1
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Mittal S, Nisler C, Szostak JW. Simulations predict preferred Mg 2+ coordination in a nonenzymatic primer-extension reaction center. Biophys J 2024; 123:1579-1591. [PMID: 38702884 PMCID: PMC11214020 DOI: 10.1016/j.bpj.2024.04.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 04/24/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024] Open
Abstract
The mechanism by which genetic information was copied prior to the evolution of ribozymes is of great interest because of its importance to the origin of life. The most effective known process for the nonenzymatic copying of an RNA template is primer extension by a two-step pathway in which 2-aminoimidazole-activated nucleotides first react with each other to form an imidazolium-bridged intermediate that subsequently reacts with the primer. Reaction kinetics, structure-activity relationships, and X-ray crystallography have provided insight into the overall reaction mechanism, but many puzzles remain. In particular, high concentrations of Mg2+ are required for efficient primer extension, but the mechanism by which Mg2+ accelerates primer extension remains unknown. By analogy with the mechanism of DNA and RNA polymerases, a role for Mg2+ in facilitating the deprotonation of the primer 3'-hydroxyl is often assumed, but no catalytic metal ion is seen in crystal structures of the primer-extension complex. To explore the potential effects of Mg2+ binding in the reaction center, we performed atomistic molecular dynamics simulations of a series of modeled complexes in which a Mg2+ ion was placed in the reaction center with inner-sphere coordination with different sets of functional groups. Our simulations suggest that coordination of a Mg2+ ion with both O3' of the terminal primer nucleotide and the pro-Sp nonbridging oxygen of the reactive phosphate of an imidazolium-bridged dinucleotide would help to pre-organize the structure of the primer/template substrate complex to favor the primer-extension reaction. Our results suggest that the catalytic metal ion may play an important role in overcoming electrostatic repulsion between a deprotonated O3' and the reactive phosphate of the bridged dinucleotide and lead to testable predictions of the mode of Mg2+ binding that is most relevant to catalysis of primer extension.
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Affiliation(s)
- Shriyaa Mittal
- Howard Hughes Medical Institute, Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts; Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Collin Nisler
- Howard Hughes Medical Institute, Department of Chemistry, University of Chicago, Chicago, Illinois
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts; Department of Genetics, Harvard Medical School, Boston, Massachusetts; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts; Howard Hughes Medical Institute, Department of Chemistry, University of Chicago, Chicago, Illinois.
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2
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Jia X, Zhang SJ, Zhou L, Szostak J. Constraints on the emergence of RNA through non-templated primer extension with mixtures of potentially prebiotic nucleotides. Nucleic Acids Res 2024; 52:5451-5464. [PMID: 38726871 PMCID: PMC11162797 DOI: 10.1093/nar/gkae355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/10/2024] [Accepted: 04/22/2024] [Indexed: 06/11/2024] Open
Abstract
The emergence of RNA on the early Earth is likely to have been influenced by chemical and physical processes that acted to filter out various alternative nucleic acids. For example, UV photostability is thought to have favored the survival of the canonical nucleotides. In a recent proposal for the prebiotic synthesis of the building blocks of RNA, ribonucleotides share a common pathway with arabino- and threo-nucleotides. We have therefore investigated non-templated primer extension with 2-aminoimidazole-activated forms of these alternative nucleotides to see if the synthesis of the first oligonucleotides might have been biased in favor of RNA. We show that non-templated primer extension occurs predominantly through 5'-5' imidazolium-bridged dinucleotides, echoing the mechanism of template-directed primer extension. Ribo- and arabino-nucleotides exhibited comparable rates and yields of non-templated primer extension, whereas threo-nucleotides showed lower reactivity. Competition experiments confirmed the bias against the incorporation of threo-nucleotides. The incorporation of an arabino-nucleotide at the end of the primer acts as a chain terminator and blocks subsequent extension. These biases, coupled with potentially selective prebiotic synthesis, and the templated copying that is known to favour the incorporation of ribonucleotides, provide a plausible model for the effective exclusion of arabino- and threo-nucleotides from primordial oligonucleotides.
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Affiliation(s)
- Xiwen Jia
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
- Howard Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Stephanie J Zhang
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
| | - Lijun Zhou
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Institute for RNA Innovation, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
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3
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Edri R, Fisher S, Menor-Salvan C, Williams LD, Frenkel-Pinter M. Assembly-driven protection from hydrolysis as key selective force during chemical evolution. FEBS Lett 2023; 597:2879-2896. [PMID: 37884438 DOI: 10.1002/1873-3468.14766] [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: 07/13/2023] [Revised: 09/07/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023]
Abstract
The origins of biopolymers pose fascinating questions in prebiotic chemistry. The marvelous assembly proficiencies of biopolymers suggest they are winners of a competitive evolutionary process. Sophisticated molecular assembly is ubiquitous in life where it is often emergent upon polymerization. We focus on the influence of molecular assembly on hydrolysis rates in aqueous media and suggest that assembly was crucial for biopolymer selection. In this model, incremental enrichment of some molecular species during chemical evolution was partially driven by the interplay of kinetics of synthesis and hydrolysis. We document a general attenuation of hydrolysis by assembly (i.e., recalcitrance) for all universal biopolymers and highlight the likely role of assembly in the survival of the 'fittest' molecules during chemical evolution.
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Affiliation(s)
- Rotem Edri
- Institute of Chemistry, The Hebrew University of Jerusalem, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Israel
| | - Sarah Fisher
- Institute of Chemistry, The Hebrew University of Jerusalem, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Israel
| | - Cesar Menor-Salvan
- Department of Biología de Sistemas, Universidad de Alcalá, Madrid, Spain
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA
| | - Moran Frenkel-Pinter
- Institute of Chemistry, The Hebrew University of Jerusalem, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Israel
- Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA
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4
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Mandal R, Ghosh A, Rout NK, Prasad M, Hazra B, Sar S, Das S, Datta A, Tarafdar PK. Self-assembled prebiotic amphiphile-mixture exhibits tunable catalytic properties. Org Biomol Chem 2023; 21:4473-4481. [PMID: 37194351 DOI: 10.1039/d3ob00606a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Protocellular surface formation via the self-assembly of amphiphiles, and catalysis by simple peptides/proto-RNA are two important pillars in the evolution of protocells. To hunt for prebiotic self-assembly-supported catalytic reactions, we thought that amino-acid-based amphiphiles might play an important role. In this paper, we investigate the formation of histidine-based and serine-based amphiphiles under mild prebiotic conditions from amino acid : fatty alcohol and amino acid : fatty acid mixtures. The histidine-based amphiphiles were able to catalyze hydrolytic reactions at the self-assembled surface (with a rate increase of ∼1000-fold), and the catalytic ability can be tuned by linkage of the fatty carbon part to histidine (N-acylated vs. O-acylated). Moreover, the presence of cationic serine-based amphiphiles on the surface enhances the catalytic efficiency by another ∼2-fold, whereas the presence of anionic aspartic acid-based amphiphiles reduces the catalytic activity. Ester partitioning into the surface, reactivity, and the accumulation of liberated fatty acid explain the substrate selectivity of the catalytic surface, where the hexyl esters were found to be more hydrolytic than other fatty acyl esters. Di-methylation of the -NH2 of OLH increases the catalytic efficacy by a further ∼2-fold, whereas trimethylation reduces the catalytic ability. The self-assembly, charge-charge repulsion, and the H-bonding to the ester carbonyl are likely to be responsible for the superior (∼2500-fold higher rate than the pre-micellar OLH) catalytic efficiency of O-lauryl dimethyl histidine (OLDMH). Thus, prebiotic amino-acid-based surfaces served as an efficient catalyst that exhibits regulation of catalytic function, substrate selectivity, and further adaptability to perform bio-catalysis.
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Affiliation(s)
- Raki Mandal
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India.
| | - Anupam Ghosh
- Indian Association for the Cultivation of Science, Raja S. C. Mullick Road, Kolkata 700032, India
| | - Nilesh K Rout
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India.
| | - Mahesh Prasad
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India.
| | - Bibhas Hazra
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India.
| | - Sanu Sar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India.
| | - Subrata Das
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India.
| | - Ayan Datta
- Indian Association for the Cultivation of Science, Raja S. C. Mullick Road, Kolkata 700032, India
| | - Pradip K Tarafdar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India.
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5
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Wozniak K, Brzezinski K. Biological Catalysis and Information Storage Have Relied on N-Glycosyl Derivatives of β-D-Ribofuranose since the Origins of Life. Biomolecules 2023; 13:biom13050782. [PMID: 37238652 DOI: 10.3390/biom13050782] [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: 03/06/2023] [Revised: 04/24/2023] [Accepted: 04/29/2023] [Indexed: 05/28/2023] Open
Abstract
Most naturally occurring nucleotides and nucleosides are N-glycosyl derivatives of β-d-ribose. These N-ribosides are involved in most metabolic processes that occur in cells. They are essential components of nucleic acids, forming the basis for genetic information storage and flow. Moreover, these compounds are involved in numerous catalytic processes, including chemical energy production and storage, in which they serve as cofactors or coribozymes. From a chemical point of view, the overall structure of nucleotides and nucleosides is very similar and simple. However, their unique chemical and structural features render these compounds versatile building blocks that are crucial for life processes in all known organisms. Notably, the universal function of these compounds in encoding genetic information and cellular catalysis strongly suggests their essential role in the origins of life. In this review, we summarize major issues related to the role of N-ribosides in biological systems, especially in the context of the origin of life and its further evolution, through the RNA-based World(s), toward the life we observe today. We also discuss possible reasons why life has arisen from derivatives of β-d-ribofuranose instead of compounds based on other sugar moieties.
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Affiliation(s)
- Katarzyna Wozniak
- Department of Structural Biology of Prokaryotic Organisms, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-074 Poznan, Poland
| | - Krzysztof Brzezinski
- Department of Structural Biology of Prokaryotic Organisms, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-074 Poznan, Poland
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6
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Ding D, Zhou L, Mittal S, Szostak JW. Experimental Tests of the Virtual Circular Genome Model for Nonenzymatic RNA Replication. J Am Chem Soc 2023; 145:7504-7515. [PMID: 36963403 PMCID: PMC10080680 DOI: 10.1021/jacs.3c00612] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
The virtual circular genome (VCG) model was proposed as a means of going beyond template copying to indefinite cycles of nonenzymatic RNA replication during the origin of life. In the VCG model, the protocellular genome is a collection of short oligonucleotides that map to both strands of a virtual circular sequence. Replication is driven by templated nonenzymatic primer extensions on a subset of kinetically trapped partially base-paired configurations, followed by the shuffling of these configurations to enable continued oligonucleotide elongation. Here, we describe initial experimental studies of the feasibility of the VCG model for replication. We designed a small 12-nucleotide model VCG and synthesized all 247 oligonucleotides of lengths 2 to 12 corresponding to this genome. We experimentally monitored the fate of individual labeled primers in the pool of VCG oligonucleotides following the addition of activated nucleotides and investigated the effect of factors such as oligonucleotide length, concentration, composition, and temperature on the extent of primer extension. We observe a surprisingly prolonged equilibration process in the VCG system that enables a considerable extent of reaction. We find that environmental fluctuations would be essential for continuous templated extension of the entire VCG system since the shortest oligonucleotides can only bind to templates at low temperatures, while the longest oligonucleotides require high-temperature spikes to escape from inactive configurations. Finally, we demonstrate that primer extension is significantly enhanced when the mix of VCG oligonucleotides is preactivated. We discuss the necessity of ongoing in situ activation chemistry for continuous and accurate VCG replication.
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Affiliation(s)
- Dian Ding
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Lijun Zhou
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Shriyaa Mittal
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Jack W Szostak
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
- Howard Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
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7
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Baron L, Hadjerci J, Thoidingjam L, Plays M, Bucci R, Morris N, Müller S, Sindikubwabo F, Solier S, Cañeque T, Colombeau L, Blouin CM, Lamaze C, Puisieux A, Bono Y, Gaillet C, Laraia L, Vauzeilles B, Taran F, Papot S, Karoyan P, Duval R, Mahuteau-Betzer F, Arimondo P, Cariou K, Guichard G, Micouin L, Ethève-Quelquejeu M, Verga D, Versini A, Gasser G, Tang C, Belmont P, Linkermann A, Bonfio C, Gillingham D, Poulsen T, Di Antonio M, Lopez M, Guianvarc'h D, Thomas C, Masson G, Gautier A, Johannes L, Rodriguez R. PSL Chemical Biology Symposia Third Edition: A Branch of Science in its Explosive Phase. Chembiochem 2023; 24:e202300093. [PMID: 36942862 DOI: 10.1002/cbic.202300093] [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: 02/03/2023] [Indexed: 03/23/2023]
Abstract
This symposium is the third PSL (Paris Sciences & Lettres) Chemical Biology meeting (2016, 2019, 2023) held at Institut Curie. This initiative originally started at Institut de Chimie des Substances Naturelles (ICSN) in Gif-sur-Yvette (2013, 2014), under the directorship of Professor Max Malacria, with a strong focus on chemistry. It was then continued at the Institut Curie (2015) covering a larger scope, before becoming the official PSL Chemical Biology meeting. This latest edition was postponed twice for the reasons that we know. This has given us the opportunity to invite additional speakers of great standing. This year, Institut Curie hosted around 300 participants, including 220 on site and over 80 online. The pandemic has had, at least, the virtue of promoting online meetings, which we came to realize is not perfect but has its own merits. In particular, it enables those with restricted time and resources to take part in events and meetings, which can now accommodate unlimited participants. We apologize to all those who could not attend in person this time due to space limitation at Institut Curie.
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Affiliation(s)
- Leeroy Baron
- Institut Curie, Department of Cellular and Chemical Biology, UMR 3666 CNRS, U1143 INSERM, PSL Université Paris, 75005, Paris, France
| | - Justine Hadjerci
- Institut Curie, Department of Cellular and Chemical Biology, UMR 3666 CNRS, U1143 INSERM, PSL Université Paris, 75005, Paris, France
| | - Leishemba Thoidingjam
- Institut Curie, Department of Cellular and Chemical Biology, UMR 3666 CNRS, U1143 INSERM, PSL Université Paris, 75005, Paris, France
| | - Marina Plays
- Institut Curie, Department of Cellular and Chemical Biology, UMR 3666 CNRS, U1143 INSERM, PSL Université Paris, 75005, Paris, France
| | - Romain Bucci
- Institut Curie, Department of Cellular and Chemical Biology, UMR 3666 CNRS, U1143 INSERM, PSL Université Paris, 75005, Paris, France
| | - Nolwenn Morris
- Institut Curie, Department of Cellular and Chemical Biology, UMR 3666 CNRS, U1143 INSERM, PSL Université Paris, 75005, Paris, France
| | - Sebastian Müller
- Institut Curie, Department of Cellular and Chemical Biology, UMR 3666 CNRS, U1143 INSERM, PSL Université Paris, 75005, Paris, France
| | - Fabien Sindikubwabo
- Institut Curie, Department of Cellular and Chemical Biology, UMR 3666 CNRS, U1143 INSERM, PSL Université Paris, 75005, Paris, France
| | - Stéphanie Solier
- Institut Curie, Department of Cellular and Chemical Biology, UMR 3666 CNRS, U1143 INSERM, PSL Université Paris, 75005, Paris, France
| | - Tatiana Cañeque
- Institut Curie, Department of Cellular and Chemical Biology, UMR 3666 CNRS, U1143 INSERM, PSL Université Paris, 75005, Paris, France
| | - Ludovic Colombeau
- Institut Curie, Department of Cellular and Chemical Biology, UMR 3666 CNRS, U1143 INSERM, PSL Université Paris, 75005, Paris, France
| | - Cedric M Blouin
- Institut Curie, Department of Cellular and Chemical Biology, UMR 3666 CNRS, U1143 INSERM, PSL Université Paris, 75005, Paris, France
| | - Christophe Lamaze
- Institut Curie, Department of Cellular and Chemical Biology, UMR 3666 CNRS, U1143 INSERM, PSL Université Paris, 75005, Paris, France
| | - Alain Puisieux
- Institut Curie, Department of Cellular and Chemical Biology, UMR 3666 CNRS, U1143 INSERM, PSL Université Paris, 75005, Paris, France
| | - Yannick Bono
- Institut Curie, Department of Cellular and Chemical Biology, UMR 3666 CNRS, U1143 INSERM, PSL Université Paris, 75005, Paris, France
| | - Christine Gaillet
- Institut Curie, Department of Cellular and Chemical Biology, UMR 3666 CNRS, U1143 INSERM, PSL Université Paris, 75005, Paris, France
| | - Luca Laraia
- Technical University of Denmark, Department of Chemistry, 2800, Kgs. Lyngby, Denmark
| | - Boris Vauzeilles
- Université Paris-Saclay, CNRS UPR 2301, 91198, Gif-sur-Yvette, France
| | - Frédéric Taran
- Université Paris-Saclay, CEA, 91191, Gif-sur-Yvette, France
| | - Sébastien Papot
- Université de Poitiers, CNRS UMR 7285, 86073, Poitiers, France
| | - Philippe Karoyan
- PSL Université Paris, Sorbonne Université Ecole Normale Supérieure, CNRS UMR 7203, 75005, Paris, France
| | - Romain Duval
- Faculté de Pharmacie de Paris, Université Paris Cité CNRS UMR 261, 75006, Paris, France
| | | | | | - Kevin Cariou
- PSL Université Paris, Chimie ParisTech, CNRS, Institute of Chemistry and Health Sciences CNRS UMR 8060, 75005, Paris, France
| | - Gilles Guichard
- Université de Bordeaux, CNRS, Bordeaux INP CBMN, UMR 5248, 33600, Pessac, France
| | | | | | - Daniela Verga
- PSL Université Paris, Institut Curie CNRS UMR 9187, INSERM U1196, 91405, Orsay, France
| | - Antoine Versini
- University of Zurich, Department of Chemistry, 8057, Zurich, Switzerland
| | - Gilles Gasser
- PSL Université Paris, Chimie ParisTech, CNRS, Institute of Chemistry and Health Sciences CNRS UMR 8060, 75005, Paris, France
| | - Cong Tang
- Universidade de Lisboa, Instituto de Medicina Molecular João Lobo Antunes, 1649-028, Lisboa, Portugal
| | | | - Andreas Linkermann
- Technische Universität Dresden Department of Internal Medicine 3, 01062, Dresden, Germany
| | - Claudia Bonfio
- Université de Strasbourg, CNRS UMR 7006, 67000, Strasbourg, France
| | | | - Thomas Poulsen
- Aarhus University, Department of Chemistry, 8000, Aarhus C Aarhus, Denmark
| | - Marco Di Antonio
- Imperial College London, Molecular Sciences Research Hub, London, W12 0BZ, UK
| | - Marie Lopez
- Université de Montpellier, CNRS UMR 5247, 34000, Montpellier, France
| | | | - Christophe Thomas
- PSL Université Paris, Chimie ParisTech CNRS UMR 6226, 75005, Paris, France
| | - Géraldine Masson
- Université Paris-Saclay, CNRS UPR 2301, 91198, Gif-sur-Yvette, France
| | - Arnaud Gautier
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, LBM, 75005, Paris, France
| | - Ludger Johannes
- Institut Curie, Department of Cellular and Chemical Biology, UMR 3666 CNRS, U1143 INSERM, PSL Université Paris, 75005, Paris, France
| | - Raphaël Rodriguez
- Institut Curie, Department of Cellular and Chemical Biology, UMR 3666 CNRS, U1143 INSERM, PSL Université Paris, 75005, Paris, France
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8
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Katke C, Pedrueza-Villalmanzo E, Spustova K, Ryskulov R, Kaplan CN, Gözen I. Colony-like Protocell Superstructures. ACS NANO 2023; 17:3368-3382. [PMID: 36795609 PMCID: PMC9979656 DOI: 10.1021/acsnano.2c08093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
We report the formation, growth, and dynamics of model protocell superstructures on solid surfaces, resembling single cell colonies. These structures, consisting of several layers of lipidic compartments enveloped in a dome-shaped outer lipid bilayer, emerged as a result of spontaneous shape transformation of lipid agglomerates deposited on thin film aluminum surfaces. Collective protocell structures were observed to be mechanically more stable compared to isolated spherical compartments. We show that the model colonies encapsulate DNA and accommodate nonenzymatic, strand displacement DNA reactions. The membrane envelope is able to disassemble and expose individual daughter protocells, which can migrate and attach via nanotethers to distant surface locations, while maintaining their encapsulated contents. Some colonies feature "exocompartments", which spontaneously extend out of the enveloping bilayer, internalize DNA, and merge again with the superstructure. A continuum elastohydrodynamic theory that we developed suggests that a plausible driving force behind subcompartment formation is attractive van der Waals (vdW) interactions between the membrane and surface. The balance between membrane bending and vdW interactions yields a critical length scale of 236 nm, above which the membrane invaginations can form subcompartments. The findings support our hypotheses that in extension of the "lipid world hypothesis", protocells may have existed in the form of colonies, potentially benefiting from the increased mechanical stability provided by a superstructure.
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Affiliation(s)
- Chinmay Katke
- Department
of Physics, Virginia Polytechnic Institute
and State University, Blacksburg, Virginia 24061, United States
- Center
for Soft Matter and Biological Physics, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Esteban Pedrueza-Villalmanzo
- Department
of Chemistry and Chemical Engineering, Chalmers
University of Technology, Göteborg SE-412 96, Sweden
- Department
of Physics, University of Gothenburg, Universitetsplatsen 1, Gothenburg 405 30, Sweden
| | - Karolina Spustova
- Centre
for Molecular Medicine Norway, Faculty of Medicine, University of Oslo, 0318 Oslo, Norway
| | - Ruslan Ryskulov
- Department
of Chemistry and Chemical Engineering, Chalmers
University of Technology, Göteborg SE-412 96, Sweden
| | - C. Nadir Kaplan
- Department
of Physics, Virginia Polytechnic Institute
and State University, Blacksburg, Virginia 24061, United States
- Center
for Soft Matter and Biological Physics, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Irep Gözen
- Centre
for Molecular Medicine Norway, Faculty of Medicine, University of Oslo, 0318 Oslo, Norway
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9
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Pavlinova P, Lambert CN, Malaterre C, Nghe P. Abiogenesis through gradual evolution of autocatalysis into template-based replication. FEBS Lett 2023; 597:344-379. [PMID: 36203246 DOI: 10.1002/1873-3468.14507] [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: 07/15/2022] [Revised: 09/20/2022] [Accepted: 09/29/2022] [Indexed: 11/11/2022]
Abstract
How life emerged from inanimate matter is one of the most intriguing questions posed to modern science. Central to this research are experimental attempts to build systems capable of Darwinian evolution. RNA catalysts (ribozymes) are a promising avenue, in line with the RNA world hypothesis whereby RNA pre-dated DNA and proteins. Since evolution in living organisms relies on template-based replication, the identification of a ribozyme capable of replicating itself (an RNA self-replicase) has been a major objective. However, no self-replicase has been identified to date. Alternatively, autocatalytic systems involving multiple RNA species capable of ligation and recombination may enable self-reproduction. However, it remains unclear how evolution could emerge in autocatalytic systems. In this review, we examine how experimentally feasible RNA reactions catalysed by ribozymes could implement the evolutionary properties of variation, heredity and reproduction, and ultimately allow for Darwinian evolution. We propose a gradual path for the emergence of evolution, initially supported by autocatalytic systems leading to the later appearance of RNA replicases.
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Affiliation(s)
- Polina Pavlinova
- Laboratoire de Biophysique et Evolution, UMR CNRS-ESPCI 8231 Chimie Biologie Innovation, PSL University, Paris, France
| | - Camille N Lambert
- Laboratoire de Biophysique et Evolution, UMR CNRS-ESPCI 8231 Chimie Biologie Innovation, PSL University, Paris, France
| | - Christophe Malaterre
- Laboratory of Philosophy of Science (LAPS) and Centre Interuniversitaire de Recherche sur la Science et la Technologie (CIRST), Université du Québec à Montréal (UQAM), Canada
| | - Philippe Nghe
- Laboratoire de Biophysique et Evolution, UMR CNRS-ESPCI 8231 Chimie Biologie Innovation, PSL University, Paris, France
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10
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Guo X, Fu S, Ying J, Zhao Y. Prebiotic chemistry: a review of nucleoside phosphorylation and polymerization. Open Biol 2023; 13:220234. [PMID: 36629018 PMCID: PMC9832566 DOI: 10.1098/rsob.220234] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 12/06/2022] [Indexed: 01/12/2023] Open
Abstract
The phosphorylation of nucleosides and their polymerization are crucial issues concerning the origin of life. The question of how these plausible chemical processes took place in the prebiotic Earth is still perplexing, despite several studies that have attempted to explain these prebiotic processes. The purpose of this article is to review these chemical reactions with respect to chemical evolution in the primeval Earth. Meanwhile, from our perspective, the chiral properties and selection of biomolecules should be considered in the prebiotic chemical origin of life, which may contribute to further research in this field to some extent.
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Affiliation(s)
- Xiaofan Guo
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, People's Republic of China
| | - Songsen Fu
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, People's Republic of China
| | - Jianxi Ying
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, People's Republic of China
| | - Yufen Zhao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, People's Republic of China
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, Fujian, People's Republic of China
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11
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Wei D, Wang Y, Song D, Zhang Z, Wang J, Chen JY, Li Z, Yu H. A Nucleic Acid Sequence That is Catalytically Active in Both RNA and TNA Backbones. ACS Synth Biol 2022; 11:3874-3885. [PMID: 36278399 DOI: 10.1021/acssynbio.2c00479] [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] [Indexed: 01/27/2023]
Abstract
Threose nucleic acid (TNA) is considered a potential RNA progenitor due to its chemical simplicity, base pairing property, and capability of folding into a functional tertiary structure. However, it is unknown whether the functional property can be maintained during transition from TNA to RNA. Here, we use a toggle in vitro selection to identify nucleic acid catalyst sequences that are active in both TNA and RNA backbones. One such nucleic acid enzyme with exchangeable backbone (CAMELEON) catalyzes an RNA cleavage reaction when prepared as TNA (T) and RNA (R). Further biochemical characterization reveals that CAMELEON R and T exhibit different catalytic behaviors such as rate enhancement and magnesium dependence. Structural probing and mutagenesis experiments suggest that they likely fold into distinct tertiary structures. This work demonstrates that the catalytic activity can be preserved during backbone transition from TNA to RNA and provides further experimental support for TNA as an RNA precursor in evolution.
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Affiliation(s)
- Dongying Wei
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu210023, China
| | - Yueyao Wang
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu210023, China
| | - Dongfan Song
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, Jiangsu210023, China
| | - Ze Zhang
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu210023, China
| | - Juan Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, Jiangsu210023, China
| | - Jia-Yu Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing210023, China
| | - Zhe Li
- State Key Laboratory of Analytical Chemistry for Life Science, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu210023, China
| | - Hanyang Yu
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu210023, China
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12
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Ikehara K. How Did Life Emerge in Chemically Complex Messy Environments? Life (Basel) 2022; 12:life12091319. [PMID: 36143356 PMCID: PMC9503616 DOI: 10.3390/life12091319] [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] [Received: 06/27/2022] [Revised: 08/18/2022] [Accepted: 08/25/2022] [Indexed: 11/18/2022] Open
Abstract
One of the problems that make it difficult to solve the mystery of the origin of life is determining how life emerged in chemically complex messy environments on primitive Earth. In this article, the “chemically complex messy environments” that are focused on are a mixed state of various organic compounds produced via prebiotic means and accumulated on primitive earth. The five factors described below are thought to have contributed to opening the way for the emergence of life: (1) A characteristic inherent in [GADV]-amino acids, which are easily produced via prebiotic means. [GADV] stands for four amino acids, Gly [G], Ala [A], Asp [D] and Val [V], which are indicated by a one-letter symbol. (2) The protein 0th-order structure or a [GADV]-amino acid composition generating water-soluble globular protein with some flexibility, which can be produced even by the random joining of [GADV]-amino acids. (3) The formation of versatile [GADV]-microspheres, which can grow, divide and proliferate even without a genetic system, was the emergence of proto-life. (4) The [GADV]-microspheres with a higher proliferation ability than others were able to be selected. Proto-Darwin evolution made it possible to proceed forward to the creation of a core life system composed of the (GNC)n gene, anticodon stem-loop tRNA or AntiC-SL tRNA (GNC genetic code), and [GADV]-protein. (5) Eventually, the first genuine life with a core life system emerged. Thus, the formation processes of [GADV]-protein and the (GNC)n gene in chemically complex messy environments were the steps to the emergence of genuine life.
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Affiliation(s)
- Kenji Ikehara
- G&L Kyosei Institute, The Keihanna Academy of Science and Culture (KASC), Keihanna Interaction Plaza, Lab. Wing 3F, 1-7 Hikaridai, Seika-cho, Souraku, Kyoto 619-0237, Japan; ; Tel.: +81-774-73-4478
- International Institute for Advanced Studies, Kizugawadai 9-3, Kizugawa, Kyoto 619-0225, Japan
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13
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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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14
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Imai M, Sakuma Y, Kurisu M, Walde P. From vesicles toward protocells and minimal cells. SOFT MATTER 2022; 18:4823-4849. [PMID: 35722879 DOI: 10.1039/d1sm01695d] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In contrast to ordinary condensed matter systems, "living systems" are unique. They are based on molecular compartments that reproduce themselves through (i) an uptake of ingredients and energy from the environment, and (ii) spatially and timely coordinated internal chemical transformations. These occur on the basis of instructions encoded in information molecules (DNAs). Life originated on Earth about 4 billion years ago as self-organised systems of inorganic compounds and organic molecules including macromolecules (e.g. nucleic acids and proteins) and low molar mass amphiphiles (lipids). Before the first living systems emerged from non-living forms of matter, functional molecules and dynamic molecular assemblies must have been formed as prebiotic soft matter systems. These hypothetical cell-like compartment systems often are called "protocells". Other systems that are considered as bridging units between non-living and living systems are called "minimal cells". They are synthetic, autonomous and sustainable reproducing compartment systems, but their constituents are not limited to prebiotic substances. In this review, we focus on both membrane-bounded (vesicular) protocells and minimal cells, and provide a membrane physics background which helps to understand how morphological transformations of vesicle systems might have happened and how vesicle reproduction might be coupled with metabolic reactions and information molecules. This research, which bridges matter and life, is a great challenge in which soft matter physics, systems chemistry, and synthetic biology must take joined efforts to better understand how the transformation of protocells into living systems might have occurred at the origin of life.
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Affiliation(s)
- Masayuki Imai
- Department of Physics, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba, Sendai 980-8578, Japan.
| | - Yuka Sakuma
- Department of Physics, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba, Sendai 980-8578, Japan.
| | - Minoru Kurisu
- Department of Physics, Graduate School of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba, Sendai 980-8578, Japan.
| | - Peter Walde
- Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, CH-8093 Zürich, Switzerland
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15
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Making nucleic acid monomers. Nat Chem 2022; 14:725-727. [PMID: 35778560 DOI: 10.1038/s41557-022-00985-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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16
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Frenkel-Pinter M, Jacobson KC, Eskew-Martin J, Forsythe JG, Grover MA, Williams LD, Hud NV. Differential Oligomerization of Alpha versus Beta Amino Acids and Hydroxy Acids in Abiotic Proto-Peptide Synthesis Reactions. Life (Basel) 2022; 12:265. [PMID: 35207553 PMCID: PMC8876357 DOI: 10.3390/life12020265] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/24/2022] [Accepted: 01/28/2022] [Indexed: 12/13/2022] Open
Abstract
The origin of biopolymers is a central question in origins of life research. In extant life, proteins are coded linear polymers made of a fixed set of twenty alpha-L-amino acids. It is likely that the prebiotic forerunners of proteins, or protopeptides, were more heterogenous polymers with a greater diversity of building blocks and linkage stereochemistry. To investigate a possible chemical selection for alpha versus beta amino acids in abiotic polymerization reactions, we subjected mixtures of alpha and beta hydroxy and amino acids to single-step dry-down or wet-dry cycling conditions. The resulting model protopeptide mixtures were analyzed by a variety of analytical techniques, including mass spectrometry and NMR spectroscopy. We observed that amino acids typically exhibited a higher extent of polymerization in reactions that also contained alpha hydroxy acids over beta hydroxy acids, whereas the extent of polymerization by beta amino acids was higher compared to their alpha amino acid analogs. Our results suggest that a variety of heterogenous protopeptide backbones existed during the prebiotic epoch, and that selection towards alpha backbones occurred later as a result of polymer evolution.
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Affiliation(s)
- Moran Frenkel-Pinter
- NSF-NASA Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, GA 30332, USA; (M.F.-P.); (K.C.J.); (J.E.-M.); (J.G.F.); (M.A.G.)
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Kaitlin C. Jacobson
- NSF-NASA Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, GA 30332, USA; (M.F.-P.); (K.C.J.); (J.E.-M.); (J.G.F.); (M.A.G.)
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Jonathan Eskew-Martin
- NSF-NASA Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, GA 30332, USA; (M.F.-P.); (K.C.J.); (J.E.-M.); (J.G.F.); (M.A.G.)
- Department of Chemistry and Biochemistry, College of Charleston, Charleston, SC 29424, USA
| | - Jay G. Forsythe
- NSF-NASA Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, GA 30332, USA; (M.F.-P.); (K.C.J.); (J.E.-M.); (J.G.F.); (M.A.G.)
- Department of Chemistry and Biochemistry, College of Charleston, Charleston, SC 29424, USA
| | - Martha A. Grover
- NSF-NASA Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, GA 30332, USA; (M.F.-P.); (K.C.J.); (J.E.-M.); (J.G.F.); (M.A.G.)
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Loren Dean Williams
- NSF-NASA Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, GA 30332, USA; (M.F.-P.); (K.C.J.); (J.E.-M.); (J.G.F.); (M.A.G.)
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Nicholas V. Hud
- NSF-NASA Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, GA 30332, USA; (M.F.-P.); (K.C.J.); (J.E.-M.); (J.G.F.); (M.A.G.)
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
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17
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Kristoffersen EL, Burman M, Noy A, Holliger P. Rolling circle RNA synthesis catalysed by RNA. eLife 2022; 11:75186. [PMID: 35108196 PMCID: PMC8937235 DOI: 10.7554/elife.75186] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/01/2022] [Indexed: 11/13/2022] Open
Abstract
RNA-catalyzed RNA replication is widely considered a key step in the emergence of life’s first genetic system. However, RNA replication can be impeded by the extraordinary stability of duplex RNA products, which must be dissociated for re-initiation of the next replication cycle. Here, we have explored rolling circle synthesis (RCS) as a potential solution to this strand separation problem. We observe sustained RCS by a triplet polymerase ribozyme beyond full-length circle synthesis with strand displacement yielding concatemeric RNA products. Furthermore, we show RCS of a circular Hammerhead ribozyme capable of self-cleavage and re-circularization. Thus, all steps of a viroid-like RNA replication pathway can be catalyzed by RNA alone. Finally, we explore potential RCS mechanisms by molecular dynamics simulations, which indicate a progressive build-up of conformational strain upon RCS with destabilization of nascent strand 5′- and 3′-ends. Our results have implications for the emergence of RNA replication and for understanding the potential of RNA to support complex genetic processes. Many organisms today rely on a trio of molecules for their survival: DNA, to store their genetic information; proteins, to conduct the biological processes required for growth or replication; and RNA, to mainly act as an intermediary between DNA and proteins. Yet, how these inanimate molecules first came together to form a living system remains unclear. Circumstantial evidence suggests that the first lifeforms relied to a much greater exrtent on RNA to conduct all necessary biological processes. There is no trace of this ‘RNA world’ today, but molecular ‘fossils’ may exist in current biology. Viroids, for example, are agents which can infect and replicate inside plant cells. They are formed of nothing but a circular strand of RNA that serves not only as genetic storage but also as ribozymes (RNA-based enzymes). Viroids need proteins from the host plant to replicate, but scientists have been able to engineer ribozymes that can copy complex RNA strands. This suggests that viroid-like replication could be achieved using only RNA. Kristoffersen et al. put this idea to the test and showed that it is possible to use RNA enzymatic activity alone to carry out all the steps of a viroid-like copying mechanism. This process included copying a viroid-like RNA circle with RNA, followed by trimming the copy to the right size and reforming the circle. These two latter steps could be carried out by a ribozyme that could itself be encoded on the RNA circle. A computer simulation indicated that RNA synthesis on the circle caused increasing tension that could ease some of the barriers to replication. These results increase our understanding of how RNA copying by RNA could be possible. This may lead to developing molecular models of a primordial RNA-based replication, which could be used to investigate early genetic systems and may have potential applications in synthetic biology.
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Affiliation(s)
| | - Matthew Burman
- Department of Physics, University of York, York, United Kingdom
| | - Agnes Noy
- Department of Physics, University of York, York, United Kingdom
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18
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Closs AC, Bechtel M, Trapp O. Dynamic Exchange of Substituents in a Prebiotic Organocatalyst: Initial Steps towards an Evolutionary System. Angew Chem Int Ed Engl 2022; 61:e202112563. [PMID: 34705315 PMCID: PMC9298921 DOI: 10.1002/anie.202112563] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Indexed: 11/07/2022]
Abstract
All evolutionary biological processes lead to a change in heritable traits over successive generations. The responsible genetic information encoded in DNA is altered, selected, and inherited by mutation of the base sequence. While this is well known at the biological level, an evolutionary change at the molecular level of small organic molecules is unknown but represents an important prerequisite for the emergence of life. Here, we present a class of prebiotic imidazolidine-4-thione organocatalysts able to dynamically change their constitution and potentially capable to form an evolutionary system. These catalysts functionalize their building blocks and dynamically adapt to their (self-modified) environment by mutation of their own structure. Depending on the surrounding conditions, they show pronounced and opposing selectivity in their formation. Remarkably, the preferentially formed species can be associated with different catalytic properties, which enable multiple pathways for the transition from abiotic matter to functional biomolecules.
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Affiliation(s)
- Anna C. Closs
- Department of ChemistryLudwig-Maximilians-University MunichButenandtstr. 5–1381377MunichGermany
- Max-Planck-Institute for AstronomyKönigstuhl 1769117HeidelbergGermany
| | - Maximilian Bechtel
- Department of ChemistryLudwig-Maximilians-University MunichButenandtstr. 5–1381377MunichGermany
| | - Oliver Trapp
- Department of ChemistryLudwig-Maximilians-University MunichButenandtstr. 5–1381377MunichGermany
- Max-Planck-Institute for AstronomyKönigstuhl 1769117HeidelbergGermany
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19
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Closs AC, Bechtel M, Trapp O. Dynamischer Austausch von Substituenten in einem präbiotischen Organokatalysator: Erste Schritte auf dem Weg zu einem evolutionären System. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Anna C. Closs
- Department Chemie Ludwig-Maximilians-Universität München Butenandtstr. 5–13 81377 München Deutschland
- Max-Planck-Institut für Astronomie Königstuhl 17 69117 Heidelberg Deutschland
| | - Maximilian Bechtel
- Department Chemie Ludwig-Maximilians-Universität München Butenandtstr. 5–13 81377 München Deutschland
| | - Oliver Trapp
- Department Chemie Ludwig-Maximilians-Universität München Butenandtstr. 5–13 81377 München Deutschland
- Max-Planck-Institut für Astronomie Königstuhl 17 69117 Heidelberg Deutschland
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20
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Giurgiu C, Fang Z, Aitken HRM, Kim SC, Pazienza L, Mittal S, Szostak JW. Structure–Activity Relationships in Nonenzymatic Template‐Directed RNA Synthesis. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Constantin Giurgiu
- Howard Hughes Medical Institute Department of Molecular Biology, and Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Department of Chemistry and Chemical Biology Harvard University Cambridge MA 02138 USA
| | - Ziyuan Fang
- Howard Hughes Medical Institute Department of Molecular Biology, and Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Department of Genetics Harvard Medical School Boston MA 02115 USA
| | - Harry R. M. Aitken
- Howard Hughes Medical Institute Department of Molecular Biology, and Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Department of Genetics Harvard Medical School Boston MA 02115 USA
| | - Seohyun Chris Kim
- Howard Hughes Medical Institute Department of Molecular Biology, and Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Department of Genetics Harvard Medical School Boston MA 02115 USA
| | - Lydia Pazienza
- Howard Hughes Medical Institute Department of Molecular Biology, and Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Department of Chemistry and Chemical Biology Harvard University Cambridge MA 02138 USA
| | - Shriyaa Mittal
- Howard Hughes Medical Institute Department of Molecular Biology, and Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Department of Chemistry and Chemical Biology Harvard University Cambridge MA 02138 USA
| | - Jack W. Szostak
- Howard Hughes Medical Institute Department of Molecular Biology, and Center for Computational and Integrative Biology Massachusetts General Hospital Boston MA 02114 USA
- Department of Chemistry and Chemical Biology Harvard University Cambridge MA 02138 USA
- Department of Genetics Harvard Medical School Boston MA 02115 USA
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21
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Giurgiu C, Fang Z, Aitken HRM, Kim SC, Pazienza L, Mittal S, Szostak JW. Structure-Activity Relationships in Nonenzymatic Template-Directed RNA Synthesis. Angew Chem Int Ed Engl 2021; 60:22925-22932. [PMID: 34428345 PMCID: PMC8490286 DOI: 10.1002/anie.202109714] [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: 07/21/2021] [Indexed: 11/11/2022]
Abstract
The template-directed synthesis of RNA played an important role in the transition from prebiotic chemistry to the beginnings of RNA based life, but the mechanism of RNA copying chemistry is incompletely understood. We measured the kinetics of template copying with a set of primers with modified 3'-nucleotides and determined the crystal structures of these modified nucleotides in the context of a primer/template/substrate-analog complex. pH-rate profiles and solvent isotope effects show that deprotonation of the primer 3'-hydroxyl occurs prior to the rate limiting step, the attack of the alkoxide on the activated phosphate of the incoming nucleotide. The analogs with a 3 E ribose conformation show the fastest formation of 3'-5' phosphodiester bonds. Among those derivatives, the reaction rate is strongly correlated with the electronegativity of the 2'-substituent. We interpret our results in terms of differences in steric bulk and charge distribution in the ground vs. transition states.
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Affiliation(s)
- Constantin Giurgiu
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Ziyuan Fang
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Harry R M Aitken
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Seohyun Chris Kim
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Lydia Pazienza
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Shriyaa Mittal
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, 02114, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
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22
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Jiménez EI, Gibard C, Krishnamurthy R. Prebiotic Phosphorylation and Concomitant Oligomerization of Deoxynucleosides to form DNA. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015910] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Eddy I. Jiménez
- The Department of Chemistry The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - Clémentine Gibard
- The Department of Chemistry The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - Ramanarayanan Krishnamurthy
- The Department of Chemistry The Scripps Research Institute 10550 North Torrey Pines Road La Jolla CA 92037 USA
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23
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Jiménez EI, Gibard C, Krishnamurthy R. Prebiotic Phosphorylation and Concomitant Oligomerization of Deoxynucleosides to form DNA. Angew Chem Int Ed Engl 2021; 60:10775-10783. [PMID: 33325148 DOI: 10.1002/anie.202015910] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Indexed: 12/14/2022]
Abstract
Recent demonstrations of RNA-DNA chimeras (RDNA) enabling RNA and DNA replication, coupled with prebiotic co-synthesis of deoxyribo- and ribo-nucleotides, have resurrected the hypothesis of co-emergence of RNA and DNA. As further support, we show that diamidophosphate (DAP) with 2-aminoimidazole (amido)phosphorylates and oligomerizes deoxynucleosides to form DNA-under conditions similar to those of ribonucleosides. The pyrimidine deoxynucleoside 5'-O-amidophosphates are formed in good (≈60 %) yields. Intriguingly, the presence of pyrimidine deoxynucleos(t)ides increased the yields of purine deoxynucleotides (≈20 %). Concomitantly, oligomerization (≈18-31 %) is observed with predominantly 3',5'-phosphodiester DNA linkages, and some (<5 %) pyrophosphates. Combined with previous observations of DAP-mediated chemistries and the constructive role of RDNA chimeras, the results reported here help set the stage for systematic investigation of a systems chemistry approach of RNA-DNA coevolution.
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Affiliation(s)
- Eddy I Jiménez
- The Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Clémentine Gibard
- The Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Ramanarayanan Krishnamurthy
- The Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
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24
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Chatragadda R, Dufossé L. Ecological and Biotechnological Aspects of Pigmented Microbes: A Way Forward in Development of Food and Pharmaceutical Grade Pigments. Microorganisms 2021; 9:637. [PMID: 33803896 PMCID: PMC8003166 DOI: 10.3390/microorganisms9030637] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/04/2021] [Accepted: 03/15/2021] [Indexed: 12/17/2022] Open
Abstract
Microbial pigments play multiple roles in the ecosystem construction, survival, and fitness of all kinds of organisms. Considerably, microbial (bacteria, fungi, yeast, and microalgae) pigments offer a wide array of food, drug, colorants, dyes, and imaging applications. In contrast to the natural pigments from microbes, synthetic colorants are widely used due to high production, high intensity, and low cost. Nevertheless, natural pigments are gaining more demand over synthetic pigments as synthetic pigments have demonstrated side effects on human health. Therefore, research on microbial pigments needs to be extended, explored, and exploited to find potential industrial applications. In this review, the evolutionary aspects, the spatial significance of important pigments, biomedical applications, research gaps, and future perspectives are detailed briefly. The pathogenic nature of some pigmented bacteria is also detailed for awareness and safe handling. In addition, pigments from macro-organisms are also discussed in some sections for comparison with microbes.
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Affiliation(s)
- Ramesh Chatragadda
- Biological Oceanography Division (BOD), Council of Scientific and Industrial Research-National Institute of Oceanography (CSIR-NIO), Dona Paula 403004, Goa, India
| | - Laurent Dufossé
- Chemistry and Biotechnology of Natural Products (CHEMBIOPRO Lab), Ecole Supérieure d’Ingénieurs Réunion Océan Indien (ESIROI), Département Agroalimentaire, Université de La Réunion, F-97744 Saint-Denis, France
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25
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Kim HJ, Benner SA. Abiotic Synthesis of Nucleoside 5'-Triphosphates with Nickel Borate and Cyclic Trimetaphosphate (CTMP). ASTROBIOLOGY 2021; 21:298-306. [PMID: 33533695 DOI: 10.1089/ast.2020.2264] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
While nucleoside 5'-triphosphates are precursors for RNA in modern biology, the presumed difficulty of making these triphosphates on Hadean Earth has caused many prebiotic researchers to consider other activated species for the prebiotic synthesis of RNA. We report here that nickel(II), in the presence of borate, gives substantial amounts (2-3%) of nucleoside 5'-triphosphates upon evaporative heating in the presence of urea, salts, and cyclic trimetaphosphate (CTMP). Also recovered are nucleoside 5'-diphosphates and nucleoside 5'-monophosphates, both likely arising from 5'-triphosphate intermediates. The total level of 5'-phosphorylation is typically 30%. Borate enhances the regiospecificity of phosphorylation, with increased amounts of other phosphorylated species seen in its absence. Experimentally supported paths are already available to make nucleosides in environments likely to have been present on Hadean Earth soon after a midsized 1021 to 1023 kg impactor, which would also have delivered nickel to the Hadean surface. Further, sources of prebiotic CTMP continue to be proposed. Thus, these results fill in one of the few remaining steps needed to demystify the prebiotic synthesis of RNA and support a continuous model from atmospheric components to oligomeric RNA that is lacking only a mechanism to obtain homochirality in the product RNA.
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Affiliation(s)
- Hyo-Joong Kim
- Foundation for Applied Molecular Evolution and Firebird Biomolecular Sciences LLC, Alachua, Florida, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution and Firebird Biomolecular Sciences LLC, Alachua, Florida, USA
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26
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Kim SC, O'Flaherty DK, Giurgiu C, Zhou L, Szostak JW. The Emergence of RNA from the Heterogeneous Products of Prebiotic Nucleotide Synthesis. J Am Chem Soc 2021; 143:3267-3279. [PMID: 33636080 DOI: 10.1021/jacs.0c12955] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent advances in prebiotic chemistry are beginning to outline plausible pathways for the synthesis of the canonical ribonucleotides and their assembly into oligoribonucleotides. However, these reaction pathways suggest that many noncanonical nucleotides are likely to have been generated alongside the standard ribonucleotides. Thus, the oligomerization of prebiotically synthesized nucleotides is likely to have led to a highly heterogeneous collection of oligonucleotides comprised of a wide range of types of nucleotides connected by a variety of backbone linkages. How then did relatively homogeneous RNA emerge from this primordial heterogeneity? Here we focus on nonenzymatic template-directed primer extension as a process that would have strongly enriched for homogeneous RNA over the course of multiple cycles of replication. We review the effects on copying the kinetics of nucleotides with altered nucleobase and sugar moieties, when they are present as activated monomers and when they are incorporated into primer and template oligonucleotides. We also discuss three variations in backbone connectivity, all of which are nonheritable and regenerate native RNA upon being copied. The kinetic superiority of RNA synthesis suggests that nonenzymatic copying served as a chemical selection mechanism that allowed relatively homogeneous RNA to emerge from a complex mixture of prebiotically synthesized nucleotides and oligonucleotides.
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Affiliation(s)
- Seohyun Chris Kim
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Derek K O'Flaherty
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Constantin Giurgiu
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Lijun Zhou
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
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27
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Zhang W, Kim SC, Tam CP, Lelyveld VS, Bala S, Chaput JC, Szostak JW. Structural interpretation of the effects of threo-nucleotides on nonenzymatic template-directed polymerization. Nucleic Acids Res 2021; 49:646-656. [PMID: 33347562 PMCID: PMC7826252 DOI: 10.1093/nar/gkaa1215] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/25/2020] [Accepted: 12/17/2020] [Indexed: 11/13/2022] Open
Abstract
The prebiotic synthesis of ribonucleotides is likely to have been accompanied by the synthesis of noncanonical nucleotides including the threo-nucleotide building blocks of TNA. Here, we examine the ability of activated threo-nucleotides to participate in nonenzymatic template-directed polymerization. We find that primer extension by multiple sequential threo-nucleotide monomers is strongly disfavored relative to ribo-nucleotides. Kinetic, NMR and crystallographic studies suggest that this is due in part to the slow formation of the imidazolium-bridged TNA dinucleotide intermediate in primer extension, and in part because of the greater distance between the attacking RNA primer 3'-hydroxyl and the phosphate of the incoming threo-nucleotide intermediate. Even a single activated threo-nucleotide in the presence of an activated downstream RNA oligonucleotide is added to the primer 10-fold more slowly than an activated ribonucleotide. In contrast, a single activated threo-nucleotide at the end of an RNA primer or in an RNA template results in only a modest decrease in the rate of primer extension, consistent with the minor and local structural distortions revealed by crystal structures. Our results are consistent with a model in which heterogeneous primordial oligonucleotides would, through cycles of replication, have given rise to increasingly homogeneous RNA strands.
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Affiliation(s)
- Wen Zhang
- Howard Hughes Medical Institute and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02114, USA.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Seohyun Chris Kim
- Howard Hughes Medical Institute and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Chun Pong Tam
- Howard Hughes Medical Institute and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Victor S Lelyveld
- Howard Hughes Medical Institute and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Saikat Bala
- Department of Chemistry and of Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA
| | - John C Chaput
- Department of Chemistry and of Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA
| | - Jack W Szostak
- Howard Hughes Medical Institute and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02114, USA.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
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28
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Zhou L, Ding D, Szostak JW. The virtual circular genome model for primordial RNA replication. RNA (NEW YORK, N.Y.) 2021; 27:1-11. [PMID: 33028653 PMCID: PMC7749632 DOI: 10.1261/rna.077693.120] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 10/02/2020] [Indexed: 05/13/2023]
Abstract
We propose a model for the replication of primordial protocell genomes that builds upon recent advances in the nonenzymatic copying of RNA. We suggest that the original genomes consisted of collections of oligonucleotides beginning and ending at all possible positions on both strands of one or more virtual circular sequences. Replication is driven by feeding with activated monomers and by the activation of monomers and oligonucleotides in situ. A fraction of the annealed configurations of the protocellular oligonucleotides would allow for template-directed oligonucleotide growth by primer extension or ligation. Rearrangements of these annealed configurations, driven either by environmental fluctuations or occurring spontaneously, would allow for continued oligonucleotide elongation. Assuming that shorter oligonucleotides were more abundant than longer ones, replication of the entire genome could occur by the growth of all oligonucleotides by as little as one nucleotide on average. We consider possible scenarios that could have given rise to such protocell genomes, as well as potential routes to the emergence of catalytically active ribozymes and thus the more complex cells of the RNA World.
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Affiliation(s)
- Lijun Zhou
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Dian Ding
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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29
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Kovalenko SP. Physicochemical Processes That Probably Originated Life. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162020040093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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30
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Zhou L, O'Flaherty DK, Szostak JW. Assembly of a Ribozyme Ligase from Short Oligomers by Nonenzymatic Ligation. J Am Chem Soc 2020; 142:15961-15965. [PMID: 32820909 PMCID: PMC9594310 DOI: 10.1021/jacs.0c06722] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Our current understanding of the chemistry of the primordial genetic material is fragmentary at best. The chemical replication of oligonucleotides long enough to perform catalytic functions is particularly problematic because of the low efficiency of nonenzymatic template copying. Here we show that this problem can be circumvented by assembling a functional ribozyme by the templated ligation of short oligonucleotides. However, this approach creates a new problem because the splint oligonucleotides used to drive ribozyme assembly strongly inhibit the resulting ribozyme. We explored three approaches to the design of splint oligonucleotides that enable efficient ligation but which allow the assembled ribozyme to remain active. DNA splints, splints with G:U wobble pairs, and splints with G to I (Inosine) substitutions all allowed for the efficient assembly of an active ribozyme ligase. Our work demonstrates the possibility of a transition from nonenzymatic ligation to enzymatic ligation and reveals the importance of avoiding ribozyme inhibition by complementary oligonucleotides.
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Affiliation(s)
- Lijun Zhou
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States.,Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Derek K O'Flaherty
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States.,Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States.,Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.,Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
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31
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32
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Fialho DM, Roche TP, Hud NV. Prebiotic Syntheses of Noncanonical Nucleosides and Nucleotides. Chem Rev 2020; 120:4806-4830. [PMID: 32421316 DOI: 10.1021/acs.chemrev.0c00069] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The origin of nucleotides is a major question in origins-of-life research. Given the central importance of RNA in biology and the influential RNA World hypothesis, a great deal of this research has focused on finding possible prebiotic syntheses of the four canonical nucleotides of coding RNA. However, the use of nucleotides in other roles across the tree of life might be evidence that nucleotides have been used in noncoding roles for even longer than RNA has been used as a genetic polymer. Likewise, it is possible that early life utilized nucleotides other than the extant nucleotides as the monomers of informational polymers. Therefore, finding plausible prebiotic syntheses of potentially ancestral noncanonical nucleotides may be of great importance for understanding the origins and early evolution of life. Experimental investigations into abiotic noncanonical nucleotide synthesis reveal that many noncanonical nucleotides and related glycosides are formed much more easily than the canonical nucleotides. An analysis of the mechanisms by which nucleosides and nucleotides form in the solution phase or in drying-heating reactions from pre-existing sugars and heterocycles suggests that a wide variety of noncanonical nucleotides and related glycosides would have been present on the prebiotic Earth, if any such molecules were present.
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Affiliation(s)
- David M Fialho
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0440, United States
| | - Tyler P Roche
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0440, United States
| | - Nicholas V Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0440, United States
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33
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Abstract
Life on Earth depends on polymerases. These enzymes copy genetic information to produce the DNA and RNA strands at the core of the central dogma. Polymerases act by forming phosphodiester linkages to produce polynucleotide strands. While synthetic chemistry can generate a broad range of alternative genetic materials with unnatural linkages, polymerases have so far been limited to forming O-P bonds. Here, we show that, in fact, unnatural N-P bonds can also be formed by a modified DNA polymerase. This template-directed activity generates complementary strands linked by phosphoramidate (NP) esters, an alternative backbone linkage only known to exist in the laboratory. The emergence of NP-DNA polymerase activity implies the biochemical plausibility of alternative central dogmas for cellular life. All known polymerases copy genetic material by catalyzing phosphodiester bond formation. This highly conserved activity proceeds by a common mechanism, such that incorporated nucleoside analogs terminate chain elongation if the resulting primer strand lacks a terminal hydroxyl group. Even conservatively substituted 3′-amino nucleotides generally act as chain terminators, and no enzymatic pathway for their polymerization has yet been found. Although 3′-amino nucleotides can be chemically coupled to yield stable oligonucleotides containing N3′→P5′ phosphoramidate (NP) bonds, no such internucleotide linkages are known to occur in nature. Here, we report that 3′-amino terminated primers are, in fact, slowly extended by the DNA polymerase from B. stearothermophilus in a template-directed manner. When its cofactor is Ca2+ rather than Mg2+, the reaction is fivefold faster, permitting multiple turnover NP bond formation to yield NP-DNA strands from the corresponding 3′-amino-2′,3′-dideoxynucleoside 5′-triphosphates. A single active site mutation further enhances the rate of NP-DNA synthesis by an additional 21-fold. We show that DNA-dependent NP-DNA polymerase activity depends on conserved active site residues and propose a likely mechanism for this activity based on a series of crystal structures of bound complexes. Our results significantly broaden the catalytic scope of polymerase activity and suggest the feasibility of a genetic transition between native nucleic acids and NP-DNA.
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