor to the O5'-oxygen leaving group that eventually leads to the self-cleavage. Indeed, systematic high-pressure simulations of catalytically relevant states confirm these findings and, moreover, provide support to the role of ribozymes as piezophilic biocatalysts with regard to their relevance in early life under extreme conditions in the realm of RNA world hypothesis.
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Affiliation(s)
- Narendra Kumar
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany.
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Schuabb C, Kumar N, Pataraia S, Marx D, Winter R. Pressure modulates the self-cleavage step of the hairpin ribozyme. Nat Commun 2017; 8:14661. [PMID: 28358002 PMCID: PMC5379106 DOI: 10.1038/ncomms14661] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 01/20/2017] [Indexed: 01/01/2023] Open
Abstract
The ability of certain RNAs, denoted as ribozymes, to not only store genetic information but also catalyse chemical reactions gave support to the RNA world hypothesis as a putative step in the development of early life on Earth. This, however, might have evolved under extreme environmental conditions, including the deep sea with pressures in the kbar regime. Here we study pressure-induced effects on the self-cleavage of hairpin ribozyme by following structural changes in real-time. Our results suggest that compression of the ribozyme leads to an accelerated transesterification reaction, being the self-cleavage step, although the overall process is retarded in the high-pressure regime. The results reveal that favourable interactions between the reaction site and neighbouring nucleobases are strengthened under pressure, resulting therefore in an accelerated self-cleavage step upon compression. These results suggest that properly engineered ribozymes may also act as piezophilic biocatalysts in addition to their hitherto known properties.
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Affiliation(s)
- Caroline Schuabb
- Physikalische Chemie I-Biophysikalische Chemie, Fakultät für Chemie und Chemische Biologie, TU Dortmund, Otto-Hahn-Strasse 4a, Dortmund 44227, Germany
| | - Narendra Kumar
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, Bochum 44780, Germany
| | - Salome Pataraia
- Physikalische Chemie I-Biophysikalische Chemie, Fakultät für Chemie und Chemische Biologie, TU Dortmund, Otto-Hahn-Strasse 4a, Dortmund 44227, Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, Bochum 44780, Germany
| | - Roland Winter
- Physikalische Chemie I-Biophysikalische Chemie, Fakultät für Chemie und Chemische Biologie, TU Dortmund, Otto-Hahn-Strasse 4a, Dortmund 44227, Germany
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Maurel MC. From neontsto filiontsand their progenies... BIO WEB OF CONFERENCES 2015. [DOI: 10.1051/bioconf/20150400014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Kaddour H, Vergne J, Herve G, Maurel MC. Inhibition by polyamines of the hammerhead ribozyme from a Chrysanthemum chlorotic mottle viroid. Biochim Biophys Acta Gen Subj 2014; 1840:1670-5. [PMID: 24412330 DOI: 10.1016/j.bbagen.2014.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 12/26/2013] [Accepted: 01/02/2014] [Indexed: 12/17/2022]
Abstract
BACKGROUND Viroids are the smallest pathogens known to date. They infect plants and cause considerable economic losses. The members of the Avsunviroidae family are known for their capability to form hammerhead ribozymes (HHR) that catalyze self-cleavage during their rolling circle replication. METHODS In vitro inhibition assays, based on the self-cleavage kinetics of the hammerhead ribozyme from a Chrysanthemum chlorotic mottle viroid (CChMVd-HHR) were performed in the presence of various putative inhibitors. RESULTS Aminated compounds appear to be inhibitors of the self-cleavage activity of the CChMVd HHR. Surprisingly the spermine, a known activator of the autocatalytic activity of another hammerhead ribozyme in the presence or absence of divalent cations, is a potent inhibitor of the CChMVd-HHR with Ki of 17±5μM. Ruthenium hexamine and TMPyP4 are also efficient inhibitors with Ki of 32±5μM and IC50 of 177±5nM, respectively. CONCLUSIONS This study shows that polyamines are inhibitors of the CChMVd-HHR self-cleavage activity, with an efficiency that increases with the number of their amino groups. GENERAL SIGNIFICANCE This fundamental investigation is of interest in understanding the catalytic activity of HHR as it is now known that HHR are present in the three domains of life including in the human genome. In addition these results emphasize again the remarkable plasticity and adaptability of ribozymes, a property which might have played a role in the early developments of life and must be also of significance nowadays for the multiple functions played by non-coding RNAs.
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Affiliation(s)
- Hussein Kaddour
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7205, F-75005 Paris, France
| | - Jacques Vergne
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7205, F-75005 Paris, France
| | - Guy Herve
- Laboratoire BIOSIPE, CNRS, ER3 UPMC Université Paris 06, France
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Nakano SI, Miyoshi D, Sugimoto N. Effects of molecular crowding on the structures, interactions, and functions of nucleic acids. Chem Rev 2013; 114:2733-58. [PMID: 24364729 DOI: 10.1021/cr400113m] [Citation(s) in RCA: 367] [Impact Index Per Article: 33.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Shu-ichi Nakano
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST) and Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University , 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
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El-Murr N, Maurel MC, Rihova M, Vergne J, Hervé G, Kato M, Kawamura K. Behavior of a hammerhead ribozyme in aqueous solution at medium to high temperatures. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 2012; 99:731-8. [PMID: 22915317 DOI: 10.1007/s00114-012-0954-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 07/17/2012] [Accepted: 07/19/2012] [Indexed: 11/28/2022]
Abstract
The "RNA world" hypothesis proposes that--early in the evolution of life--RNA molecules played important roles both in information storage and in enzymatic functions. However, this hypothesis seems to be inconsistent with the concept that life may have emerged under hydrothermal conditions since RNA molecules are considered to be labile under such extreme conditions. Presently, the possibility that the last common ancestor of the present organisms was a hyperthermophilic organism which is important to support the hypothesis of the hydrothermal origin of life has been subject of strong discussions. Consequently, it is of importance to study the behavior of RNA molecules under hydrothermal conditions from the viewpoints of stability, catalytic functions, and storage of genetic information of RNA molecules and determination of the upper limit of temperature where life could have emerged. In the present work, self-cleavage of a natural hammerhead ribozyme was examined at temperatures 10-200 °C. Self-cleavage was investigated in the presence of Mg(2+), which facilitates and accelerates this reaction. Self-cleavage of the hammerhead ribozyme was clearly observed at temperatures up to 60 °C, but at higher temperatures self-cleavage occurs together with hydrolysis and with increasing temperature hydrolysis becomes dominant. The influence of the amount of Mg(2+) on the reaction rate was also investigated. In addition, we discovered that the reaction proceeds in the presence of high concentrations of monovalent cations (Na(+) or K(+)), although very slowly. Furthermore, at high temperatures (above 60 °C), monovalent cations protect the ribozyme against degradation.
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Affiliation(s)
- Nizar El-Murr
- ER12, ANBioPhy, Fonctions et Interactions des Acides Nucléiques, UPMC Univ Paris 6, 75005, Paris, France
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Saladino R, Crestini C, Pino S, Costanzo G, Di Mauro E. Formamide and the origin of life. Phys Life Rev 2012; 9:84-104. [DOI: 10.1016/j.plrev.2011.12.002] [Citation(s) in RCA: 194] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Accepted: 12/06/2011] [Indexed: 11/16/2022]
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Müller S, Appel B, Krellenberg T, Petkovic S. The many faces of the hairpin ribozyme: Structural and functional variants of a small catalytic rna. IUBMB Life 2011; 64:36-47. [DOI: 10.1002/iub.575] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 08/18/2011] [Indexed: 12/15/2022]
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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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Residue propensities, discrimination and binding site prediction of adenine and guanine phosphates. BMC BIOCHEMISTRY 2011; 12:20. [PMID: 21569447 PMCID: PMC3113737 DOI: 10.1186/1471-2091-12-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Accepted: 05/13/2011] [Indexed: 11/15/2022]
Abstract
Background Adenine and guanine phosphates are involved in a number of biological processes such as cell signaling, metabolism and enzymatic cofactor functions. Binding sites in proteins for these ligands are often detected by looking for a previously known motif by alignment based search. This is likely to miss those where a similar binding site has not been previously characterized and when the binding sites do not follow the rule described by predefined motif. Also, it is intriguing how proteins select between adenine and guanine derivative with high specificity. Results Residue preferences for AMP, GMP, ADP, GDP, ATP and GTP have been investigated in details with additional comparison with cyclic variants cAMP and cGMP. We also attempt to predict residues interacting with these nucleotides using information derived from local sequence and evolutionary profiles. Results indicate that subtle differences exist between single residue preferences for specific nucleotides and taking neighbor environment and evolutionary context into account, successful models of their binding site prediction can be developed. Conclusion In this work, we explore how single amino acid propensities for these nucleotides play a role in the affinity and specificity of this set of nucleotides. This is expected to be helpful in identifying novel binding sites for adenine and guanine phosphates, especially when a known binding motif is not detectable.
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Abstract
Viroids are the smallest known pathogenic agents. They are noncoding, single-stranded, closed-circular, "naked" RNAs, which replicate through RNA-RNA transcription. Viroids of the Avsunviroidae family possess a hammerhead ribozyme in their sequence, allowing self-cleavage during their replication. To date, viroids have only been detected in plant cells. Here, we investigate the replication of Avocado sunblotch viroid (ASBVd) of the Avsunviroidae family in a nonconventional host, the yeast Saccharomyces cerevisiae. We demonstrate that ASBVd RNA strands of both polarities are able to self-cleave and to replicate in a unicellular eukaryote cell. We show that the viroid monomeric RNA is destabilized by the nuclear 3' and the cytoplasmic 5' RNA degradation pathways. For the first time, our results provide evidence that viroids can replicate in other organisms than plants and that yeast contains all of the essential cellular elements for the replication of ASBVd.
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Abstract
The manipulation of biological materials using elevated pressure is providing an ever-growing number of opportunities in both the applied and basic sciences. Manipulation of pressure is a useful parameter for enhancing food quality and shelf life; inactivating microbes, viruses, prions, and deleterious enzymes; affecting recombinant protein production; controlling DNA hybridization; and improving vaccine preparation. In biophysics and biochemistry, pressure is used as a tool to study intermediates in protein folding, enzyme kinetics, macromolecular interactions, amyloid fibrous protein aggregation, lipid structural changes, and to discern the role of solvation and void volumes in these processes. Biologists, including many microbiologists, examine the utility and basis of pressure inactivation of cells and cellular processes, and conversely seek to discover how deep-sea life has evolved a preference for high-pressure environments. This introduction and the papers that follow provide information on the nature and promise of the highly interdisciplinary field of high-pressure bioscience and biotechnology (HPBB).
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Affiliation(s)
- Douglas H Bartlett
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, USA.
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