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Fontecilla-Camps JC. Reflections on the Origin of Coded Protein Biosynthesis. Biomolecules 2024; 14:518. [PMID: 38785925 PMCID: PMC11117964 DOI: 10.3390/biom14050518] [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: 04/09/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024] Open
Abstract
The principle of continuity posits that some central features of primordial biocatalytic mechanisms should still be present in the genetically dependent pathway of protein synthesis, a crucial step in the emergence of life. Key bimolecular reactions of this process are catalyzed by DNA-dependent RNA polymerases, aminoacyl-tRNA synthetases, and ribosomes. Remarkably, none of these biocatalysts contribute chemically active groups to their respective reactions. Instead, structural and functional studies have demonstrated that nucleotidic α-phosphate and β-d-ribosyl 2' OH and 3' OH groups can help their own catalysis, a process which, consequently, has been called "substrate-assisted". Furthermore, upon binding, the substrates significantly lower the entropy of activation, exclude water from these catalysts' active sites, and are readily positioned for a reaction. This binding mode has been described as an "entropy trap". The combination of this effect with substrate-assisted catalysis results in reactions that are stereochemically and mechanistically simpler than the ones found in most modern enzymes. This observation is consistent with the way in which primordial catalysts could have operated; it may also explain why, thanks to their complementary reactivities, β-d-ribose and phosphate were naturally selected to be the central components of early coding polymers.
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2
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Rodrigues F, Georgelin T, Rigaud B, Zhuang G, Fonseca MG, Valtchev V, Jaber M. Deadlocks of adenine ribonucleotide synthesis: evaluation of adsorption and condensation reactions in a zeolite micropore space. Inorg Chem Front 2022. [DOI: 10.1039/d2qi00837h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, we report on adenine, d-ribose, and monophosphate adsorption/co-adsorption into the synthetic analog of the zeolite mineral mordenite followed by drying at 50 °C and thermal activation at 150 °C under an argon atmosphere.
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Affiliation(s)
- Francisco Rodrigues
- Sorbonne University, CNRS UMR 8220, Laboratoire d'Archéologie Moléculaire et Structurale, 4 place Jussieu, F-75005 Paris, France
- State University of Paraíba, UEPB, Department of Chemistry, Campina Grande, Paraíba, Brazil
| | - Thomas Georgelin
- Centre de Biophysique Moléculaire, CNRS, Rue Charles Sadron, 45000 Orléans, France
| | - Baptiste Rigaud
- CNRS Institut des Matériaux de Paris Centre (FR2482), 4 place jussieu, 75005 Paris, France
| | - Guanzheng Zhuang
- Sorbonne University, CNRS UMR 8220, Laboratoire d'Archéologie Moléculaire et Structurale, 4 place Jussieu, F-75005 Paris, France
| | | | - Valentin Valtchev
- Normandy University, Laboratoire Catalyse & Spectrochimie, ENSICAEN, 6 bl Maréchal Juin, 14050 Caen, France
| | - Maguy Jaber
- Sorbonne University, CNRS UMR 8220, Laboratoire d'Archéologie Moléculaire et Structurale, 4 place Jussieu, F-75005 Paris, France
- Institut Universitaire de France, France
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3
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Zhao ZR, Wang X. A plausible prebiotic selection of ribose for RNA - formation, dynamic isolation, and nucleotide synthesis based on metal-doped-clays. Chem 2021. [DOI: 10.1016/j.chempr.2021.09.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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4
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Banfalvi G. Prebiotic Pathway from Ribose to RNA Formation. Int J Mol Sci 2021; 22:ijms22083857. [PMID: 33917807 PMCID: PMC8068141 DOI: 10.3390/ijms22083857] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/31/2021] [Accepted: 04/06/2021] [Indexed: 01/12/2023] Open
Abstract
At the focus of abiotic chemical reactions is the synthesis of ribose. No satisfactory explanation was provided as to the missing link between the prebiotic synthesis of ribose and prebiotic RNA (preRNA). Hydrogen cyanide (HCN) is assumed to have been the principal precursor in the prebiotic formation of aldopentoses in the formose reaction and in the synthesis of ribose. Ribose as the best fitting aldopentose became the exclusive sugar component of RNA. The elevated yield of ribose synthesis at higher temperatures and its protection from decomposition could have driven the polymerization of the ribose-phosphate backbone and the coupling of nucleobases to the backbone. RNA could have come into being without the involvement of nucleotide precursors. The first nucleoside monophosphate is likely to have appeared upon the hydrolysis of preRNA contributed by the presence of reactive 2′-OH moieties in the preRNA chain. As a result of phosphorylation, nucleoside monophosphates became nucleoside triphosphates, substrates for the selective synthesis of genRNA.
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Affiliation(s)
- Gaspar Banfalvi
- Department of Molecular Biotechnology and Microbiology, University of Debrecen, 1 Egyetem Square, 4010 Debrecen, Hungary
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5
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Bizzarri BM, Šponer JE, Šponer J, Cassone G, Kapralov M, Timoshenko GN, Krasavin E, Fanelli G, Timperio AM, Di Mauro E, Saladino R. Meteorite‐Assisted Phosphorylation of Adenosine Under Proton Irradiation Conditions. CHEMSYSTEMSCHEM 2019. [DOI: 10.1002/syst.201900039] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Bruno M. Bizzarri
- Department of Ecological and Biological SciencesUniversity of Tuscia Via S. Camillo de Lellis 01100 Viterbo Italy
| | - Judit E. Šponer
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 CZ-61265 Brno Czech Republic
- Regional Centre of Advanced Technologies and Materials Faculty of SciencePalacky University 17 listopadu 771 46 Olomouc Czech Republic
| | - Jiri Šponer
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 CZ-61265 Brno Czech Republic
- Regional Centre of Advanced Technologies and Materials Faculty of SciencePalacky University 17 listopadu 771 46 Olomouc Czech Republic
| | - Giuseppe Cassone
- Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 CZ-61265 Brno Czech Republic
| | - Michail Kapralov
- Joint Institute for Nuclear ResearchJINR's Laboratory of Radiation Biology Dubna Russia
| | - Gennady N. Timoshenko
- Joint Institute for Nuclear ResearchJINR's Laboratory of Radiation Biology Dubna Russia
| | - Eugene Krasavin
- Joint Institute for Nuclear ResearchJINR's Laboratory of Radiation Biology Dubna Russia
| | - Giuseppina Fanelli
- Department of Science and Technology for Agriculture, Forestry, Nature, and EnergyUniversity of Tuscia Via S. Camillo de Lellis 01100 Viterbo Italy
| | - Anna Maria Timperio
- Department of Ecological and Biological SciencesUniversity of Tuscia Via S. Camillo de Lellis 01100 Viterbo Italy
| | - Ernesto Di Mauro
- Department of Ecological and Biological SciencesUniversity of Tuscia Via S. Camillo de Lellis 01100 Viterbo Italy
| | - Raffaele Saladino
- Department of Ecological and Biological SciencesUniversity of Tuscia Via S. Camillo de Lellis 01100 Viterbo Italy
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6
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Franco A, Ascenso J, Ilharco L, Diogo H, André V, da Silva J. Ribose-borate esters as potential components for prebiological evolution. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.02.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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7
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Fontecilla-Camps JC. Geochemical Continuity and Catalyst/Cofactor Replacement in the Emergence and Evolution of Life. Angew Chem Int Ed Engl 2018; 58:42-48. [DOI: 10.1002/anie.201808438] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/27/2018] [Indexed: 12/29/2022]
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8
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Fontecilla-Camps JC. Geochemische Kontinuität und Katalysator/Cofaktor-Austausch für Ursprung und Evolution des Lebens. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201808438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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9
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Nakashima S, Kebukawa Y, Kitadai N, Igisu M, Matsuoka N. Geochemistry and the Origin of Life: From Extraterrestrial Processes, Chemical Evolution on Earth, Fossilized Life's Records, to Natures of the Extant Life. Life (Basel) 2018; 8:E39. [PMID: 30241342 PMCID: PMC6315873 DOI: 10.3390/life8040039] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 09/15/2018] [Accepted: 09/17/2018] [Indexed: 11/18/2022] Open
Abstract
In 2001, the first author (S.N.) led the publication of a book entitled "Geochemistry and the origin of life" in collaboration with Dr. Andre Brack aiming to figure out geo- and astro-chemical processes essential for the emergence of life. Since then, a great number of research progress has been achieved in the relevant topics from our group and others, ranging from the extraterrestrial inputs of life's building blocks, the chemical evolution on Earth with the aid of mineral catalysts, to the fossilized records of ancient microorganisms. Here, in addition to summarizing these findings for the origin and early evolution of life, we propose a new hypothesis for the generation and co-evolution of photosynthesis with the redox and photochemical conditions on the Earth's surface. Besides these bottom-up approaches, we introduce an experimental study on the role of water molecules in the life's function, focusing on the transition from live, dormant, and dead states through dehydration/hydration. Further spectroscopic studies on the hydrogen bonding behaviors of water molecules in living cells will provide important clues to solve the complex nature of life.
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Affiliation(s)
- Satoru Nakashima
- Department of Earth and Space Science, Osaka University, Toyonaka, Osaka 560-0043, Japan.
- Undergraduate School of Physics, Osaka University, Toyonaka, Osaka 560-0043, Japan.
| | - Yoko Kebukawa
- Department of Earth and Space Science, Osaka University, Toyonaka, Osaka 560-0043, Japan.
- Faculty of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan.
| | - Norio Kitadai
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1, Ookayama, Meguro-ku, Tokyo 152-8550, Japan.
| | - Motoko Igisu
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Kanagawa 237-0061, Japan.
| | - Natsuki Matsuoka
- Undergraduate School of Physics, Osaka University, Toyonaka, Osaka 560-0043, Japan.
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Westall F, Hickman-Lewis K, Hinman N, Gautret P, Campbell KA, Bréhéret JG, Foucher F, Hubert A, Sorieul S, Dass AV, Kee TP, Georgelin T, Brack A. A Hydrothermal-Sedimentary Context for the Origin of Life. ASTROBIOLOGY 2018; 18:259-293. [PMID: 29489386 PMCID: PMC5867533 DOI: 10.1089/ast.2017.1680] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 09/07/2017] [Indexed: 05/02/2023]
Abstract
Critical to the origin of life are the ingredients of life, of course, but also the physical and chemical conditions in which prebiotic chemical reactions can take place. These factors place constraints on the types of Hadean environment in which life could have emerged. Many locations, ranging from hydrothermal vents and pumice rafts, through volcanic-hosted splash pools to continental springs and rivers, have been proposed for the emergence of life on Earth, each with respective advantages and certain disadvantages. However, there is another, hitherto unrecognized environment that, on the Hadean Earth (4.5-4.0 Ga), would have been more important than any other in terms of spatial and temporal scale: the sedimentary layer between oceanic crust and seawater. Using as an example sediments from the 3.5-3.33 Ga Barberton Greenstone Belt, South Africa, analogous at least on a local scale to those of the Hadean eon, we document constant permeation of the porous, carbonaceous, and reactive sedimentary layer by hydrothermal fluids emanating from the crust. This partially UV-protected, subaqueous sedimentary environment, characterized by physical and chemical gradients, represented a widespread system of miniature chemical reactors in which the production and complexification of prebiotic molecules could have led to the origin of life. Key Words: Origin of life-Hadean environment-Mineral surface reactions-Hydrothermal fluids-Archean volcanic sediments. Astrobiology 18, 259-293.
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Affiliation(s)
- F Westall
- 1 CNRS-Centre de Biophysique Moléculaire , Orléans, France
| | - K Hickman-Lewis
- 1 CNRS-Centre de Biophysique Moléculaire , Orléans, France
- 2 Dipartmento di Scienze biologiche, geologiche e ambientale, Università di Bologna , Bologna, Italy
| | - N Hinman
- 3 Geosciences, University of Montana , Missoula, Montana, USA
| | - P Gautret
- 4 University of Orléans , ISTO, UMR 7327, Orléans, France, and CNRS, ISTO, UMR 7327, Orléans, France, and BRGM, ISTO, UMR 7327, Orléans, France
| | - K A Campbell
- 5 School of Environment, The University of Auckland , Auckland, New Zealand
| | - J G Bréhéret
- 6 GéoHydrosytèmes Continentaux, Faculté des Sciences et Techniques, Université François-Rabelais de Tours , Tours, France
| | - F Foucher
- 1 CNRS-Centre de Biophysique Moléculaire , Orléans, France
| | - A Hubert
- 1 CNRS-Centre de Biophysique Moléculaire , Orléans, France
| | - S Sorieul
- 7 University of Bordeaux , CNRS, IN2P3, CENBG, UMR5797, Gradignan, France
| | - A V Dass
- 1 CNRS-Centre de Biophysique Moléculaire , Orléans, France
| | - T P Kee
- 8 School of Chemistry, University of Leeds , Leeds, UK
| | - T Georgelin
- 1 CNRS-Centre de Biophysique Moléculaire , Orléans, France
- 9 Sorbonne Universités , UPMC Paris 06, CNRS UMR 7197, Laboratoire de Réactivité de Surface, Paris, France
| | - A Brack
- 1 CNRS-Centre de Biophysique Moléculaire , Orléans, France
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11
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Saladino R, Bizzarri BM, Botta L, Šponer J, Šponer JE, Georgelin T, Jaber M, Rigaud B, Kapralov M, Timoshenko GN, Rozanov A, Krasavin E, Timperio AM, Mauro ED. Proton irradiation: a key to the challenge of N-glycosidic bond formation in a prebiotic context. Sci Rep 2017; 7:14709. [PMID: 29116184 PMCID: PMC5677017 DOI: 10.1038/s41598-017-15392-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/26/2017] [Indexed: 11/10/2022] Open
Abstract
The formation of nucleosides in abiotic conditions is a major hurdle in origin-of-life studies. We have determined the pathway of a general reaction leading to the one-pot synthesis of ribo- and 2'-deoxy-ribonucleosides from sugars and purine nucleobases under proton irradiation in the presence of a chondrite meteorite. These conditions simulate the presumptive conditions in space or on an early Earth fluxed by slow protons from the solar wind, potentially mimicking a plausible prebiotic scenario. The reaction (i) requires neither pre-activated precursors nor intermediate purification/concentration steps, (ii) is based on a defined radical mechanism, and (iii) is characterized by stereoselectivity, regioselectivity and (poly)glycosylation. The yield is enhanced by formamide and meteorite relative to the control reaction.
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Affiliation(s)
- Raffaele Saladino
- Department of Ecological and Biological Sciences, Via S. Camillo de Lellis, University of Tuscia, 01100, Viterbo, Italy.
| | - Bruno M Bizzarri
- Department of Ecological and Biological Sciences, Via S. Camillo de Lellis, University of Tuscia, 01100, Viterbo, Italy
| | - Lorenzo Botta
- Department of Ecological and Biological Sciences, Via S. Camillo de Lellis, University of Tuscia, 01100, Viterbo, Italy
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-61265, Brno, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17. Listopadu, 771 46, Olomouc, Czech Republic
| | - Judit E Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-61265, Brno, Czech Republic
| | - Thomas Georgelin
- Sorbonne Universités, UPMC Paris 06, CNRS UMR 7197, Laboratoire de Réactivité de Surface 4 place Jussieu, F-75005, Paris, France
- Centre de Biophysique Moleculaire, UPR CNRS4301, Orléans, France
| | - Maguy Jaber
- Sorbonne Universités, UPMC Paris06, CNRS UMR 8220, Laboratoire d'Archéologie Moléculaire et Structurale, Paris, France
| | - Baptiste Rigaud
- CNRS Institut des Matériaux de Paris Centre (FR2482), Paris, France
| | - Mikhail Kapralov
- Joint Institute for Nuclear Research, JINR's Laboratory of Radiation Biology, Dubna, Russia
| | - Gennady N Timoshenko
- Joint Institute for Nuclear Research, JINR's Laboratory of Radiation Biology, Dubna, Russia
| | - Alexei Rozanov
- Joint Institute for Nuclear Research, JINR's Laboratory of Radiation Biology, Dubna, Russia
| | - Eugene Krasavin
- Joint Institute for Nuclear Research, JINR's Laboratory of Radiation Biology, Dubna, Russia
| | - Anna Maria Timperio
- Department of Ecological and Biological Sciences, Via S. Camillo de Lellis, University of Tuscia, 01100, Viterbo, Italy
| | - Ernesto Di Mauro
- Department of Ecological and Biological Sciences, Via S. Camillo de Lellis, University of Tuscia, 01100, Viterbo, Italy.
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12
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Kawamura K, Maurel MC. Walking over 4 Gya: Chemical Evolution from Photochemistry to Mineral and Organic Chemistries Leading to an RNA World. ORIGINS LIFE EVOL B 2017; 47:281-296. [PMID: 28432500 DOI: 10.1007/s11084-017-9537-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Accepted: 01/20/2017] [Indexed: 01/25/2023]
Abstract
Here we overview the chemical evolution of RNA molecules from inorganic material through mineral-mediated RNA formation compatible with the plausible early Earth environments. Pathways from the gas-phase reaction to the formation of nucleotides, activation and oligomerization of nucleotides, seem to be compatible with specific environments. However, how these steps interacted is not clear since the chemical conditions are frequently different and can be incompatible between them; thus the products would have migrated from one place to another, suitable for further chemical evolution. In this review, we summarize certain points to scrutinize the RNA World hypothesis.
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Affiliation(s)
- Kunio Kawamura
- Department of Human Environmental Studies, Hiroshima Shudo University, 1-1-1 Ozuka-higashi, Asaminami-ku, Hiroshima, 731-3195, Japan.
| | - Marie-Christine Maurel
- Institut de Systématique, Evolution, Biodiversité (ISYEB), UMR 7205 CNRS MNHN UPMC EPHE, Sorbonne Universités, 50, 57 rue Cuvier, 75005, Paris, CP, France
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