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Takahashi S, Sugimoto N. Pressure-temperature control of activity of RNA polymerase ribozyme. Biophys Chem 2023; 292:106914. [PMID: 36327693 DOI: 10.1016/j.bpc.2022.106914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/07/2022] [Accepted: 10/18/2022] [Indexed: 12/03/2022]
Abstract
A representative role of nucleic acids (DNA and RNA) is in the storage of genetic information. In contrast, RNAs act as ribozymes that catalyze various biochemical reactions. The "RNA world" hypothesis suggests that the origin of life was RNA because a ribozyme that shows RNA replication activity has been identified. However, prebiotic conditions in the RNA world remain unknown. In this study, we investigated the effect of high pressure and temperature on RNA replication using an RNA polymerase ribozyme tC9Y. We found that pressure accelerated the RNA replication activity of tC9Y ribozyme at higher temperatures than physiological conditions. Furthermore, molecular crowding by concentrated polyethylene glycol 200 (average molecular weight 200) synergistically enhanced the replication activity at higher pressure and temperature because the negative effect of a volumetric contribution of hydration on the tC9Y ribozyme activity decreased under crowding conditions. As a comparison, proteinaceous RNA polymerase that exists in the modern era did not show accelerated activity under high pressure and temperature. Thus, these results imply that the prebiotic conditions for the RNA world were at high pressure and temperatures under crowding conditions.
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Affiliation(s)
- Shuntaro Takahashi
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan.
| | - Naoki Sugimoto
- FIBER (Frontier Institute for Biomolecular Engineering Research), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan; FIRST (Graduate School of Frontiers of Innovative Research in Science and Technology), Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
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2
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A High-Pressure, High-Temperature Flow Reactor Simulating the Hadean Earth Environment, with Application to the Pressure Dependence of the Cleavage of Avocado Viroid Hammerhead Ribozyme. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081224. [PMID: 36013404 PMCID: PMC9410335 DOI: 10.3390/life12081224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/08/2022] [Accepted: 08/11/2022] [Indexed: 11/24/2022]
Abstract
The RNA world hypothesis suggests that chemical networks consisting of functional RNA molecules could have constructed a primitive life-like system leading a first living system. The chemical evolution scenario of RNA molecules should be consistent with the Hadean Earth environment. We have demonstrated the importance of the environment at both high temperature and high pressure, using different types of hydrothermal flow reactor systems and high-pressure equipment. In the present study, we have attempted to develop an alternative easy-to-implement method for high-pressure measurements and demonstrate that the system is applicable as an efficient research tool for high-pressure experiments at pressures up to 30 MPa. We demonstrate the usefulness of the system by detecting the high-pressure influence for the self-cleavage of avocado hammerhead ribozyme (ASBVd(−):HHR) at 45–65 °C. A kinetic analysis of the high-pressure behavior of ASBVd(−):HHR shows that the ribozyme is active at 30 MPa and its activity is sensitive to pressures between 0.1–30 MPa. The surprising finding that such a short ribozyme is effective for self-cleavage at a high pressure suggests the importance of pressure as a factor for selection of adaptable RNA molecules towards an RNA-based life-like system in the Hadean Earth environment deep in the ocean.
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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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Le Vay K, Salibi E, Song EY, Mutschler H. Nucleic Acid Catalysis under Potential Prebiotic Conditions. Chem Asian J 2020; 15:214-230. [PMID: 31714665 PMCID: PMC7003795 DOI: 10.1002/asia.201901205] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 11/05/2019] [Indexed: 01/25/2023]
Abstract
Catalysis by nucleic acids is indispensable for extant cellular life, and it is widely accepted that nucleic acid enzymes were crucial for the emergence of primitive life 3.5-4 billion years ago. However, geochemical conditions on early Earth must have differed greatly from the constant internal milieus of today's cells. In order to explore plausible scenarios for early molecular evolution, it is therefore essential to understand how different physicochemical parameters, such as temperature, pH, and ionic composition, influence nucleic acid catalysis and to explore to what extent nucleic acid enzymes can adapt to non-physiological conditions. In this article, we give an overview of the research on catalysis of nucleic acids, in particular catalytic RNAs (ribozymes) and DNAs (deoxyribozymes), under extreme and/or unusual conditions that may relate to prebiotic environments.
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Affiliation(s)
- Kristian Le Vay
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Elia Salibi
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Emilie Y. Song
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Hannes Mutschler
- Biomimetic SystemsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
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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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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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Kawamura K. Hydrothermal Microflow Technology as a Research Tool for Origin-of-Life Studies in Extreme Earth Environments. Life (Basel) 2017; 7:E37. [PMID: 28974048 PMCID: PMC5745550 DOI: 10.3390/life7040037] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 09/25/2017] [Accepted: 09/30/2017] [Indexed: 11/16/2022] Open
Abstract
Although studies about the origin of life are a frontier in science and a number of effective approaches have been developed, drawbacks still exist. Examples include: (1) simulation of chemical evolution experiments (which were demonstrated for the first time by Stanley Miller); (2) approaches tracing back the most primitive life-like systems (on the basis of investigations of present organisms); and (3) constructive approaches for making life-like systems (on the basis of molecular biology), such as in vitro construction of the RNA world. Naturally, simulation experiments of chemical evolution under plausible ancient Earth environments have been recognized as a potentially fruitful approach. Nevertheless, simulation experiments seem not to be sufficient for identifying the scenario from molecules to life. This is because primitive Earth environments are still not clearly defined and a number of possibilities should be taken into account. In addition, such environments frequently comprise extreme conditions when compared to the environments of present organisms. Therefore, we need to realize the importance of accurate and convenient experimental approaches that use practical research tools, which are resistant to high temperature and pressure, to facilitate chemical evolution studies. This review summarizes improvements made in such experimental approaches over the last two decades, focusing primarily on our hydrothermal microflow reactor technology. Microflow reactor systems are a powerful tool for performing simulation experiments in diverse simulated hydrothermal Earth conditions in order to measure the kinetics of formation and degradation and the interactions of biopolymers.
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Affiliation(s)
- Kunio Kawamura
- Department of Human Environmental Studies, Hiroshima Shudo University, Ozuka-higashi, Asaminami-ku, Hiroshima 731-3195, Japan.
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Kawamura K, Maurel MC. Walking over 4 Gya: Chemical Evolution from Photochemistry to Mineral and Organic Chemistries Leading to an RNA World. ORIGINS LIFE EVOL B 2017; 47:281-296. [PMID: 28432500 DOI: 10.1007/s11084-017-9537-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 01/20/2017] [Indexed: 01/25/2023]
Abstract
Here we overview the chemical evolution of RNA molecules from inorganic material through mineral-mediated RNA formation compatible with the plausible early Earth environments. Pathways from the gas-phase reaction to the formation of nucleotides, activation and oligomerization of nucleotides, seem to be compatible with specific environments. However, how these steps interacted is not clear since the chemical conditions are frequently different and can be incompatible between them; thus the products would have migrated from one place to another, suitable for further chemical evolution. In this review, we summarize certain points to scrutinize the RNA World hypothesis.
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Affiliation(s)
- Kunio Kawamura
- Department of Human Environmental Studies, Hiroshima Shudo University, 1-1-1 Ozuka-higashi, Asaminami-ku, Hiroshima, 731-3195, Japan.
| | - Marie-Christine Maurel
- Institut de Systématique, Evolution, Biodiversité (ISYEB), UMR 7205 CNRS MNHN UPMC EPHE, Sorbonne Universités, 50, 57 rue Cuvier, 75005, Paris, CP, France
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Kawamura K. A Hypothesis: Life Initiated from Two Genes, as Deduced from the RNA World Hypothesis and the Characteristics of Life-Like Systems. Life (Basel) 2016; 6:life6030029. [PMID: 27490571 PMCID: PMC5041005 DOI: 10.3390/life6030029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 07/22/2016] [Accepted: 07/25/2016] [Indexed: 11/18/2022] Open
Abstract
RNA played a central role in the emergence of the first life-like system on primitive Earth since RNA molecules contain both genetic information and catalytic activity. However, there are several drawbacks regarding the RNA world hypothesis. Here, I briefly discuss the feasibility of the RNA world hypothesis to deduce the RNA functions that are essential for forming a life-like system. At the same time, I have conducted a conceptual analysis of the characteristics of biosystems as a useful approach to deduce a realistic life-like system in relation to the definition of life. For instance, an RNA-based life-like system should possess enough stability to resist environmental perturbations, by developing a cell-like compartment, for instance. Here, a conceptual viewpoint is summarized to provide a realistic life-like system that is compatible with the primitive Earth environment and the capabilities of RNA molecules. According to the empirical and conceptual analysis, I propose the hypothesis that the first life-like system could have initiated from only two genes.
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Affiliation(s)
- Kunio Kawamura
- Department of Human Environmental Studies, Hiroshima Shudo University, 1-1-1, Ozuka-higashi, Asaminami-ku, Hiroshima 731-3195, Japan.
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Kawamura K, Da Silva L, Ogawa M, Konagaya N, Maurel MC. Verification of chemical evolution of RNA under hydrothermal environments on the primitive Earth. BIO WEB OF CONFERENCES 2015. [DOI: 10.1051/bioconf/20150400011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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13
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Schuabb C, Berghaus M, Rosin C, Winter R. Exploring the Free Energy and Conformational Landscape of tRNA at High Temperature and Pressure. Chemphyschem 2014; 16:138-46. [DOI: 10.1002/cphc.201402676] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Indexed: 11/10/2022]
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Hui-Bon-Hoa G, Kaddour H, Vergne J, Kruglik SG, Maurel MC. Raman characterization of Avocado Sunblotch viroid and its response to external perturbations and self-cleavage. BMC BIOPHYSICS 2014; 7:2. [PMID: 24655924 PMCID: PMC3994434 DOI: 10.1186/2046-1682-7-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 02/10/2014] [Indexed: 11/24/2022]
Abstract
Background Viroids are the smallest pathogens of plants. To date the structural and conformational details of the cleavage of Avocado sunblotch viroid (ASBVd) and the catalytic role of Mg2+ ions in efficient self-cleavage are of crucial interest. Results We report the first Raman characterization of the structure and activity of ASBVd, for plus and minus viroid strands. Both strands exhibit a typical A-type RNA conformation with an ordered double-helical content and a C3′-endo/anti sugar pucker configuration, although small but specific differences are found in the sugar puckering and base-stacking regions. The ASBVd(-) is shown to self-cleave 3.5 times more actively than ASBVd(+). Deuteration and temperature increase perturb differently the double-helical content and the phosphodiester conformation, as revealed by corresponding characteristic Raman spectral changes. Our data suggest that the structure rigidity and stability are higher and the D2O accessibility to H-bonding network is lower for ASBVd(+) than for ASBVd(-). Remarkably, the Mg2+-activated self-cleavage of the viroid does not induce any significant alterations of the secondary viroid structure, as evidenced from the absence of intensity changes of Raman marker bands that, however exhibit small but noticeable frequency downshifts suggesting several minor changes in phosphodioxy, internal loops and hairpins of the cleaved viroids. Conclusions Our results demonstrate the sensitivity of Raman spectroscopy in monitoring structural and conformational changes of the viroid and constitute the basis for further studies of its interactions with therapeutic agents and cell membranes.
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Affiliation(s)
- Gaston Hui-Bon-Hoa
- Unité 779, INSERM, 78 rue du Général Leclerc, 94276 Le Kremlin Bicêtre, France.
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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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Cho WK, Jo Y, Jo KM, Kim KH. A current overview of two viroids that infect chrysanthemums: Chrysanthemum stunt viroid and Chrysanthemum chlorotic mottle viroid. Viruses 2013; 5:1099-113. [PMID: 23594461 PMCID: PMC3705267 DOI: 10.3390/v5041099] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 04/08/2013] [Accepted: 04/08/2013] [Indexed: 11/17/2022] Open
Abstract
The chrysanthemum (Dendranthema X grandiflorum) belongs to the family Asteraceae and it is one of the most popular flowers in the world. Viroids are the smallest known plant pathogens. They consist of a circular, single-stranded RNA, which does not encode a protein. Chrysanthemums are a common host for two different viroids, the Chrysanthemum stunt viroid (CSVd) and the Chrysanthemum chlorotic mottle viroid (CChMVd). These viroids are quite different from each other in structure and function. Here, we reviewed research associated with CSVd and CChMVd that covered disease symptoms, identification, host range, nucleotide sequences, phylogenetic relationships, structures, replication mechanisms, symptom determinants, detection methods, viroid elimination, and development of viroid resistant chrysanthemums, among other studies. We propose that the chrysanthemum and these two viroids represent convenient genetic resources for host-viroid interaction studies.
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Affiliation(s)
- Won Kyong Cho
- Department of Agricultural Biotechnology, Plant Genomics and Breeding Institute, Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.
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Prediction of hammerhead ribozyme intracellular activity with the catalytic core fingerprint. Biochem J 2013; 451:439-51. [DOI: 10.1042/bj20121761] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Hammerhead ribozyme is a versatile tool for down-regulation of gene expression in vivo. Owing to its small size and high activity, it is used as a model for RNA structure–function relationship studies. In the present paper we describe a new extended hammerhead ribozyme HH-2 with a tertiary stabilizing motif constructed on the basis of the tetraloop receptor sequence. This ribozyme is very active in living cells, but shows low activity in vitro. To understand it, we analysed tertiary structure models of substrate–ribozyme complexes. We calculated six unique catalytic core geometry parameters as distances and angles between particular atoms that we call the ribozyme fingerprint. A flanking sequence and tertiary motif change the geometry of the general base, general acid, nucleophile and leaving group. We found almost complete correlation between these parameters and the decrease of target gene expression in the cells. The tertiary structure model calculations allow us to predict ribozyme intracellular activity. Our approach could be widely adapted to characterize catalytic properties of other RNAs.
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Paz-Y-Miño-C G, Espinosa A. Galapagos III World Evolution Summit: why evolution matters. Evolution 2013; 6. [PMID: 26925190 PMCID: PMC4767162 DOI: 10.1186/1936-6434-6-28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
There is no place on Earth like the Galapagos Islands and no better destination to discuss the reality of evolution. Under the theme ‘Why Does Evolution Matter’, the University San Francisco of Quito (USFQ), Ecuador, and its Galapagos Institute for the Arts and Sciences (GAIAS), organized the III World Evolution Summit in San Cristóbal Island. The 200-attendee meeting took place on 1 to 5 June 2013; it included 12 keynote speakers, 20 oral presentations by international scholars, and 31 posters by faculty, postdocs, and graduate and undergraduate students. The Summit encompassed five sessions: evolution and society, pre-cellular evolution and the RNA world, behavior and environment, genome, and microbes and diseases. USFQ and GAIAS launched officially the Lynn Margulis Center for Evolutionary Biology and showcased the Galapagos Science Center, in San Cristóbal, an impressive research facility conceptualized in partnership with the University of North Carolina at Chapel Hill, USA. USFQ and GAIAS excelled at managing the conference with exceptional vision and at highlighting the relevance of Galapagos in the history of modern evolutionary thinking; Charles Darwin’s visit to this volcanic archipelago in 1835 unfolded unprecedented scientific interest in what today is a matchless World Heritage.
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Affiliation(s)
- Guillermo Paz-Y-Miño-C
- Department of Biology, University of Massachusetts Dartmouth, 285 Old Westport Road, North Dartmouth, Massachusetts 02747-2300, USA
| | - Avelina Espinosa
- Department of Biology, Roger Williams University, One Old Ferry Road, Bristol, Rhode Island 02809, USA
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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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