1
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Banfalvi G. The Origin of RNA and the Formose-Ribose-RNA Pathway. Int J Mol Sci 2024; 25:6727. [PMID: 38928433 PMCID: PMC11203418 DOI: 10.3390/ijms25126727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/03/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Prebiotic pre-Darwinian reactions continued throughout biochemical or Darwinian evolution. Early chemical processes could have occurred on Earth between 4.5 and 3.6 billion years ago when cellular life was about to come into being. Pre-Darwinian evolution assumes the development of hereditary elements but does not regard them as self-organizing processes. The presence of biochemical self-organization after the pre-Darwinian evolution did not justify distinguishing between different types of evolution. From the many possible solutions, evolution selected from among those stable reactions that led to catalytic networks, and under gradually changing external conditions produced a reproducible, yet constantly evolving and adaptable, living system. Major abiotic factors included sunlight, precipitation, air, minerals, soil and the Earth's atmosphere, hydrosphere and lithosphere. Abiotic sources of chemicals contributed to the formation of prebiotic RNA, the development of genetic RNA, the RNA World and the initial life forms on Earth and the transition of genRNA to the DNA Empire, and eventually to the multitude of life forms today. The transition from the RNA World to the DNA Empire generated new processes such as oxygenic photosynthesis and the hierarchical arrangement of processes involved in the transfer of genetic information. The objective of this work is to unite earlier work dealing with the formose, the origin and synthesis of ribose and RNA reactions that were published as a series of independent reactions. These reactions are now regarded as the first metabolic pathway.
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Affiliation(s)
- Gaspar Banfalvi
- Department of Molecular Biotechnology and Microbiology, University of Debrecen, 4032 Debrecen, Hungary
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2
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Balloi V, Diaz-Perez MA, Lara-Angulo MA, Villalgordo-Hernández D, Narciso J, Ramos-Fernandez EV, Serrano-Ruiz JC. Metal-Organic Frameworks as Formose Reaction Catalysts with Enhanced Selectivity. Molecules 2023; 28:6095. [PMID: 37630347 PMCID: PMC10458508 DOI: 10.3390/molecules28166095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 07/28/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
The formose reaction is an autocatalytic series of aldol condensations that allows one to obtain monosaccharides from formaldehyde. The formose reaction suffers from a lack of selectivity, which hinders practical applications at the industrial level. Over the years, many attempts have been made to overcome this selectivity issue, with modest results. Heterogeneous porous catalysts with acid-base properties, such as Metal-Organic Frameworks (MOFs), can offer advantages compared to homogeneous strong bases (e.g., calcium hydroxide) for increasing the selectivity of this important reaction. For the very first time, four different Zeolite Imidazolate Frameworks are presented in this work as catalysts for the formose reaction in liquid phase, and their catalytic performances were compared with those of the typical homogeneous catalyst (i.e., calcium hydroxide). The heterogeneous nature of the catalysis, the possible contribution of leached metal or linkers to the solution, and the stability of the materials were investigated. The porous structure of these solids and their mild basicity make them suitable for obtaining enhanced selectivity at 30% formaldehyde conversion. Most of the MOFs tested showed low structural stability under reaction conditions, thereby indicating the need to search for new MOF families with higher robustness. However, this important result opens the path for future research on porous heterogeneous basic catalysts for the formose reaction.
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Affiliation(s)
- Valentina Balloi
- Materials and Sustainability Group, Department of Engineering, Universidad Loyola Andalucía, Avenida de las Universidades, s/n, 41704 Sevilla, Spain; (V.B.); (M.A.D.-P.); (M.A.L.-A.)
| | - Manuel Antonio Diaz-Perez
- Materials and Sustainability Group, Department of Engineering, Universidad Loyola Andalucía, Avenida de las Universidades, s/n, 41704 Sevilla, Spain; (V.B.); (M.A.D.-P.); (M.A.L.-A.)
| | - Mayra Anabel Lara-Angulo
- Materials and Sustainability Group, Department of Engineering, Universidad Loyola Andalucía, Avenida de las Universidades, s/n, 41704 Sevilla, Spain; (V.B.); (M.A.D.-P.); (M.A.L.-A.)
| | - David Villalgordo-Hernández
- Laboratory of Advanced Materials, Inorganic Chemistry Department, University Materials Institute of Alicante, University of Alicante, Apartado 99, 03080 Alicante, Spain; (D.V.-H.); (J.N.); (E.V.R.-F.)
| | - Javier Narciso
- Laboratory of Advanced Materials, Inorganic Chemistry Department, University Materials Institute of Alicante, University of Alicante, Apartado 99, 03080 Alicante, Spain; (D.V.-H.); (J.N.); (E.V.R.-F.)
| | - Enrique V. Ramos-Fernandez
- Laboratory of Advanced Materials, Inorganic Chemistry Department, University Materials Institute of Alicante, University of Alicante, Apartado 99, 03080 Alicante, Spain; (D.V.-H.); (J.N.); (E.V.R.-F.)
| | - Juan Carlos Serrano-Ruiz
- Materials and Sustainability Group, Department of Engineering, Universidad Loyola Andalucía, Avenida de las Universidades, s/n, 41704 Sevilla, Spain; (V.B.); (M.A.D.-P.); (M.A.L.-A.)
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3
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Amante G, Sponer JE, Sponer J, Saija F, Cassone G. A Computational Quantum-Based Perspective on the Molecular Origins of Life’s Building Blocks. ENTROPY 2022; 24:e24081012. [PMID: 35892991 PMCID: PMC9394336 DOI: 10.3390/e24081012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/25/2022] [Accepted: 07/18/2022] [Indexed: 12/04/2022]
Abstract
The search for the chemical origins of life represents a long-standing and continuously debated enigma. Despite its exceptional complexity, in the last decades the field has experienced a revival, also owing to the exponential growth of the computing power allowing for efficiently simulating the behavior of matter—including its quantum nature—under disparate conditions found, e.g., on the primordial Earth and on Earth-like planetary systems (i.e., exoplanets). In this minireview, we focus on some advanced computational methods capable of efficiently solving the Schro¨dinger equation at different levels of approximation (i.e., density functional theory)—such as ab initio molecular dynamics—and which are capable to realistically simulate the behavior of matter under the action of energy sources available in prebiotic contexts. In addition, recently developed metadynamics methods coupled with first-principles simulations are here reviewed and exploited to answer to old enigmas and to propose novel scenarios in the exponentially growing research field embedding the study of the chemical origins of life.
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Affiliation(s)
- Gabriele Amante
- Department of Mathematical and Computer Science, Physical Sciences and Earth Sciences, Università degli Studi di Messina, V. le F. Stagno d’Alcontres 31, 98166 Messina, Italy;
| | - Judit E. Sponer
- Institute of Biophysics of the Czech Academy of Sciences (IBP-CAS), Kràlovopolskà 135, 61265 Brno, Czech Republic; (J.E.S.); (J.S.)
| | - Jiri Sponer
- Institute of Biophysics of the Czech Academy of Sciences (IBP-CAS), Kràlovopolskà 135, 61265 Brno, Czech Republic; (J.E.S.); (J.S.)
| | - Franz Saija
- Institute for Physical-Chemical Processes, National Research Council of Italy (IPCF-CNR), V. le F. Stagno d’Alcontres 37, 98158 Messina, Italy
- Correspondence: (F.S.); (G.C.)
| | - Giuseppe Cassone
- Institute for Physical-Chemical Processes, National Research Council of Italy (IPCF-CNR), V. le F. Stagno d’Alcontres 37, 98158 Messina, Italy
- Correspondence: (F.S.); (G.C.)
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4
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Martínez RF, Cuccia LA, Viedma C, Cintas P. On the Origin of Sugar Handedness: Facts, Hypotheses and Missing Links-A Review. ORIGINS LIFE EVOL B 2022; 52:21-56. [PMID: 35796896 DOI: 10.1007/s11084-022-09624-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 05/24/2022] [Indexed: 11/30/2022]
Abstract
By paraphrasing one of Kipling's most amazing short stories (How the Leopard Got His Spots), this article could be entitled "How Sugars Became Homochiral". Obviously, we have no answer to this still unsolved mystery, and this perspective simply brings recent models, experiments and hypotheses into the homochiral homogeneity of sugars on earth. We shall revisit the past and current understanding of sugar chirality in the context of prebiotic chemistry, with attention to recent developments and insights. Different scenarios and pathways will be discussed, from the widely known formose-type processes to less familiar ones, often viewed as unorthodox chemical routes. In particular, problems associated with the spontaneous generation of enantiomeric imbalances and the transfer of chirality will be tackled. As carbohydrates are essential components of all cellular systems, astrochemical and terrestrial observations suggest that saccharides originated from environmentally available feedstocks. Such substances would have been capable of sustaining autotrophic and heterotrophic mechanisms integrating nutrients, metabolism and the genome after compartmentalization. Recent findings likewise indicate that sugars' enantiomeric bias may have emerged by a transfer of chirality mechanisms, rather than by deracemization of sugar backbones, yet providing an evolutionary advantage that fueled the cellular machinery.
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Affiliation(s)
- R Fernando Martínez
- Departamento de Química Orgánica E Inorgánica, Facultad de Ciencias, and Instituto Universitario de Investigación del Agua, Cambio Climático Y Sostenibilidad, (IACYS), Universidad de Extremadura, Avenida de Elvas s/n, 06006, Badajoz, Spain.
| | - Louis A Cuccia
- Department of Chemistry and Biochemistry, Quebec Centre for Advanced Materials (QCAM/CQMF), FRQNT, Concordia University, 7141 Sherbrooke St. West, Montreal, QC, H4B 1R6, Canada
| | - Cristóbal Viedma
- Department of Crystallography and Mineralogy, University Complutense, 28040, Madrid, Spain
| | - Pedro Cintas
- Departamento de Química Orgánica E Inorgánica, Facultad de Ciencias, and Instituto Universitario de Investigación del Agua, Cambio Climático Y Sostenibilidad, (IACYS), Universidad de Extremadura, Avenida de Elvas s/n, 06006, Badajoz, Spain.
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5
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Melosso M, Bizzocchi L, Gazzeh H, Tonolo F, Guillemin JC, Alessandrini S, Rivilla VM, Dore L, Barone V, Puzzarini C. Gas-phase identification of ( Z)-1,2-ethenediol, a key prebiotic intermediate in the formose reaction. Chem Commun (Camb) 2022; 58:2750-2753. [PMID: 35119446 DOI: 10.1039/d1cc06919e] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Prebiotic sugars are thought to be formed on primitive Earth by the formose reaction. However, their formation is not fully understood and it is plausible that key intermediates could have formed in extraterrestrial environments and subsequently delivered on early Earth by cometary bodies. 1,2-Ethenediol, the enol form of glycolaldehyde, represents a highly reactive intermediate of the formose reaction and is likely detectable in the interstellar medium. Here, we report the identification and first characterization of (Z)-1,2-ethenediol by means of rotational spectroscopy. The title compound has been produced in the gas phase by flash vacuum pyrolysis of bis-exo-5-norbornene-2,3-diol at 750 °C, through a retro-Diels-Alder reaction. The spectral analysis was guided by high-level quantum-chemical calculations, which predicted spectroscopic parameters in very good agreement with the experiment. Our study provides accurate spectral data to be used for searches of (Z)-1,2-ethenediol in the interstellar space.
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Affiliation(s)
- Mattia Melosso
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy. .,Scuola Superiore Meridionale, Università di Napoli Federico II, Largo San Marcellino 10, 80138 Naples, Italy
| | - Luca Bizzocchi
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy. .,Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Houda Gazzeh
- Univ Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR - UMR6226, F-35000 Rennes, France.,Université de Monastir, Avenue Taher Hadded B. P 56, Monastir 5000, Tunisia
| | - Francesca Tonolo
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy. .,Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Jean-Claude Guillemin
- Univ Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR - UMR6226, F-35000 Rennes, France
| | - Silvia Alessandrini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy. .,Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Víctor M Rivilla
- Centro de Astrobiología (CSIC-INTA), Ctra. de Ajalvir Km. 4, Torrejón de Ardoz, 28850 Madrid, Spain.,INAF - Osservatorio Astrofisico di Arcetri, Largo E. Fermi 5, 50125 Florence, Italy
| | - Luca Dore
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Cristina Puzzarini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
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6
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Cassone G, Sponer J, Saija F. Ab Initio Molecular Dynamics Studies of the Electric-Field-Induced Catalytic Effects on Liquids. Top Catal 2021. [DOI: 10.1007/s11244-021-01487-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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7
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Zellner NEB, McCaffrey VP, Butler JHE. Cometary Glycolaldehyde as a Source of pre-RNA Molecules. ASTROBIOLOGY 2020; 20:1377-1388. [PMID: 32985898 DOI: 10.1089/ast.2020.2216] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Over 200 molecules have been detected in multiple extraterrestrial environments, including glycolaldehyde (C2(H2O)2, GLA), a two-carbon sugar precursor that has been detected in regions of the interstellar medium. Its recent in situ detection on the nucleus of comet 67P/Churyumov-Gerasimenko and through remote observations in the comae of others provides tantalizing evidence that it is common on most (if not all) comets. Impact experiments conducted at the Experimental Impact Laboratory at NASA's Johnson Space Center have shown that samples of GLA and GLA mixed with montmorillonite clays can survive impact delivery in the pressure range of 4.5 to 25 GPa. Extrapolated to amounts of GLA observed on individual comets and assuming a monotonic impact rate in the first billion years of Solar System history, these experimental results show that up to 1023 kg of cometary GLA could have survived impact delivery, with substantial amounts of threose, erythrose, glycolic acid, and ethylene glycol also produced or delivered. Importantly, independent of the profile of the impact flux in the early Solar System, comet delivery of GLA would have provided (and may continue to provide) a reservoir of starting material for the formose reaction (to form ribose) and the Strecker reaction (to form amino acids). Thus, comets may have been important delivery vehicles for starting molecules necessary for life as we know it.
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Affiliation(s)
| | | | - Jayden H E Butler
- Department of Physics, Albion College, Albion, Michigan, USA
- Department of Physics, California State University - Los Angeles, Los Angeles, California, USA
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8
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Lamport DTA, Tan L, Held M, Kieliszewski MJ. The Role of the Primary Cell Wall in Plant Morphogenesis. Int J Mol Sci 2018; 19:E2674. [PMID: 30205598 PMCID: PMC6165521 DOI: 10.3390/ijms19092674] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 09/04/2018] [Accepted: 09/04/2018] [Indexed: 01/16/2023] Open
Abstract
Morphogenesis remains a riddle, wrapped in a mystery, inside an enigma. It remains a formidable problem viewed from many different perspectives of morphology, genetics, and computational modelling. We propose a biochemical reductionist approach that shows how both internal and external physical forces contribute to plant morphogenesis via mechanical stress⁻strain transduction from the primary cell wall tethered to the plasma membrane by a specific arabinogalactan protein (AGP). The resulting stress vector, with direction defined by Hechtian adhesion sites, has a magnitude of a few piconewtons amplified by a hypothetical Hechtian growth oscillator. This paradigm shift involves stress-activated plasma membrane Ca2+ channels and auxin-activated H⁺-ATPase. The proton pump dissociates periplasmic AGP-glycomodules that bind Ca2+. Thus, as the immediate source of cytosolic Ca2+, an AGP-Ca2+ capacitor directs the vectorial exocytosis of cell wall precursors and auxin efflux (PIN) proteins. In toto, these components comprise the Hechtian oscillator and also the gravisensor. Thus, interdependent auxin and Ca2+ morphogen gradients account for the predominance of AGPs. The size and location of a cell surface AGP-Ca2+ capacitor is essential to differentiation and explains AGP correlation with all stages of morphogenetic patterning from embryogenesis to root and shoot. Finally, the evolutionary origins of the Hechtian oscillator in the unicellular Chlorophycean algae reflect the ubiquitous role of chemiosmotic proton pumps that preceded DNA at the dawn of life.
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Affiliation(s)
- Derek T A Lamport
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK.
| | - Li Tan
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA.
| | - Michael Held
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA.
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9
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Irradiation of glyceraldehyde under simulated prebiotic conditions: Study in solid and aqueous state. J Radioanal Nucl Chem 2018. [DOI: 10.1007/s10967-018-5830-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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10
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Cassone G, Sponer J, Sponer JE, Pietrucci F, Saitta AM, Saija F. Synthesis of (d)-erythrose from glycolaldehyde aqueous solutions under electric field. Chem Commun (Camb) 2018; 54:3211-3214. [DOI: 10.1039/c8cc00045j] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A Miller-like numerical experiment demonstrates that ubiquitarious molecules such as water and glycolaldehyde can synthesize (d)-erythrose, one of the direct precursors of ribose.
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Affiliation(s)
- Giuseppe Cassone
- Institute of Biophysics, Czech Academy of Sciences
- 61265 Brno
- Czech Republic
| | - Jiri Sponer
- Institute of Biophysics, Czech Academy of Sciences
- 61265 Brno
- Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University
- 77146 Olomouc
| | - Judit E. Sponer
- Institute of Biophysics, Czech Academy of Sciences
- 61265 Brno
- Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University
- 77146 Olomouc
| | - Fabio Pietrucci
- Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, CNRS, Muséum national d’Histoire naturelle, Institut de Recherche pour le Développement
- F-75005 Paris
- France
| | - A. Marco Saitta
- Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, CNRS, Muséum national d’Histoire naturelle, Institut de Recherche pour le Développement
- F-75005 Paris
- France
| | - Franz Saija
- CNR-IPCF, Viale Ferdinando Stagno d’Alcontres 37
- 98158 Messina
- Italy
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11
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Wagner JP, McDonald DC, Duncan MA. Infrared Spectroscopy of the Astrochemically Relevant Protonated Formaldehyde Dimer. J Phys Chem A 2017; 122:192-198. [DOI: 10.1021/acs.jpca.7b10573] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- J. Philipp Wagner
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, United States
| | - David C. McDonald
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, United States
| | - Michael A. Duncan
- Department of Chemistry, University of Georgia, 140 Cedar Street, Athens, Georgia 30602, United States
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12
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Metal-Ion- and Hydrogen-Bond-Mediated Interstellar Prebiotic Chemistry: The First Step in the Formose Reaction. J Phys Chem A 2017; 121:8659-8674. [DOI: 10.1021/acs.jpca.7b08002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Formose Reaction Controlled by a Copolymer of N,N-Dimethylacrylamide and 4-Vinylphenylboronic Acid. Polymers (Basel) 2017; 9:polym9110549. [PMID: 30965856 PMCID: PMC6418552 DOI: 10.3390/polym9110549] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 10/21/2017] [Accepted: 10/24/2017] [Indexed: 12/24/2022] Open
Abstract
The formose reaction is an oligomerization of formaldehyde under basic conditions, which produces a complicated mixture of monosaccharides and sugar alcohols. Selective formation of useful monosaccharides by the formose reaction has been an important challenge. In this study, we have investigated the formose reaction controlled by N,N-dimethylacrylamide/4-vinylphenylboronic acid copolymer (pDMA/VBA) and phenylboronic acid (PBA) because boronic acid compounds form esters with polyols, e.g., monosaccharides and sugar alcohols. We obtained time⁻conversion data in the presence of these boronic acid compounds, and characterized the products by liquid chromatography-mass spectroscopy and NMR measurements. pDMA/VBA and PBA decelerated the formose reaction because of the formation of boronic acid esters with products. It is noteworthy that the formose reaction in the presence of pDMA/VBA and PBA formed favorably six- and seven-carbon branched monosaccharides and sugar alcohols.
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14
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Phosphoribosyl Pyrophosphate: A Molecular Vestige of the Origin of Life on Minerals. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702633] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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15
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Akouche M, Jaber M, Maurel MC, Lambert JF, Georgelin T. Phosphoribosyl Pyrophosphate: A Molecular Vestige of the Origin of Life on Minerals. Angew Chem Int Ed Engl 2017; 56:7920-7923. [PMID: 28558156 DOI: 10.1002/anie.201702633] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 04/15/2017] [Indexed: 11/07/2022]
Abstract
In this contribution, we report the formation under prebiotic conditions of phosphoribosyl pyrophosphate (PRPP) as a molecular precursor in the one-pot synthesis of a canonical nucleotide, namely adenosine monophosphate (AMP) from its building blocks (KH2 PO4 or Pi , adenine, and d-ribose), on a fumed silica surface. The on-the-rocks approach has been successfully applied to the simultaneous phosphorylation and glycosylation of ribose. The one-pot formation mechanism of AMP involves a two-step pathway via an activated intermediate, namely PRPP, obtained by multiple ribose phosphorylations upon mild thermal activation.
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Affiliation(s)
- Mariame Akouche
- Sorbonne Universités, UPMC Paris 06, CNRS UMR 7197, Laboratoire de Réactivité de Surface, 4 place Jussieu, 75005, Paris, France
| | - Maguy Jaber
- Sorbonne Universités, UPMC Paris06, CNRS UMR 8220, Laboratoire d'Archéologie Moléculaire et Structurale, 4 place Jussieu, 75005, Paris, France
| | | | - Jean-Francois Lambert
- Sorbonne Universités, UPMC Paris 06, CNRS UMR 7197, Laboratoire de Réactivité de Surface, 4 place Jussieu, 75005, Paris, France
| | - Thomas Georgelin
- Sorbonne Universités, UPMC Paris 06, CNRS UMR 7197, Laboratoire de Réactivité de Surface, 4 place Jussieu, 75005, Paris, France
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16
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Sandford SA, Bera PP, Lee TJ, Materese CK, Nuevo M. Photosynthesis and photo-stability of nucleic acids in prebiotic extraterrestrial environments. Top Curr Chem (Cham) 2015; 356:123-64. [PMID: 24500331 PMCID: PMC5737941 DOI: 10.1007/128_2013_499] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Laboratory experiments have shown that the UV photo-irradiation of low-temperature ices of astrophysical interest leads to the formation of organic molecules, including molecules important for biology such as amino acids, quinones, and amphiphiles. When pyrimidine is introduced into these ices, the products of irradiation include the nucleobases uracil, cytosine, and thymine, the informational sub-units of DNA and RNA, as well as some of their isomers. The formation of these compounds, which has been studied both experimentally and theoretically, requires a succession of additions of OH, NH₂, and CH₃groups to pyrimidine. Results show that H₂O ice plays key roles in the formation of the nucleobases, as an oxidant, as a matrix in which reactions can take place, and as a catalyst that assists proton abstraction from intermediate compounds. As H₂O is also the most abundant icy component in most cold astrophysical environments, it probably plays the same roles in space in the formation of biologically relevant compounds. Results also show that although the formation of uracil and cytosine from pyrimidine in ices is fairly straightforward, the formation of thymine is not. This is mostly due to the fact that methylation is a limiting step for its formation, particularly in H₂O-rich ices, where methylation must compete with oxidation. The relative inefficiency of the abiotic formation of thymine to that of uracil and cytosine, together with the fact that thymine has not been detected in meteorites, are not inconsistent with the RNA world hypothesis. Indeed, a lack of abiotically produced thymine delivered to the early Earth may have forced the choice for an RNA world, in which only uracil and cytosine are needed, but not thymine.
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Affiliation(s)
- Scott A Sandford
- Space Science and Astrobiology Division, NASA Ames Research Center, MS 245-6, Moffett Field, CA, 94035, USA,
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17
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McCaffrey VP, Zellner NEB, Waun CM, Bennett ER, Earl EK. Reactivity and survivability of glycolaldehyde in simulated meteorite impact experiments. ORIGINS LIFE EVOL B 2014; 44:29-42. [PMID: 24934564 DOI: 10.1007/s11084-014-9358-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 05/01/2014] [Indexed: 10/25/2022]
Abstract
Sugars of extraterrestrial origin have been observed in the interstellar medium (ISM), in at least one comet spectrum, and in several carbonaceous chondritic meteorites that have been recovered from the surface of the Earth. The origins of these sugars within the meteorites have been debated. To explore the possibility that sugars could be generated during shock events, this paper reports on the results of the first laboratory impact experiments wherein glycolaldehyde, found in the ISM, as well as glycolaldehyde mixed with montmorillonite clay, have been subjected to reverberated shocks from ~5 to >25 GPa. New biologically relevant molecules, including threose, erythrose and ethylene glycol, were identified in the resulting samples. These results show that sugar molecules can not only survive but also become more complex during impact delivery to planetary bodies.
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Affiliation(s)
- V P McCaffrey
- Department of Chemistry, Albion College, Albion, MI, 49224, USA,
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18
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Kua J, Avila JE, Lee CG, Smith WD. Mapping the Kinetic and Thermodynamic Landscape of Formaldehyde Oligomerization under Neutral Conditions. J Phys Chem A 2013; 117:12658-67. [DOI: 10.1021/jp4098292] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jeremy Kua
- Department
of Chemistry and Biochemistry, University of San Diego, 5998 Alcala
Park, San Diego, California 92110, United States
- Yale-NUS
College, 6 College Avenue East #B1-01, Singapore 138614
| | - Joseph E. Avila
- Department
of Chemistry and Biochemistry, University of San Diego, 5998 Alcala
Park, San Diego, California 92110, United States
| | - Christopher G. Lee
- Department
of Chemistry and Biochemistry, University of San Diego, 5998 Alcala
Park, San Diego, California 92110, United States
| | - William D. Smith
- Christian High School, 2100 Greenfield Drive, El
Cajon, California 92019, United States
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19
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Toxvaerd S. The role of carbohydrates at the origin of homochirality in biosystems. ORIGINS LIFE EVOL B 2013; 43:391-409. [PMID: 23996458 DOI: 10.1007/s11084-013-9342-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Accepted: 07/12/2013] [Indexed: 01/18/2023]
Abstract
Pasteur has demonstrated that the chiral components in a racemic mixture can separate in homochiral crystals. But with a strong chiral discrimination the chiral components in a concentrated mixture can also phase separate into homochiral fluid domains, and the isomerization kinetics can then perform a symmetry breaking into one thermodynamical stable homochiral system. Glyceraldehyde has a sufficient chiral discrimination to perform such a symmetry breaking. The requirement of a high concentration of the chiral reactant(s) in an aqueous solution in order to perform and maintain homochirality; the appearance of phosphorylation of almost all carbohydrates in the central machinery of life; the basic ideas that the biochemistry and the glycolysis and gluconeogenesis contain the trace of the biochemical evolution, all point in the direction of that homochirality was obtained just after- or at a phosphorylation of the very first products of the formose reaction, at high concentrations of the reactants in phosphate rich compartments in submarine hydrothermal vents. A racemic solution of D,L-glyceraldehyde-3-phosphate could be the template for obtaining homochiral D-glyceraldehyde-3-phosphate(aq) as well as L-amino acids.
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Affiliation(s)
- Søren Toxvaerd
- DNRF centre "Glass and Time", IMFUFA, Department of Sciences, Roskilde University, Postbox 260, 4000, Roskilde, Denmark,
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20
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Wang T, Bowie JH. Hydrogen tunnelling influences the isomerisation of some small radicals of interstellar importance. A theoretical investigation. Org Biomol Chem 2012; 10:3219-28. [DOI: 10.1039/c2ob07102a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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21
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Simakov A, Sekiguchi O, Bunkan AJC, Uggerud E. Energetics and Mechanisms for the Unimolecular Dissociation of Protonated Trioses and Relationship to Proton-Mediated Formaldehyde Polymerization to Carbohydrates in Interstellar Environments. J Am Chem Soc 2011; 133:20816-22. [DOI: 10.1021/ja206600w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anton Simakov
- Mass Spectrometry Laboratory and Centre for Theoretical and Computational Chemistry (CTCC), Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway
| | - Osamu Sekiguchi
- Mass Spectrometry Laboratory and Centre for Theoretical and Computational Chemistry (CTCC), Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway
| | - Arne Joakim C. Bunkan
- Mass Spectrometry Laboratory and Centre for Theoretical and Computational Chemistry (CTCC), Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway
| | - Einar Uggerud
- Mass Spectrometry Laboratory and Centre for Theoretical and Computational Chemistry (CTCC), Department of Chemistry, University of Oslo, P.O. Box 1033 Blindern, N-0315 Oslo, Norway
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22
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Osburn S, O'Hair RA, Black SM, Ryzhov V. Post-translational modification in the gas phase: mechanism of cysteine S-nitrosylation via ion-molecule reactions. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:3216-22. [PMID: 22006383 PMCID: PMC3908822 DOI: 10.1002/rcm.5219] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The gas-phase mechanism of S-nitrosylation of thiols was studied in a quadrupole ion trap mass spectrometer. This was done via ion-molecule reactions of protonated cysteine and many of its derivatives and other thiol ions with neutral tert-butyl nitrite or nitrous acid. Our results showed that the presence of the carboxylic acid functional group, -COOH, in the vicinity of the thiol group is essential for the gas-phase nitrosylation of thiols. When the carboxyl proton is replaced by a methyl group (cysteine methyl ester) no nitrosylation was observed. Other thiols lacking a carboxylic acid functional group displayed no S-nitrosylation, strongly suggesting that the carboxyl hydrogen plays a key role in the nitrosylation process. These results are in excellent agreement with a solution-phase mechanism proposed by Stamler et al. (J. S. Stamler, E. J. Toone, S. A. Lipton, N. J. Sucher. Neuron 1997, 18, 691-696) who suggested a catalytic role for the carboxylic acid group adjacent to cysteine residues and with later additions by Ascenzi et al. (P. Ascenzi, M. Colasanti, T. Persichini, M. Muolo, F. Polticelli, G. Venturini, D. Bordo, M. Bolognesi. Biol. Chem. 2000, 381, 623-627) who postulated that the presence of the carboxyl in the cysteine microenvironment in proteins is crucial for S-nitrosylation. A concerted mechanism for the gas-phase S-nitrosylation was proposed based on our results and was further studied using theoretical calculations. Our calculations showed that this proposed pathway is exothermic by 44.0 kJ mol(-1). This is one of the few recent examples when a gas-phase mechanism matches one in solution.
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Affiliation(s)
- Sandra Osburn
- Department of Chemistry and Biochemistry, and Center for Biochemical and Biophysical Studies, Northern Illinois University, DeKalb, IL 60115, USA
| | - Richard A.J. O'Hair
- School of Chemistry, University of Melbourne; Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne; and ARC Centre of Excellence for Free Radical Chemistry and Biotechnology, Melbourne, VIC 3010, Australia
| | - Stephen M. Black
- Pulmonary Vascular Disease Program, Vascular Biology Center, Georgia Health Sciences University, Augusta, GA 30912, USA
| | - Victor Ryzhov
- Department of Chemistry and Biochemistry, and Center for Biochemical and Biophysical Studies, Northern Illinois University, DeKalb, IL 60115, USA
- Correspondence to: V. Ryzhov, Department of Chemistry and Biochemistry, Northern Illinois University, DeKalb, IL 60115, USA.
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23
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Wang T, Bowie JH. Radical routes to interstellar glycolaldehyde. The possibility of stereoselectivity in gas-phase polymerization reactions involving CH2O and ˙CH2OH. Org Biomol Chem 2010; 8:4757-66. [DOI: 10.1039/c0ob00125b] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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Jalbout AF. Prebiotic synthesis of simple sugars by an interstellar formose reaction. ORIGINS LIFE EVOL B 2008; 38:489-97. [PMID: 18998238 DOI: 10.1007/s11084-008-9151-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Accepted: 01/13/2008] [Indexed: 11/26/2022]
Abstract
The prebiotic possibilities for the synthesis of interstellar carbohydrates through a protic variant of the formose reaction under gas phase conditions were studied. Ab initio calculations were used to evaluate potential mechanisms. Based on considerations of barrier heights and temperature variations in the Interstellar Medium the plausibility of extended sugar synthesis will be discussed.
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Affiliation(s)
- Abraham F Jalbout
- Instituto de Química, Universidad Nacional Autónoma de Mexico, México DF, Mexico.
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25
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The ribose and glycine Maillard reaction in the interstellar medium (ISM): A theoretical study. J CHEM SCI 2008. [DOI: 10.1007/s12039-008-0056-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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