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Bechtel M, Hümmer E, Trapp O. Selective Phosphorylation of RNA‐ and DNA‐Nucleosides under Prebiotically Plausible Conditions. CHEMSYSTEMSCHEM 2022. [DOI: 10.1002/syst.202200020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Maximilian Bechtel
- Department of Chemistry Ludwig-Maximilians-University Munich Butenandtstr. 5–13 81377 Munich Germany
| | - Eva Hümmer
- Department of Chemistry Ludwig-Maximilians-University Munich Butenandtstr. 5–13 81377 Munich Germany
| | - Oliver Trapp
- Department of Chemistry Ludwig-Maximilians-University Munich Butenandtstr. 5–13 81377 Munich Germany
- Max-Planck-Institute for Astronomy Königstuhl 17 69117 Heidelberg Germany
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2
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Yi J, Kaur H, Kazöne W, Rauscher SA, Gravillier L, Muchowska KB, Moran J. A Nonenzymatic Analog of Pyrimidine Nucleobase Biosynthesis. Angew Chem Int Ed Engl 2022; 61:e202117211. [PMID: 35304939 PMCID: PMC9325535 DOI: 10.1002/anie.202117211] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Indexed: 11/28/2022]
Abstract
Metabolic theories for the origin of life posit that inorganic catalysts enabled self‐organized chemical precursors to the pathways of metabolism, including those that make genetic molecules. Recently, experiments showing nonenzymatic versions of a number of core metabolic pathways have started to support this idea. However, experimental demonstrations of nonenzymatic reaction sequences along the de novo ribonucleotide biosynthesis pathways are limited. Here we show that all three reactions of pyrimidine nucleobase biosynthesis that convert aspartate to orotate proceed at 60 °C without photochemistry under aqueous conditions in the presence of metals such as Cu2+ and Mn4+. Combining reactions into one‐pot variants is also possible. Life may not have invented pyrimidine nucleobase biosynthesis from scratch, but simply refined existing nonenzymatic reaction channels. This work is a first step towards uniting metabolic theories of life's origin with those centered around genetic molecules.
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Affiliation(s)
- Jing Yi
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS) CNRS UMR 7006 Université de Strasbourg 8 Allée Gaspard Monge 67000 Strasbourg France
| | - Harpreet Kaur
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS) CNRS UMR 7006 Université de Strasbourg 8 Allée Gaspard Monge 67000 Strasbourg France
| | - Wahnyalo Kazöne
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS) CNRS UMR 7006 Université de Strasbourg 8 Allée Gaspard Monge 67000 Strasbourg France
| | - Sophia A. Rauscher
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS) CNRS UMR 7006 Université de Strasbourg 8 Allée Gaspard Monge 67000 Strasbourg France
| | - Louis‐Albin Gravillier
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS) CNRS UMR 7006 Université de Strasbourg 8 Allée Gaspard Monge 67000 Strasbourg France
| | - Kamila B. Muchowska
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS) CNRS UMR 7006 Université de Strasbourg 8 Allée Gaspard Monge 67000 Strasbourg France
| | - Joseph Moran
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS) CNRS UMR 7006 Université de Strasbourg 8 Allée Gaspard Monge 67000 Strasbourg France
- Institut Universitaire de France (IUF) France
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3
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Yi J, Kaur H, Kazöne W, Rauscher SA, Gravillier LA, Muchowska KB, Moran J. A Nonenzymatic Analog of Pyrimidine Nucleobase Biosynthesis. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202117211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jing Yi
- University of Strasbourg: Universite de Strasbourg ISIS FRANCE
| | - Harpreet Kaur
- University of Strasbourg: Universite de Strasbourg ISIS FRANCE
| | - Wahnyalo Kazöne
- Université de Strasbourg: Universite de Strasbourg ISIS FRANCE
| | | | | | | | - Joseph Moran
- University of Strasbourg ISIS 8 allée Gaspard MongeBP 70028 67083 Strasbourg FRANCE
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Franco A, da Silva JAL. Boron in Prebiological Evolution. Angew Chem Int Ed Engl 2021; 60:10458-10468. [PMID: 32997879 DOI: 10.1002/anie.202010616] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Indexed: 01/02/2023]
Abstract
Boron(III), as borate (or boric acid), mediates the synthesis of ribose, ribonucleosides, and ribonucleotides. These reactions are carried out under moderate temperatures (typically 70-95 °C) with organic molecules (or their derivatives) detected in interstellar space and inorganic ions found in minerals on Earth (and could occur during early stages of prebiotic evolution). Research in this century suggests that borate was a relevant prebiological reagent, thus reinforcing the RNA world hypothesis as an explanation for the origin of life. Herein, these developments on prebiological chemistry related to boron species are reviewed.
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Affiliation(s)
- Ana Franco
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - José Armando L da Silva
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
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5
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Affiliation(s)
- Ana Franco
- Centro de Química Estrutural Instituto Superior Técnico, Universidade de Lisboa Av. Rovisco Pais 1049-001 Lisbon Portugal
| | - José Armando L. Silva
- Centro de Química Estrutural Instituto Superior Técnico, Universidade de Lisboa Av. Rovisco Pais 1049-001 Lisbon Portugal
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6
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Prebiotic chemistry and origins of life research with atomistic computer simulations. Phys Life Rev 2020; 34-35:105-135. [DOI: 10.1016/j.plrev.2018.09.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 09/10/2018] [Indexed: 02/02/2023]
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Hu J, Lei W, Wang J, Chen HY, Xu JJ. Regioselective 5'-position phosphorylation of ribose and ribonucleosides: phosphate transfer in the activated pyrophosphate complex in the gas phase. Chem Commun (Camb) 2019; 55:310-313. [PMID: 30468222 DOI: 10.1039/c8cc08510b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, we present a rapid, efficient and regioselective phosphorylation method at the 5'-position of unprotected ribose and ribonucleosides with pyrophosphate in the gas phase, which involves the formation of anionic complexes via electrospray ionization and collisional activation to induce phosphorylation within the complexes.
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Affiliation(s)
- Jun Hu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China.
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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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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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Pérez-Villa A, Saitta AM, Georgelin T, Lambert JF, Guyot F, Maurel MC, Pietrucci F. Synthesis of RNA Nucleotides in Plausible Prebiotic Conditions from ab Initio Computer Simulations. J Phys Chem Lett 2018; 9:4981-4987. [PMID: 30107125 DOI: 10.1021/acs.jpclett.8b02077] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Understanding the mechanism of spontaneous formation of ribonucleotides under realistic prebiotic conditions is a key open issue of origins-of-life research. In cells, de novo and salvage nucleotide enzymatic synthesis combines 5-phospho-α-d-ribose-1-diphosphate (α-PRPP) and nucleobases. Interestingly, these reactants are also known as prebiotically plausible compounds. Combining ab initio molecular dynamics simulations with recently developed reaction exploration and enhanced sampling methods, we show that nucleobases and α-PRPP should spontaneously combine, under mild hydrothermal conditions, with an exothermic reaction and a facile mechanism, forming both purine and pyrimidine ribonucleotides. Surprisingly, this mechanism is very similar to the biological one and yields ribonucleotides with the same anomeric carbon chirality as in biological systems. Mass spectrometry experiments performed on solutions of adenine and PRPP in similar conditions support the formation of AMP. These results suggest that natural selection might have optimized, through enzymes, a pre-existing ribonucleotide formation mechanism, carrying it forward to modern life forms.
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Affiliation(s)
- Andrea Pérez-Villa
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matriaux et de Cosmochimie, IMPMC, F-75005 Paris , France
| | - A Marco Saitta
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matriaux et de Cosmochimie, IMPMC, F-75005 Paris , France
| | - Thomas Georgelin
- Sorbonne Université, CNRS UMR 7197, Laboratoire de Réactivité de Surface, LRS, F-75005 Paris , France
- Centre de Biophysique Moléculaire, CNRS UPR 4301, F-45071 Orléans , France
| | - Jean-François Lambert
- Sorbonne Université, CNRS UMR 7197, Laboratoire de Réactivité de Surface, LRS, F-75005 Paris , France
| | - François Guyot
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matriaux et de Cosmochimie, IMPMC, F-75005 Paris , France
| | - Marie-Christine Maurel
- Sorbonne Université, Muséum National d'Histoire Naturelle, CNRS MNHN UMR 7205, Institut de Systématique, Evolution, Biodiversité, ISyEB, F-75005 Paris , France
| | - Fabio Pietrucci
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matriaux et de Cosmochimie, IMPMC, F-75005 Paris , France
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11
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Wang T, Zhang P, Hu G, Gao Y, Wu Y, Xu P, Liu Y, Zhao Y. Mixed Anhydrides of Nucleotides and Amino Acids Give Dipeptides: A Model System for Studying the Origin of the Genetic Code? ChemistrySelect 2018. [DOI: 10.1002/slct.201800965] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Tao Wang
- Key Laboratory for Chemical Biology of Fujian ProvinceDepartment of Chemistry, College of Chemistry and Chemical EngineeringXiamen University, Xiamen 361005 China
| | - Pengbo Zhang
- Key Laboratory for Chemical Biology of Fujian ProvinceDepartment of Chemistry, College of Chemistry and Chemical EngineeringXiamen University, Xiamen 361005 China
| | - Gaobo Hu
- Key Laboratory for Chemical Biology of Fujian ProvinceDepartment of Chemistry, College of Chemistry and Chemical EngineeringXiamen University, Xiamen 361005 China
| | - Yuzhen Gao
- Key Laboratory for Chemical Biology of Fujian ProvinceDepartment of Chemistry, College of Chemistry and Chemical EngineeringXiamen University, Xiamen 361005 China
| | - Yile Wu
- Key Laboratory for Chemical Biology of Fujian ProvinceDepartment of Chemistry, College of Chemistry and Chemical EngineeringXiamen University, Xiamen 361005 China
| | - Pengxiang Xu
- Key Laboratory for Chemical Biology of Fujian ProvinceDepartment of Chemistry, College of Chemistry and Chemical EngineeringXiamen University, Xiamen 361005 China
| | - Yan Liu
- Key Laboratory for Chemical Biology of Fujian ProvinceDepartment of Chemistry, College of Chemistry and Chemical EngineeringXiamen University, Xiamen 361005 China
| | - Yufen Zhao
- Key Laboratory for Chemical Biology of Fujian ProvinceDepartment of Chemistry, College of Chemistry and Chemical EngineeringXiamen University, Xiamen 361005 China
- Institute of Drug Discovery TechnologyNingbo University Ningbo 315211 Zhejiang China
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education)Department of ChemistryTsinghua University Beijing 100084 China
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Potential Role of Inorganic Confined Environments in Prebiotic Phosphorylation. Life (Basel) 2018; 8:life8010007. [PMID: 29510574 PMCID: PMC5871939 DOI: 10.3390/life8010007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 01/25/2018] [Accepted: 02/28/2018] [Indexed: 01/19/2023] Open
Abstract
A concise outlook on the potential role of confinement in phosphorylation and phosphate condensation pertaining to prebiotic chemistry is presented. Inorganic confinement is a relatively uncharted domain in studies concerning prebiotic chemistry, and even more so in terms of experimentation. However, molecular crowding within confined dimensions is central to the functioning of contemporary biology. There are numerous advantages to confined environments and an attempt to highlight this fact, within this article, has been undertaken, keeping in context the limitations of aqueous phase chemistry in phosphorylation and, to a certain extent, traditional approaches in prebiotic chemistry.
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Bolm C, Mocci R, Schumacher C, Turberg M, Puccetti F, Hernández JG. Mechanochemical Activation of Iron Cyano Complexes: A Prebiotic Impact Scenario for the Synthesis of α-Amino Acid Derivatives. Angew Chem Int Ed Engl 2018; 57:2423-2426. [PMID: 29334423 DOI: 10.1002/anie.201713109] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Indexed: 11/06/2022]
Abstract
Mechanochemical activation of iron cyano complexes by ball milling results in the formation of HCN, which can be trapped and incorporated into α-aminonitriles. This prebiotic impact scenario can be extended by mechanochemically transforming the resulting α-aminonitriles into α-amino amides using a chemical route related to early Earth conditions.
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Affiliation(s)
- Carsten Bolm
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52074, Aachen, Germany
| | - Rita Mocci
- Dipartimento di Scienze Chimiche e Geologiche, Università degli Studi di Cagliari, Cittadella Universitaria, SS 554 bivio per Sestu, 09028, Monserrato (CA), Italy
| | - Christian Schumacher
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52074, Aachen, Germany
| | - Mathias Turberg
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52074, Aachen, Germany
| | - Francesco Puccetti
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52074, Aachen, Germany.,Department of Chemistry "Ugo Schiff", University of Firenze, Via della Lastruccia 3-13, 50019, Sesto Fiorentino, Italy
| | - José G Hernández
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, 52074, Aachen, Germany
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14
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Bolm C, Mocci R, Schumacher C, Turberg M, Puccetti F, Hernández JG. Mechanochemical Activation of Iron Cyano Complexes: A Prebiotic Impact Scenario for the Synthesis of α-Amino Acid Derivatives. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201713109] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Carsten Bolm
- Institute of Organic Chemistry; RWTH Aachen University; Landoltweg 1 52074 Aachen Germany
| | - Rita Mocci
- Dipartimento di Scienze Chimiche e Geologiche; Università degli Studi di Cagliari, Cittadella Universitaria; SS 554 bivio per Sestu 09028 Monserrato (CA) Italy
| | - Christian Schumacher
- Institute of Organic Chemistry; RWTH Aachen University; Landoltweg 1 52074 Aachen Germany
| | - Mathias Turberg
- Institute of Organic Chemistry; RWTH Aachen University; Landoltweg 1 52074 Aachen Germany
| | - Francesco Puccetti
- Institute of Organic Chemistry; RWTH Aachen University; Landoltweg 1 52074 Aachen Germany
- Department of Chemistry “Ugo Schiff”; University of Firenze; Via della Lastruccia 3-13 50019 Sesto Fiorentino Italy
| | - José G. Hernández
- Institute of Organic Chemistry; RWTH Aachen University; Landoltweg 1 52074 Aachen Germany
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Knappenberger AJ, Reiss CW, Strobel SA. Structures of two aptamers with differing ligand specificity reveal ruggedness in the functional landscape of RNA. eLife 2018; 7:36381. [PMID: 29877798 PMCID: PMC6031431 DOI: 10.7554/elife.36381] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 06/05/2018] [Indexed: 01/07/2023] Open
Abstract
Two classes of riboswitches related to the ykkC guanidine-I riboswitch bind phosphoribosyl pyrophosphate (PRPP) and guanosine tetraphosphate (ppGpp). Here we report the co-crystal structure of the PRPP aptamer and its ligand. We also report the structure of the G96A point mutant that prefers ppGpp over PRPP with a dramatic 40,000-fold switch in specificity. The ends of the aptamer form a helix that is not present in the guanidine aptamer and is involved in the expression platform. In the mutant, the base of ppGpp replaces G96 in three-dimensional space. This disrupts the S-turn, which is a primary structural feature of the ykkC RNA motif. These dramatic differences in ligand specificity are achieved with minimal mutations. ykkC aptamers are therefore a prime example of an RNA fold with a rugged fitness landscape. The ease with which the ykkC aptamer acquires new specificity represents a striking case of evolvability in RNA.
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Affiliation(s)
- Andrew John Knappenberger
- Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenUnited States,Chemical Biology InstituteYale UniversityWest HavenUnited States
| | - Caroline Wetherington Reiss
- Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenUnited States,Chemical Biology InstituteYale UniversityWest HavenUnited States
| | - Scott A Strobel
- Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenUnited States,Chemical Biology InstituteYale UniversityWest HavenUnited States
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