1
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Tozzi A, Mazzeo M. The First Nucleic Acid Strands May Have Grown on Peptides via Primeval Reverse Translation. Acta Biotheor 2023; 71:23. [PMID: 37947915 DOI: 10.1007/s10441-023-09474-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 10/25/2023] [Indexed: 11/12/2023]
Abstract
The central dogma of molecular biology dictates that, with only a few exceptions, information proceeds from DNA to protein through an RNA intermediate. Examining the enigmatic steps from prebiotic to biological chemistry, we take another road suggesting that primordial peptides acted as template for the self-assembly of the first nucleic acids polymers. Arguing in favour of a sort of archaic "reverse translation" from proteins to RNA, our basic premise is a Hadean Earth where key biomolecules such as amino acids, polypeptides, purines, pyrimidines, nucleosides and nucleotides were available under different prebiotically plausible conditions, including meteorites delivery, shallow ponds and hydrothermal vents scenarios. Supporting a protein-first scenario alternative to the RNA world hypothesis, we propose the primeval occurrence of short two-dimensional peptides termed "selective amino acid- and nucleotide-matching oligopeptides" (henceforward SANMAOs) that noncovalently bind at the same time the polymerized amino acids and the single nucleotides dispersed in the prebiotic milieu. In this theoretical paper, we describe the chemical features of this hypothetical oligopeptide, its biological plausibility and its virtues from an evolutionary perspective. We provide a theoretical example of SANMAO's selective pairing between amino acids and nucleosides, simulating a poly-Glycine peptide that acts as a template to build a purinic chain corresponding to the glycine's extant triplet codon GGG. Further, we discuss how SANMAO might have endorsed the formation of low-fidelity RNA's polymerized strains, well before the appearance of the accurate genetic material's transmission ensured by the current translation apparatus.
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Affiliation(s)
- Arturo Tozzi
- Center for Nonlinear Science, Department of Physics, University of North Texas, 1155 Union Circle, #311427, Denton, TX, 76203-5017, USA.
| | - Marco Mazzeo
- Erredibi Srl, Via Pazzigno 117, 80146, Naples, Italy
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2
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McCarthy E, Ekesan Ş, Giese TJ, Wilson TJ, Deng J, Huang L, Lilley DJ, York DM. Catalytic mechanism and pH dependence of a methyltransferase ribozyme (MTR1) from computational enzymology. Nucleic Acids Res 2023; 51:4508-4518. [PMID: 37070188 PMCID: PMC10201425 DOI: 10.1093/nar/gkad260] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/09/2023] [Accepted: 04/10/2023] [Indexed: 04/19/2023] Open
Abstract
A methyltransferase ribozyme (MTR1) was selected in vitro to catalyze alkyl transfer from exogenous O6-methylguanine (O6mG) to a target adenine N1, and recently, high-resolution crystal structures have become available. We use a combination of classical molecular dynamics, ab initio quantum mechanical/molecular mechanical (QM/MM) and alchemical free energy (AFE) simulations to elucidate the atomic-level solution mechanism of MTR1. Simulations identify an active reactant state involving protonation of C10 that hydrogen bonds with O6mG:N1. The deduced mechanism involves a stepwise mechanism with two transition states corresponding to proton transfer from C10:N3 to O6mG:N1 and rate-controlling methyl transfer (19.4 kcal·mol-1 barrier). AFE simulations predict the pKa for C10 to be 6.3, close to the experimental apparent pKa of 6.2, further implicating it as a critical general acid. The intrinsic rate derived from QM/MM simulations, together with pKa calculations, enables us to predict an activity-pH profile that agrees well with experiment. The insights gained provide further support for a putative RNA world and establish new design principles for RNA-based biochemical tools.
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Affiliation(s)
- Erika McCarthy
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Şölen Ekesan
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Timothy J Giese
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Timothy J Wilson
- Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Jie Deng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong–Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Lin Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong–Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - David M J Lilley
- Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
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3
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Deng J, Shi Y, Peng X, He Y, Chen X, Li M, Lin X, Liao W, Huang Y, Jiang T, Lilley DJ, Miao Z, Huang L. Ribocentre: a database of ribozymes. Nucleic Acids Res 2023; 51:D262-D268. [PMID: 36177882 PMCID: PMC9825448 DOI: 10.1093/nar/gkac840] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/14/2022] [Accepted: 09/21/2022] [Indexed: 01/29/2023] Open
Abstract
Ribozymes are excellent systems in which to study 'sequence - structure - function' relationships in RNA molecules. Understanding these relationships may greatly help structural modeling and design of functional RNA structures and some functional structural modules could be repurposed in molecular design. At present, there is no comprehensive database summarising all the natural ribozyme families. We have therefore created Ribocentre, a database that collects together sequence, structure and mechanistic data on 21 ribozyme families. This includes available information on timelines, sequence families, secondary and tertiary structures, catalytic mechanisms, applications of the ribozymes together with key publications. The database is publicly available at https://www.ribocentre.org.
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Affiliation(s)
- Jie Deng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Yaohuang Shi
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou 510005, China
| | - Xuemei Peng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Yuanlin He
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Xiaoxue Chen
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
- Department of pharmacy, Sun-Yat-Sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Mengxiao Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Xiaowei Lin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Wenjian Liao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
- Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Yuanyin Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Taijiao Jiang
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou 510005, China
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Zhichao Miao
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou 510005, China
- Translational Research Institute of Brain and Brain-Like Intelligence and Department of Anesthesiology, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine, Shanghai 200434, China
| | - Lin Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
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4
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Kumar V, Turnbull WB, Kumar A. Review on Recent Developments in Biocatalysts for Friedel–Crafts Reactions. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Vajinder Kumar
- Department of Chemistry, Akal University, Talwandi Sabo, Bathinda, Punjab 151302, India
| | - W. Bruce Turnbull
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K
| | - Avneesh Kumar
- Department of Botany, Akal University, Talwandi Sabo, Bathinda, Punjab 151302, India
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5
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Forster AC. Revisiting the Extinction of the RNA World. Biochemistry 2022; 61:749-751. [PMID: 35389627 PMCID: PMC9069686 DOI: 10.1021/acs.biochem.2c00121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The ribozyme world
is thought to have evolved the burdensome complexity
of peptide and protein synthesis because the 20 amino acid side chains
are catalytically superior. Instead, I propose that the Achilles heel
of the RNA world that led to the extinction of riboorganisms was RNA’s
polyanionic charges that could not be covalently neutralized stably
by phosphotriester formation. These charges prevented development
of hydrophobic cores essential for integration into membranes and
many enzymatic reactions. In contrast, the phosphotriester modification
of DNA is stable. So, the fact that the charge was never removed in
DNA evolution gives further credence to proteins coming before DNA.
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Affiliation(s)
- Anthony C Forster
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, Uppsala 75124, Sweden
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6
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Deng J, Wilson TJ, Wang J, Peng X, Li M, Lin X, Liao W, Lilley DMJ, Huang L. Structure and mechanism of a methyltransferase ribozyme. Nat Chem Biol 2022; 18:556-564. [PMID: 35301479 PMCID: PMC9050513 DOI: 10.1038/s41589-022-00982-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/26/2022] [Indexed: 11/09/2022]
Abstract
Known ribozymes in contemporary biology perform a limited range of chemical catalysis, but in vitro selection has generated species that catalyze a broader range of chemistry; yet, there have been few structural and mechanistic studies of selected ribozymes. A ribozyme has recently been selected that can catalyze a site-specific methyl transfer reaction. We have solved the crystal structure of this ribozyme at a resolution of 2.3 Å, showing how the RNA folds to generate a very specific binding site for the methyl donor substrate. The structure immediately suggests a catalytic mechanism involving a combination of proximity and orientation and nucleobase-mediated general acid catalysis. The mechanism is supported by the pH dependence of the rate of catalysis. A selected methyltransferase ribozyme can thus use a relatively sophisticated catalytic mechanism, broadening the range of known RNA-catalyzed chemistry. ![]()
The authors present the crystal structure of the MTR1 ribozyme that transfers the methyl group from O6-methylguanine to an adenine N1 in the target RNA and propose a catalytic mechanism based upon proximity, orientation and general acid catalysis.
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Affiliation(s)
- Jie Deng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Timothy J Wilson
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, UK
| | - Jia Wang
- College of Life Sciences, Guangzhou University, Guangzhou, China
| | - Xuemei Peng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Mengxiao Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Xiaowei Lin
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Wenjian Liao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.,Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, UK.
| | - Lin Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China. .,Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China.
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7
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Piedrafita G, Varma SJ, Castro C, Messner CB, Szyrwiel L, Griffin JL, Ralser M. Cysteine and iron accelerate the formation of ribose-5-phosphate, providing insights into the evolutionary origins of the metabolic network structure. PLoS Biol 2021; 19:e3001468. [PMID: 34860829 PMCID: PMC8673631 DOI: 10.1371/journal.pbio.3001468] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 12/15/2021] [Accepted: 11/04/2021] [Indexed: 12/21/2022] Open
Abstract
The structure of the metabolic network is highly conserved, but we know little about its evolutionary origins. Key for explaining the early evolution of metabolism is solving a chicken–egg dilemma, which describes that enzymes are made from the very same molecules they produce. The recent discovery of several nonenzymatic reaction sequences that topologically resemble central metabolism has provided experimental support for a “metabolism first” theory, in which at least part of the extant metabolic network emerged on the basis of nonenzymatic reactions. But how could evolution kick-start on the basis of a metal catalyzed reaction sequence, and how could the structure of nonenzymatic reaction sequences be imprinted on the metabolic network to remain conserved for billions of years? We performed an in vitro screening where we add the simplest components of metabolic enzymes, proteinogenic amino acids, to a nonenzymatic, iron-driven reaction network that resembles glycolysis and the pentose phosphate pathway (PPP). We observe that the presence of the amino acids enhanced several of the nonenzymatic reactions. Particular attention was triggered by a reaction that resembles a rate-limiting step in the oxidative PPP. A prebiotically available, proteinogenic amino acid cysteine accelerated the formation of RNA nucleoside precursor ribose-5-phosphate from 6-phosphogluconate. We report that iron and cysteine interact and have additive effects on the reaction rate so that ribose-5-phosphate forms at high specificity under mild, metabolism typical temperature and environmental conditions. We speculate that accelerating effects of amino acids on rate-limiting nonenzymatic reactions could have facilitated a stepwise enzymatization of nonenzymatic reaction sequences, imprinting their structure on the evolving metabolic network. The evolutionary origins of metabolism are largely unknown. This study shows that the prebiotically available proteinogenic amino acid cysteine can promote the metabolism-like rate-limiting formation of ribose-5-phosphate, suggesting that early metabolic pathways could have emerged thought the stepwise enzymatization of non-enzymatic reaction sequences.
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Affiliation(s)
- Gabriel Piedrafita
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, United Kingdom
| | - Sreejith J. Varma
- Department of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Cecilia Castro
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, United Kingdom
| | - Christoph B. Messner
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Lukasz Szyrwiel
- Department of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Julian L. Griffin
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, United Kingdom
- The Rowett Institute, The University of Aberdeen, Aberdeen, United Kingdom
| | - Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, United Kingdom
- Department of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
- * E-mail:
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8
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Maier J, Müller SM, Torvisco A, Glotz G, Fischer RC, Griesser T, Kelterer A, Haas M. Isolable Stannenolates Enable the Synthesis of Visible‐Light Photoinitiators. CHEMPHOTOCHEM 2021. [DOI: 10.1002/cptc.202100213] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Janine Maier
- Institute of Inorganic Chemistry Graz University of Technology Stremayrgasse 9/IV 8010 Graz Austria
| | - Stefanie M. Müller
- Institute of Chemistry of Polymeric Materials Montanuniversitaet Leoben Otto-Gloeckelstrasse 2 8700 Leoben Austria
| | - Ana Torvisco
- Institute of Inorganic Chemistry Graz University of Technology Stremayrgasse 9/IV 8010 Graz Austria
| | - Gabriel Glotz
- Institute of Physical and Theoretical Chemistry Technical University Graz Stremayrgasse 9/II 8010 Graz Austria
| | - Roland C. Fischer
- Institute of Inorganic Chemistry Graz University of Technology Stremayrgasse 9/IV 8010 Graz Austria
| | - Thomas Griesser
- Institute of Chemistry of Polymeric Materials Montanuniversitaet Leoben Otto-Gloeckelstrasse 2 8700 Leoben Austria
| | - Anne‐Marie Kelterer
- Institute of Physical and Theoretical Chemistry Technical University Graz Stremayrgasse 9/II 8010 Graz Austria
| | - Michael Haas
- Institute of Inorganic Chemistry Graz University of Technology Stremayrgasse 9/IV 8010 Graz Austria
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9
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Drusgala M, Frühwirt P, Glotz G, Hogrefe K, Torvisco A, Fischer RC, Wilkening HMR, Kelterer A, Gescheidt G, Haas M. Isolable Geminal Bisgermenolates: A New Synthon in Organometallic Chemistry. Angew Chem Int Ed Engl 2021; 60:23646-23650. [PMID: 34464492 PMCID: PMC8596710 DOI: 10.1002/anie.202111636] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Indexed: 11/07/2022]
Abstract
We have synthesized the first isolable geminal bisenolates L2 K2 Ge[(CO)R]2 (R=2,4,6-trimethylphenyl (2 a,b), L=THF for (2 a) or [18]-crown-6 for (2 b)), a new synthon for the synthesis of organometallic reagents. The formation of these derivatives was confirmed by NMR spectroscopy and X-ray crystallographic analysis. The UV/Vis spectra of these anions show three distinct bands, which were assigned by DFT calculations. The efficiency of 2 a,b to serve as new building block in macromolecular chemistry is demonstrated by the reactions with two different types of electrophiles (acid chlorides and alkyl halides). In all cases the salt metathesis reaction gave rise to novel Ge-based photoinitiators in good yields.
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Affiliation(s)
- Manfred Drusgala
- Institute of Inorganic ChemistryGraz University of TechnologyStremayrgasse 9/IV8010GrazAustria
| | - Philipp Frühwirt
- Institute of Physical and Theoretical ChemistryGraz University of TechnologyStremayrgasse 9/II8010GrazAustria
| | - Gabriel Glotz
- Institute of Physical and Theoretical ChemistryGraz University of TechnologyStremayrgasse 9/II8010GrazAustria
| | - Katharina Hogrefe
- Institute for Chemistry and Technology of MaterialsGraz University of TechnologyStremayrgasse 9/III8010GrazAustria
| | - Ana Torvisco
- Institute of Inorganic ChemistryGraz University of TechnologyStremayrgasse 9/IV8010GrazAustria
| | - Roland C. Fischer
- Institute of Inorganic ChemistryGraz University of TechnologyStremayrgasse 9/IV8010GrazAustria
| | - H. Martin R. Wilkening
- Institute for Chemistry and Technology of MaterialsGraz University of TechnologyStremayrgasse 9/III8010GrazAustria
| | - Anne‐Marie Kelterer
- Institute of Physical and Theoretical ChemistryGraz University of TechnologyStremayrgasse 9/II8010GrazAustria
| | - Georg Gescheidt
- Institute of Physical and Theoretical ChemistryGraz University of TechnologyStremayrgasse 9/II8010GrazAustria
| | - Michael Haas
- Institute of Inorganic ChemistryGraz University of TechnologyStremayrgasse 9/IV8010GrazAustria
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10
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Drusgala M, Frühwirt P, Glotz G, Hogrefe K, Torvisco A, Fischer RC, Wilkening HMR, Kelterer A, Gescheidt G, Haas M. Isolable Geminal Bisgermenolates: A New Synthon in Organometallic Chemistry. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 133:23838-23842. [PMID: 38505802 PMCID: PMC10946821 DOI: 10.1002/ange.202111636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Indexed: 11/07/2022]
Abstract
We have synthesized the first isolable geminal bisenolates L2K2Ge[(CO)R]2 (R=2,4,6-trimethylphenyl (2 a,b), L=THF for (2 a) or [18]-crown-6 for (2 b)), a new synthon for the synthesis of organometallic reagents. The formation of these derivatives was confirmed by NMR spectroscopy and X-ray crystallographic analysis. The UV/Vis spectra of these anions show three distinct bands, which were assigned by DFT calculations. The efficiency of 2 a,b to serve as new building block in macromolecular chemistry is demonstrated by the reactions with two different types of electrophiles (acid chlorides and alkyl halides). In all cases the salt metathesis reaction gave rise to novel Ge-based photoinitiators in good yields.
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Affiliation(s)
- Manfred Drusgala
- Institute of Inorganic ChemistryGraz University of TechnologyStremayrgasse 9/IV8010GrazAustria
| | - Philipp Frühwirt
- Institute of Physical and Theoretical ChemistryGraz University of TechnologyStremayrgasse 9/II8010GrazAustria
| | - Gabriel Glotz
- Institute of Physical and Theoretical ChemistryGraz University of TechnologyStremayrgasse 9/II8010GrazAustria
| | - Katharina Hogrefe
- Institute for Chemistry and Technology of MaterialsGraz University of TechnologyStremayrgasse 9/III8010GrazAustria
| | - Ana Torvisco
- Institute of Inorganic ChemistryGraz University of TechnologyStremayrgasse 9/IV8010GrazAustria
| | - Roland C. Fischer
- Institute of Inorganic ChemistryGraz University of TechnologyStremayrgasse 9/IV8010GrazAustria
| | - H. Martin R. Wilkening
- Institute for Chemistry and Technology of MaterialsGraz University of TechnologyStremayrgasse 9/III8010GrazAustria
| | - Anne‐Marie Kelterer
- Institute of Physical and Theoretical ChemistryGraz University of TechnologyStremayrgasse 9/II8010GrazAustria
| | - Georg Gescheidt
- Institute of Physical and Theoretical ChemistryGraz University of TechnologyStremayrgasse 9/II8010GrazAustria
| | - Michael Haas
- Institute of Inorganic ChemistryGraz University of TechnologyStremayrgasse 9/IV8010GrazAustria
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11
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Wilson TJ, Lilley DMJ. The potential versatility of RNA catalysis. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1651. [PMID: 33949113 DOI: 10.1002/wrna.1651] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 01/21/2023]
Abstract
It is commonly thought that in the early development of life on this planet RNA would have acted both as a store of genetic information and as a catalyst. While a number of RNA enzymes are known in contemporary cells, they are largely confined to phosphoryl transfer reactions, whereas an RNA based metabolism would have required a much greater chemical diversity of catalysis. Here we discuss how RNA might catalyze a wider variety of chemistries, and particularly how information gleaned from riboswitches could suggest how ribozymes might recruit coenzymes to expand their chemical range. We ask how we might seek such activities in modern biology. This article is categorized under: RNA-Based Catalysis > Miscellaneous RNA-Catalyzed Reactions Regulatory RNAs/RNAi/Riboswitches > Riboswitches RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry.
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Affiliation(s)
- Timothy J Wilson
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, UK
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, UK
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12
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Magde D, Akoopie A, Magde MD, Müller UF. Water/Oil Emulsions with Controlled Droplet Sizes for In Vitro Selection Experiments. ACS OMEGA 2021; 6:21773-21783. [PMID: 34471779 PMCID: PMC8388082 DOI: 10.1021/acsomega.1c03445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
In the early history of life, RNA might have had many catalytic functions as ribozymes that do not exist today. To explore this possibility, catalytically active RNAs can be identified by in vitro selection experiments. Some of these experiments are best performed in nanodroplets to prevent diffusion between individual RNA sequences. In order to explore the suitability for the large-scale in emulsio selection of water-in-oil emulsions made by passing a mixture of mineral oil, the emulsifier ABIL-EM90, and a few percent of an aqueous phase through a microfluidizer, we used dynamic light scattering to characterize the size of aqueous droplets dispersed throughout the oil. We found that seven or more passes through the microfluidizer at 8000 psi with close to half molar inorganic salts and 10% polyethylene glycol produced droplets with sizes below 100 nm that were ideal for our purposes. We also identified conditions that would produce larger or smaller droplets, and we demonstrate that the emulsions are stable over weeks and months, which is desirable for different types of in vitro selection experiments.
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Affiliation(s)
- Douglas Magde
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Arvin Akoopie
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Michael D. Magde
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Ulrich F. Müller
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California 92093, United States
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13
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Arriola JT, Müller UF. A combinatorial method to isolate short ribozymes from complex ribozyme libraries. Nucleic Acids Res 2020; 48:e116. [PMID: 33035338 PMCID: PMC7672470 DOI: 10.1093/nar/gkaa834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 08/28/2020] [Accepted: 10/01/2020] [Indexed: 11/13/2022] Open
Abstract
In vitro selections are the only known methods to generate catalytic RNAs (ribozymes) that do not exist in nature. Such new ribozymes are used as biochemical tools, or to address questions on early stages of life. In both cases, it is helpful to identify the shortest possible ribozymes since they are easier to deploy as a tool, and because they are more likely to have emerged in a prebiotic environment. One of our previous selection experiments led to a library containing hundreds of different ribozyme clusters that catalyze the triphosphorylation of their 5'-terminus. This selection showed that RNA systems can use the prebiotically plausible molecule cyclic trimetaphosphate as an energy source. From this selected ribozyme library, the shortest ribozyme that was previously identified had a length of 67 nucleotides. Here we describe a combinatorial method to identify short ribozymes from libraries containing many ribozymes. Using this protocol on the library of triphosphorylation ribozymes, we identified a 17-nucleotide sequence motif embedded in a 44-nucleotide pseudoknot structure. The described combinatorial approach can be used to analyze libraries obtained by different in vitro selection experiments.
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Affiliation(s)
- Joshua T Arriola
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California 92093, USA
| | - Ulrich F Müller
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California 92093, USA
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14
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Papastavrou N, Bande O, Marlière P, Groaz E, Herdewijn P. Vitamin-guanosine monophosphate conjugates for in vitro transcription priming. Chem Commun (Camb) 2020; 56:2787-2790. [PMID: 32025667 DOI: 10.1039/c9cc09427j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Expanding the catalytic repertoire of ribozymes to include vitamin synthesis requires efficient labelling of RNA with the substrate of interest, prior to in vitro selection. For this purpose, we rationally designed and synthesized six GMP-conjugates carrying a synthetic pre-thiamine or biotin precursor and investigated their transcription incorporation properties by T7 RNA polymerase.
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Affiliation(s)
- Nikolaos Papastavrou
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49-Box 1041, 3000 Leuven, Belgium.
| | - Omprakash Bande
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49-Box 1041, 3000 Leuven, Belgium.
| | - Philippe Marlière
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057 Evry, France.
| | - Elisabetta Groaz
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49-Box 1041, 3000 Leuven, Belgium.
| | - Piet Herdewijn
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49-Box 1041, 3000 Leuven, Belgium.
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15
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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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16
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Abstract
Recently heavier Group 14 enolates showed their importance and applicability in a broad range of chemical transformations. They were found to be key intermediates during the synthesis of photoinitiators, as well as during the formation of complex silicon frameworks. This Minireview presents general strategies towards the synthesis of heavier Group 14 enolates (HG 14 enolates). Structural properties, as well as their spectroscopic behavior are outlined. This study may aid future development in this research area.
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Affiliation(s)
- Michael Haas
- Institute of Inorganic ChemistryTechnische Universität GrazStremayrgasse 9/IV8010GrazAustria
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17
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Kostenbader K, York DM. Molecular simulations of the pistol ribozyme: unifying the interpretation of experimental data and establishing functional links with the hammerhead ribozyme. RNA (NEW YORK, N.Y.) 2019; 25:1439-1456. [PMID: 31363004 PMCID: PMC6795133 DOI: 10.1261/rna.071944.119] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/11/2019] [Indexed: 05/27/2023]
Abstract
The pistol ribozyme (Psr) is among the most recently discovered RNA enzymes and has been the subject of experiments aimed at elucidating the mechanism. Recent biochemical studies have revealed exciting clues about catalytic interactions in the active site not apparent from available crystallographic data. The present work unifies the interpretation of the existing body of structural and functional data on Psr by providing a dynamical model for the catalytically active state in solution from molecular simulation. Our results suggest that a catalytic Mg2+ ion makes inner-sphere contact with G33:N7 and outer-sphere coordination to the pro-RP of the scissile phosphate, promoting electrostatic stabilization of the dianionic transition state and neutralization of the developing charge of the leaving group through a metal-coordinated water molecule that is made more acidic by a hydrogen bond donated from the 2'OH of P32. This model is consistent with experimental activity-pH and mutagenesis data, including sensitivity to G33(7cG) and phosphorothioate substitution/metal ion rescue. The model suggests several experimentally testable predictions, including the response of cleavage activity to mutations at G42 and P32 positions in the ribozyme, and thio substitutions of the substrate in the presence of different divalent metal ions. Further, the model identifies striking similarities of Psr to the hammerhead ribozyme (HHr), including similar global fold, organization of secondary structure around an active site three-way junction, catalytic metal ion binding mode, and guanine general base. However, the specific binding mode and role of the Mg2+ ion, as well as a conserved 2'-OH in the active site, are interrelated but subtly different between the ribozymes.
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Affiliation(s)
- Ken Kostenbader
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-8076, USA
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry & Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-8076, USA
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18
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Yokobayashi Y. Applications of high-throughput sequencing to analyze and engineer ribozymes. Methods 2019; 161:41-45. [PMID: 30738128 DOI: 10.1016/j.ymeth.2019.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/04/2019] [Accepted: 02/03/2019] [Indexed: 01/22/2023] Open
Abstract
A large number of catalytic RNAs, or ribozymes, have been identified in the genomes of various organisms and viruses. Ribozymes are involved in biological processes such as regulation of gene expression and viral replication, but biological roles of many ribozymes still remain unknown. Ribozymes have also inspired researchers to engineer synthetic ribozymes that function as sensors or gene switches. To gain deeper understanding of the sequence-function relationship of ribozymes and to efficiently engineer synthetic ribozymes, a large number of ribozyme variants need to be examined which was limited to hundreds of sequences by Sanger sequencing. The advent of high-throughput sequencing technologies, however, has allowed us to sequence millions of ribozyme sequences at low cost. This review focuses on the recent applications of high-throughput sequencing to both characterize and engineer ribozymes, to highlight how the large-scale sequence data can advance ribozyme research and engineering.
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Affiliation(s)
- Yohei Yokobayashi
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495, Japan.
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19
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Ralser M. An appeal to magic? The discovery of a non-enzymatic metabolism and its role in the origins of life. Biochem J 2018; 475:2577-2592. [PMID: 30166494 PMCID: PMC6117946 DOI: 10.1042/bcj20160866] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 07/23/2018] [Accepted: 07/24/2018] [Indexed: 12/18/2022]
Abstract
Until recently, prebiotic precursors to metabolic pathways were not known. In parallel, chemistry achieved the synthesis of amino acids and nucleotides only in reaction sequences that do not resemble metabolic pathways, and by using condition step changes, incompatible with enzyme evolution. As a consequence, it was frequently assumed that the topological organisation of the metabolic pathway has formed in a Darwinian process. The situation changed with the discovery of a non-enzymatic glycolysis and pentose phosphate pathway. The suite of metabolism-like reactions is promoted by a metal cation, (Fe(II)), abundant in Archean sediment, and requires no condition step changes. Knowledge about metabolism-like reaction topologies has accumulated since, and supports non-enzymatic origins of gluconeogenesis, the S-adenosylmethionine pathway, the Krebs cycle, as well as CO2 fixation. It now feels that it is only a question of time until essential parts of metabolism can be replicated non-enzymatically. Here, I review the 'accidents' that led to the discovery of the non-enzymatic glycolysis, and on the example of a chemical network based on hydrogen cyanide, I provide reasoning why metabolism-like non-enzymatic reaction topologies may have been missed for a long time. Finally, I discuss that, on the basis of non-enzymatic metabolism-like networks, one can elaborate stepwise scenarios for the origin of metabolic pathways, a situation that increasingly renders the origins of metabolism a tangible problem.
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Affiliation(s)
- Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K.
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, 1 Midland Rd, London NW1 1AT, U.K
- Department of Biochemistry, Charitè, Am Chariteplatz 1, 10117 Berlin, Germany
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20
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Abstract
The emergence of functional cooperation between the three main classes of biomolecules - nucleic acids, peptides and lipids - defines life at the molecular level. However, how such mutually interdependent molecular systems emerged from prebiotic chemistry remains a mystery. A key hypothesis, formulated by Crick, Orgel and Woese over 40 year ago, posits that early life must have been simpler. Specifically, it proposed that an early primordial biology lacked proteins and DNA but instead relied on RNA as the key biopolymer responsible not just for genetic information storage and propagation, but also for catalysis, i.e. metabolism. Indeed, there is compelling evidence for such an 'RNA world', notably in the structure of the ribosome as a likely molecular fossil from that time. Nevertheless, one might justifiably ask whether RNA alone would be up to the task. From a purely chemical perspective, RNA is a molecule of rather uniform composition with all four bases comprising organic heterocycles of similar size and comparable polarity and pK a values. Thus, RNA molecules cover a much narrower range of steric, electronic and physicochemical properties than, e.g. the 20 amino acid side-chains of proteins. Herein we will examine the functional potential of RNA (and other nucleic acids) with respect to self-replication, catalysis and assembly into simple protocellular entities.
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21
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Akoopie A, Müller UF. Lower temperature optimum of a smaller, fragmented triphosphorylation ribozyme. Phys Chem Chem Phys 2018; 18:20118-25. [PMID: 27053323 DOI: 10.1039/c6cp00672h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The RNA world hypothesis describes a stage in the early evolution of life in which catalytic RNAs mediated the replication of RNA world organisms. One challenge to this hypothesis is that most existing ribozymes are much longer than what may be expected to originate from prebiotically plausible methods, or from the polymerization by currently existing polymerase ribozymes. We previously developed a 96-nucleotide long ribozyme, which generates a chemically activated 5'-phosphate (a 5'-triphosphate) from a prebiotically plausible molecule, trimetaphosphate, and an RNA 5'-hydroxyl group. Analogous ribozymes may have been important in the RNA world to access an energy source for the earliest life forms. Here we reduce the length of this ribozyme by fragmenting the ribozyme into multiple RNA strands, and by successively removing its longest double strand. The resulting ribozyme is composed of RNA fragments with none longer than 34 nucleotides. The temperature optimum was ∼20 °C, compared to ∼40 °C for the parent ribozyme. This shift in temperature dependence may be a more general phenomenon for fragmented ribozymes, and may have helped RNA world organisms to emerge at low temperature.
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Affiliation(s)
- Arvin Akoopie
- Department of Chemistry & Biochemistry, University of California, San Diego, USA.
| | - Ulrich F Müller
- Department of Chemistry & Biochemistry, University of California, San Diego, USA.
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22
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Leypold M, Schuh L, Fischer R, Torvisco A, Flock M, Stueger H, Haas M. Synthesis of Structurally Complex Silicon Frameworks through the First Sila-Aldol Reaction. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701862] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Mario Leypold
- Institute of Inorganic Chemistry; Graz University of Technology; Stremayrgasse 9/IV 8010 Graz Austria
| | - Lukas Schuh
- Institute of Inorganic Chemistry; Graz University of Technology; Stremayrgasse 9/IV 8010 Graz Austria
| | - Roland Fischer
- Institute of Inorganic Chemistry; Graz University of Technology; Stremayrgasse 9/IV 8010 Graz Austria
| | - Ana Torvisco
- Institute of Inorganic Chemistry; Graz University of Technology; Stremayrgasse 9/IV 8010 Graz Austria
| | - Michaela Flock
- Institute of Inorganic Chemistry; Graz University of Technology; Stremayrgasse 9/IV 8010 Graz Austria
| | - Harald Stueger
- Institute of Inorganic Chemistry; Graz University of Technology; Stremayrgasse 9/IV 8010 Graz Austria
| | - Michael Haas
- Institute of Inorganic Chemistry; Graz University of Technology; Stremayrgasse 9/IV 8010 Graz Austria
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23
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Leypold M, Schuh L, Fischer R, Torvisco A, Flock M, Stueger H, Haas M. Synthesis of Structurally Complex Silicon Frameworks through the First Sila-Aldol Reaction. Angew Chem Int Ed Engl 2017; 56:8089-8093. [PMID: 28481426 DOI: 10.1002/anie.201701862] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 04/04/2017] [Indexed: 11/06/2022]
Abstract
Herein, we report on the first sila-aldol reaction, which emphasizes the tight connection between silicon and carbon chemistry. This novel synthetic method provides straightforward access to 2-oxahexasilabicyclo[3.2.1]octan-8-ide, a structurally complex silicon framework, in quantitative yield. Its structure was confirmed by NMR spectroscopy and X-ray crystallography, and it displays a distinctive charge-transfer transition. The complete mechanism of this highly selective rearrangement cascade is outlined and supported by density functional theory (DFT) calculations, which highlight the thermodynamic driving force and the low activation barriers of this powerful silicon-carbon bond-forming strategy.
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Affiliation(s)
- Mario Leypold
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9/IV, 8010, Graz, Austria
| | - Lukas Schuh
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9/IV, 8010, Graz, Austria
| | - Roland Fischer
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9/IV, 8010, Graz, Austria
| | - Ana Torvisco
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9/IV, 8010, Graz, Austria
| | - Michaela Flock
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9/IV, 8010, Graz, Austria
| | - Harald Stueger
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9/IV, 8010, Graz, Austria
| | - Michael Haas
- Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9/IV, 8010, Graz, Austria
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24
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Duchemin N, Heath-Apostolopoulos I, Smietana M, Arseniyadis S. A decade of DNA-hybrid catalysis: from innovation to comprehension. Org Biomol Chem 2017; 15:7072-7087. [DOI: 10.1039/c7ob00176b] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Since the pioneering work of Roelfes and Feringa in the field of DNA-based asymmetric catalysis, the unique chirality of oligonucleotides has allowed the development of a variety of asymmetric synthetic transformations. This review offers a complete overview of the field.
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Affiliation(s)
- Nicolas Duchemin
- Queen Mary University of London
- School of Biological and Chemical Sciences
- London
- UK
| | | | - Michael Smietana
- Institut des Biomolécules Max Mousseron
- UMR 5247 CNRS
- Université de Montpellier
- 34095 Montpellier
- France
| | - Stellios Arseniyadis
- Queen Mary University of London
- School of Biological and Chemical Sciences
- London
- UK
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25
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26
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The structural stability and catalytic activity of DNA and RNA oligonucleotides in the presence of organic solvents. Biophys Rev 2016; 8:11-23. [PMID: 28510143 DOI: 10.1007/s12551-015-0188-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/03/2015] [Indexed: 01/02/2023] Open
Abstract
Organic solvents and apolar media are used in the studies of nucleic acids to modify the conformation and function of nucleic acids, to improve solubility of hydrophobic ligands, to construct molecular scaffolds for organic synthesis, and to study molecular crowding effects. Understanding how organic solvents affect nucleic acid interactions and identifying the factors that dominate solvent effects are important for the creation of oligonucleotide-based technologies. This review describes the structural and catalytic properties of DNA and RNA oligonucleotides in organic solutions and in aqueous solutions with organic cosolvents. There are several possible mechanisms underlying the effects of organic solvents on nucleic acid interactions. The reported results emphasize the significance of the osmotic pressure effect and the dielectric constant effect in addition to specific interactions with nucleic acid strands. This review will serve as a guide for the selection of solvent systems based on the purpose of the nucleic acid-based experiments.
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27
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Duchemin N, Benedetti E, Bethge L, Vonhoff S, Klussmann S, Vasseur JJ, Cossy J, Smietana M, Arseniyadis S. Expanding biohybrid-mediated asymmetric catalysis into the realm of RNA. Chem Commun (Camb) 2016; 52:8604-7. [DOI: 10.1039/c6cc03540j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report here the first example of an RNA-based catalyst involving a catalytically active metal complex interacting in a non-covalent fashion with short RNA sequences.
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Affiliation(s)
- Nicolas Duchemin
- Laboratoire de Chimie Organique
- Institute of Chemistry
- Biology and Innovation (CBI) – ESPCI ParisTech/CNRS (UMR8231)/PSL* Research University
- 75231 Paris Cedex 05
- France
| | - Erica Benedetti
- Laboratoire de Chimie Organique
- Institute of Chemistry
- Biology and Innovation (CBI) – ESPCI ParisTech/CNRS (UMR8231)/PSL* Research University
- 75231 Paris Cedex 05
- France
| | | | | | | | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron
- UMR 5247 CNRS
- Université de Montpellier
- ENSCM Place Eugène Bataillon
- 34095 Montpellier
| | - Janine Cossy
- Laboratoire de Chimie Organique
- Institute of Chemistry
- Biology and Innovation (CBI) – ESPCI ParisTech/CNRS (UMR8231)/PSL* Research University
- 75231 Paris Cedex 05
- France
| | - Michael Smietana
- Institut des Biomolécules Max Mousseron
- UMR 5247 CNRS
- Université de Montpellier
- ENSCM Place Eugène Bataillon
- 34095 Montpellier
| | - Stellios Arseniyadis
- Laboratoire de Chimie Organique
- Institute of Chemistry
- Biology and Innovation (CBI) – ESPCI ParisTech/CNRS (UMR8231)/PSL* Research University
- 75231 Paris Cedex 05
- France
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28
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Landmarks in the Evolution of (t)-RNAs from the Origin of Life up to Their Present Role in Human Cognition. Life (Basel) 2015; 6:life6010001. [PMID: 26703740 PMCID: PMC4810232 DOI: 10.3390/life6010001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 12/07/2015] [Accepted: 12/15/2015] [Indexed: 01/28/2023] Open
Abstract
How could modern life have evolved? The answer to that question still remains unclear. However, evidence is growing that, since the origin of life, RNA could have played an important role throughout evolution, right up to the development of complex organisms and even highly sophisticated features such as human cognition. RNA mediated RNA-aminoacylation can be seen as a first landmark on the path from the RNA world to modern DNA- and protein-based life. Likewise, the generation of the RNA modifications that can be found in various RNA species today may already have started in the RNA world, where such modifications most likely entailed functional advantages. This association of modification patterns with functional features was apparently maintained throughout the further course of evolution, and particularly tRNAs can now be seen as paradigms for the developing interdependence between structure, modification and function. It is in this spirit that this review highlights important stepping stones of the development of (t)RNAs and their modifications (including aminoacylation) from the ancient RNA world up until their present role in the development and maintenance of human cognition. The latter can be seen as a high point of evolution at its present stage, and the susceptibility of cognitive features to even small alterations in the proper structure and functioning of tRNAs underscores the evolutionary relevance of this RNA species.
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29
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Hollenstein M. DNA Catalysis: The Chemical Repertoire of DNAzymes. Molecules 2015; 20:20777-804. [PMID: 26610449 PMCID: PMC6332124 DOI: 10.3390/molecules201119730] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Revised: 11/10/2015] [Accepted: 11/11/2015] [Indexed: 12/24/2022] Open
Abstract
Deoxyribozymes or DNAzymes are single-stranded catalytic DNA molecules that are obtained by combinatorial in vitro selection methods. Initially conceived to function as gene silencing agents, the scope of DNAzymes has rapidly expanded into diverse fields, including biosensing, diagnostics, logic gate operations, and the development of novel synthetic and biological tools. In this review, an overview of all the different chemical reactions catalyzed by DNAzymes is given with an emphasis on RNA cleavage and the use of non-nucleosidic substrates. The use of modified nucleoside triphosphates (dN*TPs) to expand the chemical space to be explored in selection experiments and ultimately to generate DNAzymes with an expanded chemical repertoire is also highlighted.
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Affiliation(s)
- Marcel Hollenstein
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
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30
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Nakano SI, Kitagawa Y, Yamashita H, Miyoshi D, Sugimoto N. Effects of Cosolvents on the Folding and Catalytic Activities of the Hammerhead Ribozyme. Chembiochem 2015; 16:1803-10. [DOI: 10.1002/cbic.201500139] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Indexed: 11/09/2022]
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31
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Famulok M, Mayer G. Aptamers and SELEX in Chemistry & Biology. ACTA ACUST UNITED AC 2015; 21:1055-8. [PMID: 25237853 DOI: 10.1016/j.chembiol.2014.08.003] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 07/23/2014] [Accepted: 08/01/2014] [Indexed: 02/06/2023]
Abstract
Nucleic acid aptamers, or simply aptamers, are oligonucleotides that bind specific ligands that vary from small molecules to proteins. An aptamer for a specific ligand is routinely identified through the process of systematic evolution of ligands by exponential enrichment, although some aptamers are found in nature as ligand-binding sites of special RNA structures called riboswitches. Aptamers have significant value in biotechnology and for the development of aptamer-based therapeutics. This perspective briefly highlights the tight connection between the journal Chemistry & Biology and in vitro selection technologies over the past two decades. We then focus our discussion on the summary of the current state of the art of aptamer technologies and provide our view of the future challenges and opportunities for the field.
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Affiliation(s)
- Michael Famulok
- Life and Medical Sciences Institute, University of Bonn, Chemical Biology Unit, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany.
| | - Günter Mayer
- Life and Medical Sciences Institute, University of Bonn, Chemical Biology Unit, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany.
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Abstract
An RNA world has been placed centre stage for explaining the origin of life. Indeed, RNA is the most plausible molecule able to form both a (self)-replicator and to inherit information, necessities for initiating genetics. However, in parallel with self-replication, the proto-organism had to obtain the ability to catalyse supply of its chemical constituents, including the ribonucleotide metabolites required to replicate RNA. Although the possibility of an RNA-catalysed metabolic network has been considered, it is to be questioned whether RNA molecules, at least on their own, possess the required catalytic capacities. An alternative scenario for the origin of metabolism involves chemical reactions that are based on environmental catalysts. Recently, we described a non-enzymatic glycolysis and pentose phosphate pathway-like reactions catalysed by metal ions [mainly Fe(II)] and phosphate, simple inorganic molecules abundantly found in Archaean sediments. While the RNA world can serve to explain the origin of genetics, the origin of the metabolic network might thus date back to constraints of environmental chemistry. Interestingly, considering a metal-catalysed origin of metabolism gives rise to an attractive hypothesis about how the first enzymes could have formed: simple RNA or (poly)peptide molecules could have bound the metal ions, and thus increased their solubility, concentration and accessibility. In a second step, this would have allowed substrate specificity to evolve.
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McDonald RI, Guilinger JP, Mukherji S, Curtis EA, Lee WI, Liu DR. Electrophilic activity-based RNA probes reveal a self-alkylating RNA for RNA labeling. Nat Chem Biol 2014; 10:1049-54. [PMID: 25306441 PMCID: PMC4232462 DOI: 10.1038/nchembio.1655] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 08/21/2014] [Indexed: 02/08/2023]
Abstract
Probes that form covalent bonds with RNA molecules on the basis of their chemical reactivity would advance our ability to study the transcriptome. We developed a set of electrophilic activity-based RNA probes designed to react with unusually nucleophilic RNAs. We used these probes to identify reactive genome-encoded RNAs, resulting in the discovery of a 42-nt catalytic RNA from an archaebacterium that reacts with a 2,3-disubstituted epoxide at N7 of a specific guanosine. Detailed characterization of the catalytic RNA revealed the structural requirements for reactivity. We developed this catalytic RNA into a general tool to selectively conjugate a small molecule to an RNA of interest. This strategy enabled up to 500-fold enrichment of target RNA from total mammalian RNA or from cell lysate. We demonstrated the utility of this approach by selectively capturing proteins in yeast cell lysate that bind the ASH1 mRNA.
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Affiliation(s)
- Richard I. McDonald
- Department of Chemistry and Chemical Biology and Howard Hughes Medical Institute, Harvard University, 12 Oxford St., Cambridge, MA, 02138 USA
| | - John P. Guilinger
- Department of Chemistry and Chemical Biology and Howard Hughes Medical Institute, Harvard University, 12 Oxford St., Cambridge, MA, 02138 USA
| | - Shankar Mukherji
- Department of Molecular and Cellular Biology and Howard Hughes Medical Institute, Harvard University, 52 Oxford St., Cambridge, MA 02138, USA
| | - Edward A. Curtis
- Department of Chemistry and Chemical Biology and Howard Hughes Medical Institute, Harvard University, 12 Oxford St., Cambridge, MA, 02138 USA
| | - Won I. Lee
- Department of Chemistry and Chemical Biology and Howard Hughes Medical Institute, Harvard University, 12 Oxford St., Cambridge, MA, 02138 USA
| | - David R. Liu
- Department of Chemistry and Chemical Biology and Howard Hughes Medical Institute, Harvard University, 12 Oxford St., Cambridge, MA, 02138 USA
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Szilágyi A, Kun Á, Szathmáry E. Local neutral networks help maintain inaccurately replicating ribozymes. PLoS One 2014; 9:e109987. [PMID: 25299454 PMCID: PMC4192543 DOI: 10.1371/journal.pone.0109987] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 09/05/2014] [Indexed: 12/03/2022] Open
Abstract
The error threshold of replication limits the selectively maintainable genome size against recurrent deleterious mutations for most fitness landscapes. In the context of RNA replication a distinction between the genotypic and the phenotypic error threshold has been made; where the latter concerns the maintenance of secondary structure rather than sequence. RNA secondary structure is treated as a proxy for function. The phenotypic error threshold allows higher per digit mutation rates than its genotypic counterpart, and is known to increase with the frequency of neutral mutations in sequence space. Here we show that the degree of neutrality, i.e. the frequency of nearest-neighbour (one-step) neutral mutants is a remarkably accurate proxy for the overall frequency of such mutants in an experimentally verifiable formula for the phenotypic error threshold; this we achieve by the full numerical solution for the concentration of all sequences in mutation-selection balance up to length 16. We reinforce our previous result that currently known ribozymes could be selectively maintained by the accuracy known from the best available polymerase ribozymes. Furthermore, we show that in silico stabilizing selection can increase the mutational robustness of ribozymes due to the fact that they were produced by artificial directional selection in the first place. Our finding offers a better understanding of the error threshold and provides further insight into the plausibility of an ancient RNA world.
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Affiliation(s)
- András Szilágyi
- Parmenides Center for the Conceptual Foundations of Science, Munich/Pullach, Germany
- MTA-ELTE Theoretical Biology and Evolutionary Ecology Research Group, Budapest, Hungary
| | - Ádám Kun
- Parmenides Center for the Conceptual Foundations of Science, Munich/Pullach, Germany
- MTA-ELTE-MTM Ecology Research Group, Budapest, Hungary
| | - Eörs Szathmáry
- Parmenides Center for the Conceptual Foundations of Science, Munich/Pullach, Germany
- MTA-ELTE Theoretical Biology and Evolutionary Ecology Research Group, Budapest, Hungary
- Department of Plant Systematics, Ecology and Theoretical Biology, Institute of Biology, Eötvös Loránd University, Budapest, Hungary
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35
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Breaker RR, Joyce GF. The expanding view of RNA and DNA function. CHEMISTRY & BIOLOGY 2014; 21:1059-65. [PMID: 25237854 PMCID: PMC4171699 DOI: 10.1016/j.chembiol.2014.07.008] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 07/16/2014] [Accepted: 07/21/2014] [Indexed: 11/28/2022]
Abstract
RNA and DNA are simple linear polymers consisting of only four major types of subunits, and yet these molecules carry out a remarkable diversity of functions in cells and in the laboratory. Each newly discovered function of natural or engineered nucleic acids enforces the view that prior assessments of nucleic acid function were far too narrow and that many more exciting findings are yet to come. This Perspective highlights just a few of the numerous discoveries over the past 20 years pertaining to nucleic acid function, focusing on those that have been of particular interest to chemical biologists. History suggests that there will continue to be many opportunities to engage chemical biologists in the discovery, creation, and manipulation of nucleic acid function in the years to come.
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Affiliation(s)
- Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, and Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University, Box 208103, New Haven, CT 06520, USA.
| | - Gerald F Joyce
- Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA.
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36
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Rublack N, Müller S. Synthesis of a bifunctional cytidine derivative and its conjugation to RNA for in vitro selection of a cytidine deaminase ribozyme. Beilstein J Org Chem 2014; 10:1906-13. [PMID: 25246949 PMCID: PMC4168874 DOI: 10.3762/bjoc.10.198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 07/30/2014] [Indexed: 11/23/2022] Open
Abstract
Over the past 20 years, the generation of functional RNAs by in vitro selection has become a standard technique. Apart from aptamers for simple binding of defined ligands, also RNAs for catalysis of chemical reactions have been selected. In the latter case, a key step often is the conjugation of one of the two reactants to the library, requiring suitable strategies for terminal or internal RNA functionalization. With the aim of selecting a ribozyme for deamination of cytidine, we have set up a selection scheme involving the attachment of the cytidine acting as deamination substrate to the 3'-terminus of the RNAs in the library, and library immobilization. Here, we report the synthesis of a bifunctional cytidine derivative suitable for conjugation to RNA and linkage of the conjugated library to a streptavidine-coated surface. Successful conjugation of the cytidine derivative to the 3'-terminus of a model RNA is demonstrated.
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Affiliation(s)
- Nico Rublack
- Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
| | - Sabine Müller
- Institut für Biochemie, Ernst-Moritz-Arndt-Universität Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
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37
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Urata S, Miyahata T, Matsuura H, Kitamura Y, Ihara T. Alteration of DNAzyme Activity by Silver Ion. CHEM LETT 2014. [DOI: 10.1246/cl.140197] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Shoma Urata
- Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University
| | - Takaaki Miyahata
- Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University
| | - Hirotaka Matsuura
- Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University
| | - Yusuke Kitamura
- Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University
- CREST, Japan Science and Technology Agency
| | - Toshihiro Ihara
- Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University
- CREST, Japan Science and Technology Agency
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38
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Keller MA, Turchyn AV, Ralser M. Non-enzymatic glycolysis and pentose phosphate pathway-like reactions in a plausible Archean ocean. Mol Syst Biol 2014; 10:725. [PMID: 24771084 PMCID: PMC4023395 DOI: 10.1002/msb.20145228] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 03/11/2014] [Accepted: 03/18/2014] [Indexed: 11/30/2022] Open
Abstract
The reaction sequences of central metabolism, glycolysis and the pentose phosphate pathway provide essential precursors for nucleic acids, amino acids and lipids. However, their evolutionary origins are not yet understood. Here, we provide evidence that their structure could have been fundamentally shaped by the general chemical environments in earth's earliest oceans. We reconstructed potential scenarios for oceans of the prebiotic Archean based on the composition of early sediments. We report that the resultant reaction milieu catalyses the interconversion of metabolites that in modern organisms constitute glycolysis and the pentose phosphate pathway. The 29 observed reactions include the formation and/or interconversion of glucose, pyruvate, the nucleic acid precursor ribose-5-phosphate and the amino acid precursor erythrose-4-phosphate, antedating reactions sequences similar to that used by the metabolic pathways. Moreover, the Archean ocean mimetic increased the stability of the phosphorylated intermediates and accelerated the rate of intermediate reactions and pyruvate production. The catalytic capacity of the reconstructed ocean milieu was attributable to its metal content. The reactions were particularly sensitive to ferrous iron Fe(II), which is understood to have had high concentrations in the Archean oceans. These observations reveal that reaction sequences that constitute central carbon metabolism could have been constrained by the iron-rich oceanic environment of the early Archean. The origin of metabolism could thus date back to the prebiotic world.
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Affiliation(s)
- Markus A Keller
- Department of Biochemistry and Cambridge Systems Biology CentreUniversity of CambridgeCambridgeUK
| | | | - Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology CentreUniversity of CambridgeCambridgeUK
- Division of Physiology and MetabolismMRC National Institute for Medical ResearchMill HillLondonUK
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39
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Wang F, Lu CH, Willner I. From cascaded catalytic nucleic acids to enzyme-DNA nanostructures: controlling reactivity, sensing, logic operations, and assembly of complex structures. Chem Rev 2014; 114:2881-941. [PMID: 24576227 DOI: 10.1021/cr400354z] [Citation(s) in RCA: 494] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Fuan Wang
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
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40
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Generation and selection of ribozyme variants with potential application in protein engineering and synthetic biology. Appl Microbiol Biotechnol 2014; 98:3389-99. [DOI: 10.1007/s00253-014-5528-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 01/06/2014] [Accepted: 01/07/2014] [Indexed: 12/22/2022]
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41
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Ameta S, Winz ML, Previti C, Jäschke A. Next-generation sequencing reveals how RNA catalysts evolve from random space. Nucleic Acids Res 2013; 42:1303-10. [PMID: 24157838 PMCID: PMC3902939 DOI: 10.1093/nar/gkt949] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Catalytic RNAs are attractive objects for studying molecular evolution. To understand how RNA libraries can evolve from randomness toward highly active catalysts, we analyze the original samples that led to the discovery of Diels-Alderase ribozymes by next-generation sequencing. Known structure-activity relationships are used to correlate abundance with catalytic performance. We find that efficient catalysts arose not just from selection for reactivity among the members of the starting library, but from improvement of less potent precursors by mutations. We observe changes in the ribozyme population in response to increasing selection pressure. Surprisingly, even after many rounds of enrichment, the libraries are highly diverse, suggesting that potential catalysts are more abundant in random space than generally thought. To highlight the use of next-generation sequencing as a tool for in vitro selections, we also apply this technique to a recent, less characterized ribozyme selection. Making use of the correlation between sequence evolution and catalytic activity, we predict mutations that improve ribozyme activity and validate them biochemically. Our study reveals principles underlying ribozyme in vitro selections and provides guidelines to render future selections more efficient, as well as to predict the conservation of key structural elements, allowing the rational improvement of catalysts.
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Affiliation(s)
- Sandeep Ameta
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, 69120-Heidelberg, Germany and High Throughput Sequencing Core Facility, German Cancer Research Center (DKFZ), 69120-Heidelberg, Germany
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42
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Hollenstein M. Deoxynucleoside triphosphates bearing histamine, carboxylic acid, and hydroxyl residues--synthesis and biochemical characterization. Org Biomol Chem 2013; 11:5162-72. [PMID: 23817514 DOI: 10.1039/c3ob40842f] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Modified nucleoside triphosphates (dA(Hs)TP, dU(POH)TP, and dC(Val)TP) bearing imidazole, hydroxyl, and carboxylic acid residues connected to the purine and pyrimidine bases through alkyne linkers were prepared. These modified dN*TPs were excellent substrates for various DNA polymerases in primer extension reactions. Moreover, the combined use of terminal deoxynucleotidyl transferase (TdT) and the modified dNTPs led to efficient tailing reactions that rival those of natural counterparts. Finally, the triphosphates were tolerated by polymerases under PCR conditions, and the ensuing modified oligonucleotides served as templates for the regeneration of unmodified DNA. Thus, these modified dN*TPs are fully compatible with in vitro selection methods and can be used to develop artificial peptidases based on DNA.
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Affiliation(s)
- Marcel Hollenstein
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
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43
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Uzawa T, Tada S, Wang W, Ito Y. Expansion of the aptamer library from a "natural soup" to an "unnatural soup". Chem Commun (Camb) 2013; 49:1786-95. [PMID: 23283144 DOI: 10.1039/c2cc36348h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The possibility of evolving a commonly existing biomolecule into a variety of functional biomolecules has now been realized in the form of aptamers through the development of in vitro selection. In addition to their high affinity and high specificity for the desired targets, aptamers are easily synthesized chemically and can be modified for downstream applications. Although aptamers were originally selected from a library containing only natural components, the past decade has seen a wealth of new aptamers selected from libraries containing unnatural components to provide new aptamer functions artificially. In this review, we highlight this transition (the shift between selection from natural components and selection from unnatural components) and the applications of selected aptamers.
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Affiliation(s)
- Takanori Uzawa
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.
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44
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Photochemically relevant DNA-based molecular systems enabling chemical and signal transductions and their analytical applications. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2012. [DOI: 10.1016/j.jphotochemrev.2012.03.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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45
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Huang F, Shi Y. Synthesis of photolabile transcription initiators and preparation of photocleavable functional RNA by transcription. Bioorg Med Chem Lett 2012; 22:4254-8. [PMID: 22677315 DOI: 10.1016/j.bmcl.2012.05.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 05/03/2012] [Accepted: 05/08/2012] [Indexed: 12/20/2022]
Abstract
Two new photolabile adenosine-containing transcription initiators with terminal thiol and amino functionalities are chemically synthesized. Transcription in the presence of the transcription initiators under the T7 phi2.5 promoter produces 5' thiol- and amino-functionalized RNA conjugated by a photocleavable (PC) linker. Further RNA functionalization with biotin may be achieved through acyl transfer reactions from either biotinyl AMP to the RNA thiol group or biotin NHS to the RNA amino group. Photocleavage of the PC linker displays relatively fast kinetics with a half-life of 4-5 min. The availability of these transcription initiators makes new photolabile RNA accessible for affinity purification of RNA, in vitro selection of functional RNAs, and functional RNA caging.
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Affiliation(s)
- Faqing Huang
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, MS 39406-5043, USA.
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46
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Wang TP, Su YC, Chen Y, Liou YM, Lin KL, Wang EC, Hwang LC, Wang YM, Chen YH. In vitro selection and characterization of a novel Zn(II)-dependent phosphorothiolate thiolesterase ribozyme. Biochemistry 2011; 51:496-510. [PMID: 22175782 DOI: 10.1021/bi201585d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Here we present the in vitro selection of a novel ribozyme specific for Zn2+-dependent catalysis on hydrolysis of a phosphorothiolate thiolester bond. The ribozyme, called the TW17 ribozyme, was evolved and selected from an artificial RNA pool covalently linked to a biotin-containing substrate through the phosphorothiolate thiolester bond. The secondary structure for the evolved ribozyme consisted of three major helices and three loops. Biochemical and chemical studies of ribozyme-catalyzed reaction products provided evidence that the ribozyme specifically catalyzes hydrolysis of the phosphorothiolate thiolester linkage. A successful ribozyme construct with active catalysis in trans further supported the determined ribozyme structure and indicated the potential of the ribozyme for multiple-substrate turnover. The ribozyme also requires Zn2+ and Mg2+ for maximal catalysis. The TW17 ribozyme, in the presence of Zn2+ and Mg2+, conferred a rate enhancement of at least 5 orders of magnitude when compared to the estimated rate of the uncatalyzed reaction. The ribozyme completely lost catalytic activity in the absence of Zn2+, like Zn2+-dependent protein hydrolases. The discovery and characterization of the TW17 ribozyme suggest additional roles for Zn2+ in ribozyme catalysts.
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Affiliation(s)
- Tzu-Pin Wang
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.
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47
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Eschenmoser A. Ätiologie potentiell primordialer Biomolekül-Strukturen: Vom Vitamin B12 zu den Nukleinsäuren und der Frage nach der Chemie der Entstehung des Lebens - ein Rückblick. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201103672] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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48
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Eschenmoser A. Etiology of potentially primordial biomolecular structures: from vitamin B12 to the nucleic acids and an inquiry into the chemistry of life's origin: a retrospective. Angew Chem Int Ed Engl 2011; 50:12412-72. [PMID: 22162284 DOI: 10.1002/anie.201103672] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Indexed: 11/10/2022]
Abstract
"We'll never be able to know" is a truism that leads to resignation with respect to any experimental effort to search for the chemistry of life's origin. But such resignation runs radically counter to the challenge imposed upon chemistry as a natural science. Notwithstanding the prognosis according to which the shortest path to understanding the metamorphosis of the chemical into the biological is by way of experimental modeling of "artificial chemical life", the scientific search for the route nature adopted in creating the life we know will arguably never truly end. It is, after all, part of the search for our own origin.
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Affiliation(s)
- Albert Eschenmoser
- Organisch-chemisches Laboratorium der ETH Zürich, Hönggerberg, Wolfgang-Pauli-Str. 10, CHI H309, CH-8093 Zürich, Switzerland
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49
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Dong Z, Yongguo Wang, Yin Y, Liu J. Supramolecular enzyme mimics by self-assembly. Curr Opin Colloid Interface Sci 2011. [DOI: 10.1016/j.cocis.2011.08.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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50
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Talini G, Branciamore S, Gallori E. Ribozymes: Flexible molecular devices at work. Biochimie 2011; 93:1998-2005. [PMID: 21740954 DOI: 10.1016/j.biochi.2011.06.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2011] [Accepted: 06/23/2011] [Indexed: 11/17/2022]
Abstract
The discovery of ribozymes, RNAs with catalytic activity, revealed the extraordinary characteristic of this molecule, and corroborated the idea that RNA was the first informative polymer. The "RNA world" hypothesis asserts that the DNA/RNA/PROTEIN world arose from an earlier RNA world in which were present only RNA molecules able to perform both of the two functions performed separately by DNA and proteins in the present-day cells: the ability to transfer genetic information and to carry out catalytic activity. The catalytic properties of ribozymes are exclusively due to the capacity of RNA molecules to assume particular structures. Moreover, the structural versatility of RNA can allow to a single RNA sequence to fold in more than one structure, able to perform more than one function. In the first part of this work we will discuss the RNA plasticity, focusing on "bifunctional" ribozymes isolated by in vitro selection experiments, and on the consequences of this plasticity in the prospective of the emergence of new specific functions. The possibility that one sequence could have more than one structure/function, greatly increase the evolutionary potential of RNA, and the capacity of RNA to switch from a structure/function to another is probably one of the reasons of the evolutionary success also in modern-day cells. Naturally occurring ribozymes discovered in contemporary cells, demonstrate the crucial role that ribozymes still have in the modern protein world. In the second part of this paper we will discuss the capacity of natural ribozymes to modulate gene expression making use of their exclusive catalytic properties. Moreover, we will consider the possibility of their ancient origin.
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Affiliation(s)
- Giulia Talini
- Laboratory of Cancer Genetics and Gene Transfer, Core Research Laboratory, Istituto Toscano Tumori, AOU Careggi, Viale Pieraccini 6, 50139 Florence, Italy
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