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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Sydow C, Seiband C, Siegle AF, Trapp O. Phosphorylation in liquid sulfur dioxide under prebiotically plausible conditions. Commun Chem 2022; 5:143. [PMID: 36697619 PMCID: PMC9814524 DOI: 10.1038/s42004-022-00761-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022] Open
Abstract
In nature, organophosphates provide key functions such as information storage and transport, structural tasks, and energy transfer. Since condensations are unfavourable in water and nucleophilic attack at phosphate is kinetically inhibited, various abiogenesis hypotheses for the formation of organophosphate are discussed. Recently, the application of phosphites as phosphorylation agent showed promising results. However, elevated temperatures and additional reaction steps are required to obtain organophosphates. Here we show that in liquid sulfur dioxide, which acts as solvent and oxidant, efficient organophosphate formation is enabled. Phosphorous acid yields up to 32.6% 5' nucleoside monophosphate, 3.6% 5' nucleoside diphosphate, and the formation of nucleoside triphosphates and dinucleotides in a single reaction step at room temperature. In addition to the phosphorylation of organic compounds, we observed diserine formation. Thus, we suggest volcanic environments as reaction sites for biopolymer formation on Early Earth. Because of the simple recyclability of sulfur dioxide, the reaction is also interesting for synthesis chemistry.
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Affiliation(s)
- Constanze Sydow
- grid.5252.00000 0004 1936 973XDepartment of Chemistry and Pharmacy, Ludwig-Maximilians-University, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Christiane Seiband
- grid.5252.00000 0004 1936 973XDepartment of Chemistry and Pharmacy, Ludwig-Maximilians-University, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Alexander F. Siegle
- grid.5252.00000 0004 1936 973XDepartment of Chemistry and Pharmacy, Ludwig-Maximilians-University, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Oliver Trapp
- grid.5252.00000 0004 1936 973XDepartment of Chemistry and Pharmacy, Ludwig-Maximilians-University, Butenandtstr. 5-13, 81377 Munich, Germany ,grid.429508.20000 0004 0491 677XMax-Planck-Institute for Astronomy, Königstuhl 17, 69117 Heidelberg, Germany
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4
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Fried SD, Fujishima K, Makarov M, Cherepashuk I, Hlouchova K. Peptides before and during the nucleotide world: an origins story emphasizing cooperation between proteins and nucleic acids. J R Soc Interface 2022; 19:20210641. [PMID: 35135297 PMCID: PMC8833103 DOI: 10.1098/rsif.2021.0641] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 01/05/2022] [Indexed: 12/14/2022] Open
Abstract
Recent developments in Origins of Life research have focused on substantiating the narrative of an abiotic emergence of nucleic acids from organic molecules of low molecular weight, a paradigm that typically sidelines the roles of peptides. Nevertheless, the simple synthesis of amino acids, the facile nature of their activation and condensation, their ability to recognize metals and cofactors and their remarkable capacity to self-assemble make peptides (and their analogues) favourable candidates for one of the earliest functional polymers. In this mini-review, we explore the ramifications of this hypothesis. Diverse lines of research in molecular biology, bioinformatics, geochemistry, biophysics and astrobiology provide clues about the progression and early evolution of proteins, and lend credence to the idea that early peptides served many central prebiotic roles before they were encodable by a polynucleotide template, in a putative 'peptide-polynucleotide stage'. For example, early peptides and mini-proteins could have served as catalysts, compartments and structural hubs. In sum, we shed light on the role of early peptides and small proteins before and during the nucleotide world, in which nascent life fully grasped the potential of primordial proteins, and which has left an imprint on the idiosyncratic properties of extant proteins.
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Affiliation(s)
- Stephen D. Fried
- Department of Chemistry, Johns Hopkins University, Baltimore, MD 21212, USA
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21212, USA
| | - Kosuke Fujishima
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 1528550, Japan
- Graduate School of Media and Governance, Keio University, Fujisawa 2520882, Japan
| | - Mikhail Makarov
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12800, Czech Republic
| | - Ivan Cherepashuk
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12800, Czech Republic
| | - Klara Hlouchova
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague 12800, Czech Republic
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 16610, Czech Republic
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5
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Duzdevich D, Carr CE, Ding D, Zhang SJ, Walton TS, Szostak JW. Competition between bridged dinucleotides and activated mononucleotides determines the error frequency of nonenzymatic RNA primer extension. Nucleic Acids Res 2021; 49:3681-3691. [PMID: 33744957 PMCID: PMC8053118 DOI: 10.1093/nar/gkab173] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 02/12/2021] [Accepted: 03/05/2021] [Indexed: 12/15/2022] Open
Abstract
Nonenzymatic copying of RNA templates with activated nucleotides is a useful model for studying the emergence of heredity at the origin of life. Previous experiments with defined-sequence templates have pointed to the poor fidelity of primer extension as a major problem. Here we examine the origin of mismatches during primer extension on random templates in the simultaneous presence of all four 2-aminoimidazole-activated nucleotides. Using a deep sequencing approach that reports on millions of individual template-product pairs, we are able to examine correct and incorrect polymerization as a function of sequence context. We have previously shown that the predominant pathway for primer extension involves reaction with imidazolium-bridged dinucleotides, which form spontaneously by the reaction of two mononucleotides with each other. We now show that the sequences of correctly paired products reveal patterns that are expected from the bridged dinucleotide mechanism, whereas those associated with mismatches are consistent with direct reaction of the primer with activated mononucleotides. Increasing the ratio of bridged dinucleotides to activated mononucleotides, either by using purified components or by using isocyanide-based activation chemistry, reduces the error frequency. Our results point to testable strategies for the accurate nonenzymatic copying of arbitrary RNA sequences.
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Affiliation(s)
- Daniel Duzdevich
- To whom correspondence should be addressed. Tel: +1 617 726 5102; Fax: +1 617 643 332;
| | - Christopher E Carr
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Dian Ding
- Department of Molecular Biology, 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
| | - Stephanie J Zhang
- Department of Molecular Biology, 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
| | - Travis S Walton
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jack W Szostak
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Howard Hughes Medical Institute, 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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6
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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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7
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Duzdevich D, Carr CE, Szostak JW. Deep sequencing of non-enzymatic RNA primer extension. Nucleic Acids Res 2020; 48:e70. [PMID: 32427335 PMCID: PMC7337528 DOI: 10.1093/nar/gkaa400] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/02/2020] [Accepted: 05/05/2020] [Indexed: 12/02/2022] Open
Abstract
Life emerging in an RNA world is expected to propagate RNA as hereditary information, requiring some form of primitive replication without enzymes. Non-enzymatic template-directed RNA primer extension is a model of the copying step in this posited form of replication. The sequence space accessed by primer extension dictates potential pathways to self-replication and, eventually, ribozymes. Which sequences can be accessed? What is the fidelity of the reaction? Does the recently illuminated mechanism of primer extension affect the distribution of sequences that can be copied? How do sequence features respond to experimental conditions and prebiotically relevant contexts? To help answer these and related questions, we here introduce a deep-sequencing methodology for studying RNA primer extension. We have designed and vetted special RNA constructs for this purpose, honed a protocol for sample preparation and developed custom software that analyzes sequencing data. We apply this new methodology to proof-of-concept controls, and demonstrate that it works as expected and reports on key features of the sequences accessed by primer extension.
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Affiliation(s)
- Daniel Duzdevich
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Christopher E Carr
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jack W Szostak
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Howard Hughes Medical Institute, 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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8
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Motsch S, Pfeffer D, Richert C. 2'/3' Regioselectivity of Enzyme-Free Copying of RNA Detected by NMR. Chembiochem 2020; 21:2013-2018. [PMID: 32017335 PMCID: PMC7497262 DOI: 10.1002/cbic.202000014] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Indexed: 11/06/2022]
Abstract
The RNA-templated extension of oligoribonucleotides by nucleotides produces either a 3',5' or a 2',5'-phosphodiester. Nature controls the regioselectivity during RNA chain growth with polymerases, but enzyme-free versions of genetic copying have modest specificity. Thus far, enzymatic degradation of products, combined with chromatography or electrophoresis, has been the preferred mode of detecting 2',5'-diesters produced in enzyme-free reactions. This approach hinges on the substrate specificity of nucleases, and is not suitable for in situ monitoring. Here we report how 1 H NMR spectroscopy can be used to detect the extension of self-templating RNA hairpins and that this reveals the regioisomeric nature of the newly formed phosphodiesters. We studied several modes of activating nucleotides, including imidazolides, a pyridinium phosphate, an active ester, and in situ activation with carbodiimide and organocatalyst. Conversion into the desired extension product ranged from 20 to 90 %, depending on the leaving group. Integration of the resonances of H1' protons of riboses and H5 protons of pyrimidines gave regioselectivities ranging from 40:60 to 85:15 (3',5' to 2',5' diester), but no simple correlation between 3',5' selectivity and yield. Our results show how monitoring with a high-resolution technique sheds a new light on a process that may have played an important role during the emergence of life.
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Affiliation(s)
- Sebastian Motsch
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Daniel Pfeffer
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
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9
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Kim SC, Zhou L, Zhang W, O'Flaherty DK, Rondo-Brovetto V, Szostak JW. A Model for the Emergence of RNA from a Prebiotically Plausible Mixture of Ribonucleotides, Arabinonucleotides, and 2'-Deoxynucleotides. J Am Chem Soc 2020; 142:2317-2326. [PMID: 31913615 PMCID: PMC7577264 DOI: 10.1021/jacs.9b11239] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
The abiotic synthesis of ribonucleotides
is thought to have been
an essential step toward the emergence of the RNA world. However,
it is likely that the prebiotic synthesis of ribonucleotides was accompanied
by the simultaneous synthesis of arabinonucleotides, 2′-deoxyribonucleotides,
and other variations on the canonical nucleotides. In order to understand
how relatively homogeneous RNA could have emerged from such complex
mixtures, we have examined the properties of arabinonucleotides and
2′-deoxyribonucleotides in nonenzymatic template-directed primer
extension reactions. We show that nonenzymatic primer extension with
activated arabinonucleotides is much less efficient than with activated
ribonucleotides, and furthermore that once an arabinonucleotide is
incorporated, continued primer extension is strongly inhibited. As
previously shown, 2′-deoxyribonucleotides are also less efficiently
incorporated in primer extension reactions, but the difference is
more modest. Experiments with mixtures of nucleotides suggest that
the coexistence of ribo- and arabinonucleotides does not impede the
copying of RNA templates. Moreover, chimeric oligoribonucleotides
containing 2′-deoxy- or arabinonucleotides are effective templates
for RNA synthesis. We propose that the initial genetic polymers were
random sequence chimeric oligonucleotides formed by untemplated polymerization,
but that template copying chemistry favored RNA synthesis; multiple
rounds of replication may have led to pools of oligomers composed
mainly of RNA.
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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 , 185 Cambridge Street , Boston , Massachusetts 02114 , United States.,Department of Genetics , Harvard Medical School , 77 Avenue Louis Pasteur , Boston , Massachusetts 02115 , United States
| | - 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
| | - Wen Zhang
- 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
| | - Valeria Rondo-Brovetto
- 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
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10
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Fairbanks BD, Culver HR, Mavila S, Bowman CN. Towards High-Efficiency Synthesis of Xenonucleic Acids. TRENDS IN CHEMISTRY 2020. [DOI: 10.1016/j.trechm.2019.06.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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11
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Wright TH, Giurgiu C, Zhang W, Radakovic A, O'Flaherty DK, Zhou L, Szostak JW. Prebiotically Plausible "Patching" of RNA Backbone Cleavage through a 3'-5' Pyrophosphate Linkage. J Am Chem Soc 2019; 141:18104-18112. [PMID: 31651170 PMCID: PMC7577263 DOI: 10.1021/jacs.9b08237] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Achieving multiple cycles of RNA
replication within a model protocell
would be a critical step toward demonstrating a path from prebiotic
chemistry to cellular biology. Any model for early life based on an
“RNA world” must account for RNA strand cleavage and
hydrolysis, which would degrade primitive genetic information and
lead to an accumulation of truncated, phosphate-terminated strands.
We show here that cleavage of the phosphodiester backbone is not an
end point for RNA replication. Instead, 3′-phosphate-terminated
RNA strands can participate in template-directed copying reactions
with activated ribonucleotide monomers. These reactions form a pyrophosphate
linkage, the stability of which we have characterized in the context
of RNA copying chemistry. The presence of free magnesium cations results
in cleavage of the pyrophosphate bond within minutes. However, we
found that the pyrophosphate bond is relatively stable within an RNA
duplex and in the presence of chelated magnesium. We show that, under
these conditions, pyrophosphate-linked RNA can act as a template for
the polymerization of ribonucleotides into canonical 3′–5′
phosphodiester-linked RNA. We suggest that primer extension of 3′-phosphate-terminated
RNA followed by template-directed copying represents a plausible nonenzymatic
pathway for the salvage and recovery of genetic information following
strand cleavage.
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Affiliation(s)
- Tom H Wright
- 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
| | - Constantin Giurgiu
- 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
| | - Wen Zhang
- 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
| | - Aleksandar Radakovic
- 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
| | - 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
| | - 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
| | - 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
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12
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O'Flaherty DK, Zhou L, Szostak JW. Nonenzymatic Template-Directed Synthesis of Mixed-Sequence 3'-NP-DNA up to 25 Nucleotides Long Inside Model Protocells. J Am Chem Soc 2019; 141:10481-10488. [PMID: 31180644 PMCID: PMC7547854 DOI: 10.1021/jacs.9b04858] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Efficiently copying mixed-sequence oligonucleotide templates nonenzymatically is a long-standing problem both with respect to the origin of life, and with regard to bottom up efforts to synthesize artificial living systems. Here we report an efficient and sequence-general nonenzymatic process in which RNA templates direct the synthesis of a complementary strand composed of N3'→P5' phosphoramidate DNA (3'-NP-DNA) using 3'-amino-2',3'-dideoxyribonucleotides activated with 2-aminoimidazole. Using only the four canonical nucleobases (A, G, C, and T) of modern DNA, we demonstrate the chemical copying of a variety of mixed-sequence RNA templates, both in solution and within model protocells, into complementary 3'-NP-DNA strands. Templates up to 25 nucleotides long were chemically transcribed with an average stepwise yield of 96-97%. The nonenzymatic template-directed generation of primer extension products long enough to encode active ribozymes and/or aptamers inside model protocells suggests possible routes to the synthesis of evolving cellular systems.
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Affiliation(s)
- 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
| | - 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
| | - 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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13
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Zhang W, Walton T, Li L, Szostak JW. Crystallographic observation of nonenzymatic RNA primer extension. eLife 2018; 7:36422. [PMID: 29851379 PMCID: PMC5980232 DOI: 10.7554/elife.36422] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 04/26/2018] [Indexed: 12/31/2022] Open
Abstract
The importance of genome replication has inspired detailed crystallographic studies of enzymatic DNA/RNA polymerization. In contrast, the mechanism of nonenzymatic polymerization is less well understood, despite its critical role in the origin of life. Here we report the direct observation of nonenzymatic RNA primer extension through time-resolved crystallography. We soaked crystals of an RNA primer-template-dGMP complex with guanosine-5′-phosphoro-2-aminoimidazolide for increasing times. At early times we see the activated ribonucleotides bound to the template, followed by formation of the imidazolium-bridged dinucleotide intermediate. At later times, we see a new phosphodiester bond forming between the primer and the incoming nucleotide. The intermediate is pre-organized because of the constraints of base-pairing with the template and hydrogen bonding between the imidazole amino group and both flanking phosphates. Our results provide atomic-resolution insight into the mechanism of nonenzymatic primer extension, and set the stage for further structural dissection and optimization of the RNA copying process. Enzymes speed up chemical reactions that are essential to life. Most enzymes are proteins, but some are molecules of ribonucleic acid or RNA. Like DNA, RNA is made from a chain of building blocks called nucleotides. In modern organisms, protein-based enzymes build RNAs by linking nucleotides together, while the building blocks of proteins are linked by an RNA-based enzyme at the heart of a structure called a ribosome. The earliest life on Earth most likely relied only on RNA-based enzymes, but during the emergence of life, scientists believe that RNA molecules must have replicated spontaneously before dedicated RNA-based enzymes had evolved. How RNA could replicate without enzymes has been a puzzle for decades. Recently, scientists discovered a previously unsuspected chemical intermediate that forms during the process, and hypothesized that this molecule’s special structure is what enables the chemical reaction that adds new nucleotides to a growing strand of RNA. To test this hypothesis, Zhang et al. diffused free RNA nucleotides into a crystalized complex containing template strands of RNA attached to short pieces of RNA called primers, which kick-start replication. Then, the crystals were frozen at various intervals and viewed using X-rays. This allowed Zhang et al. to observe the structural changes that occurred over time as the compounds reacted. The approach first revealed that the free nucleotides had paired with complementary nucleotides on the RNA template strands. Then, pairs of free nucleotides reacted with each other to form the intermediate. Finally, the intermediate reacted with the primer, forming a new bond that connects the RNA primer to one of the nucleotides of the intermediate, while the other nucleotide of the intermediate was released as a free nucleotide. This experiment confirms that the specific structure of the intermediate molecule promotes RNA replication without help from enzymes. These findings will benefit chemists and biologists who study how RNA evolves and replicates. Future research building upon this work will deepen scientific understanding of the environmental conditions that were required for life to appear on Earth.
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Affiliation(s)
- Wen Zhang
- Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, United States.,Department of Genetics, Harvard Medical School, Boston, United States.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States
| | - Travis Walton
- Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, United States.,Department of Genetics, Harvard Medical School, Boston, United States.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States
| | - Li Li
- Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, United States.,Department of Genetics, Harvard Medical School, Boston, United States.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States
| | - Jack W Szostak
- Department of Molecular Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, United States.,Department of Genetics, Harvard Medical School, Boston, United States.,Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States
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14
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O’Flaherty D, Kamat NP, Mirza FN, Li L, Prywes N, Szostak JW. Copying of Mixed-Sequence RNA Templates inside Model Protocells. J Am Chem Soc 2018; 140:5171-5178. [PMID: 29608310 PMCID: PMC7547884 DOI: 10.1021/jacs.8b00639] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Indexed: 01/11/2023]
Abstract
The chemical replication of RNA inside fatty acid vesicles is a plausible step in the emergence of cellular life. On the primitive Earth, simple protocells with the ability to import nucleotides and short oligomers from their environment could potentially have replicated and retained larger genomic RNA oligonucleotides within a spatially defined compartment. We have previously shown that short 5'-phosphoroimidazolide-activated "helper" RNA oligomers enable the nonenzymatic copying of mixed-sequence templates in solution, using 5'-phosphoroimidazolide-activated mononucleotides. Here, we report that citrate-chelated Mg2+, a catalyst of nonenzymatic primer extension, enhances fatty acid membrane permeability to such short RNA oligomers up to the size of tetramers, without disrupting vesicle membranes. In addition, selective permeability of short, but not long, oligomers can be further enhanced by elevating the temperature. The ability to increase the permeability of fatty acid membranes to short oligonucleotides allows for the nonenzymatic copying of RNA templates containing all four nucleotides inside vesicles, bringing us one step closer to the goal of building a protocell capable of Darwinian evolution.
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Affiliation(s)
- 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
| | - Neha P. Kamat
- Howard
Hughes Medical Institute, Department of Molecular Biology, and Center
for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Biomedical
Engineering Department, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Fatima N. Mirza
- Howard
Hughes Medical Institute, Department of Molecular Biology, and Center
for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Li Li
- Howard
Hughes Medical Institute, Department of Molecular Biology, and Center
for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Noam Prywes
- Howard
Hughes Medical Institute, Department of Molecular Biology, and Center
for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, 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
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15
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Zhang W, Tam CP, Zhou L, Oh SS, Wang J, Szostak JW. Structural Rationale for the Enhanced Catalysis of Nonenzymatic RNA Primer Extension by a Downstream Oligonucleotide. J Am Chem Soc 2018; 140:2829-2840. [PMID: 29411978 PMCID: PMC6326529 DOI: 10.1021/jacs.7b11750] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Indexed: 01/28/2023]
Abstract
Nonenzymatic RNA primer extension by activated mononucleotides has long served as a model for the study of prebiotic RNA copying. We have recently shown that the rate of primer extension is greatly enhanced by the formation of an imidazolium-bridged dinucleotide between the incoming monomer and a second, downstream activated monomer. However, the rate of primer extension is further enhanced if the downstream monomer is replaced by an activated oligonucleotide. Even an unactivated downstream oligonucleotide provides a modest enhancement in the rate of reaction of a primer with a single activated monomer. Here we study the mechanism of these effects through crystallographic studies of RNA complexes with the recently synthesized nonhydrolyzable substrate analog, guanosine 5'-(4-methylimidazolyl)-phosphonate (ICG). ICG mimics 2-methylimidazole activated guanosine-5'-phosphate (2-MeImpG), a commonly used substrate in nonenzymatic primer extension experiments. We present crystal structures of primer-template complexes with either one or two ICG residues bound downstream of a primer. In both cases, the aryl-phosphonate moiety of the ICG adjacent to the primer is disordered. To investigate the effect of a downstream oligonucleotide, we transcribed a short RNA oligonucleotide with either a 5'-ICG residue, a 5'-phosphate or a 5'-hydroxyl. We then determined crystal structures of primer-template complexes with a bound ICG monomer sandwiched between the primer and each of the three downstream oligonucleotides. Surprisingly, all three oligonucleotides rigidify the ICG monomer conformation and position it for attack by the primer 3'-hydroxyl. Furthermore, when GpppG, an analog of the imidazolium-bridged intermediate, is sandwiched between an upstream primer and a downstream helper oligonucleotide, or covalently linked to the 5'-end of the downstream oligonucleotide, the complex is better preorganized for primer extension than in the absence of a downstream oligonucleotide. Our results suggest that a downstream helper oligonucleotide contributes to the catalysis of primer extension by favoring a reactive conformation of the primer-template-intermediate complex.
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Affiliation(s)
- Wen Zhang
- Howard
Hughes Medical Institute and Center for Computational and Integrative
Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department
of Genetics, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Chun Pong Tam
- Howard
Hughes Medical Institute 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 and Center for Computational and Integrative
Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department
of Genetics, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Seung Soo Oh
- Howard
Hughes Medical Institute and Center for Computational and Integrative
Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department
of Genetics, Harvard Medical School, Boston, Massachusetts 02114, United States
| | - Jiawei Wang
- School
of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jack W. Szostak
- Howard
Hughes Medical Institute and Center for Computational and Integrative
Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
- Department
of Genetics, Harvard Medical School, Boston, Massachusetts 02114, United States
- Department
of Chemistry and Chemical Biology, Harvard
University, Cambridge, Massachusetts 02138, United States
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16
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Tam CP, Zhou L, Fahrenbach AC, Zhang W, Walton T, Szostak JW. Synthesis of a Nonhydrolyzable Nucleotide Phosphoroimidazolide Analogue That Catalyzes Nonenzymatic RNA Primer Extension. J Am Chem Soc 2018; 140:783-792. [PMID: 29251930 PMCID: PMC6326531 DOI: 10.1021/jacs.7b11623] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
We
report the synthesis of guanosine 5′-(4-methylimidazolyl)phosphonate
(ICG), the third member of a series of nonhydrolyzable nucleoside
5′-phosphoro-2-methylimidazolide (2-MeImpN) analogues designed
for mechanistic studies of nonenzymatic RNA primer extension. The
addition of a 2-MeImpN monomer to a primer is catalyzed by the presence
of a downstream activated monomer, yet the three nonhydrolyzable analogues
do not show catalytic effects under standard mildly basic primer extension
conditions. Surprisingly, ICG, which has a pKa similar to that of 2-MeImpG, is a modest catalyst of nonenzymatic
primer extension at acidic pH. Here we show that ICG reacts with 2-MeImpC
to form a stable 5′–5′-imidazole-bridged guanosine-cytosine
dinucleotide, with both a labile nitrogen–phosphorus and a
stable carbon–phosphorus linkage flanking the central imidazole
bridge. Cognate RNA primer–template complexes react with this
GC-dinucleotide by attack of the primer 3′-hydroxyl on the
activated N–P side of the 5′-5′-imidazole bridge.
These observations support the hypothesis that 5′–5′-imidazole-bridged
dinucleotides can bind to cognate RNA primer–template duplexes
and adopt appropriate conformations for subsequent phosphodiester
bond formation, consistent with our recent mechanistic proposal that
the formation of activated 5′–5′-imidazolium-bridged
dinucleotides is responsible for 2-MeImpN-driven primer extension.
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Affiliation(s)
- Chun Pong Tam
- 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 Chemistry and Chemical Biology, Harvard University , 12 Oxford Street, 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 , 185 Cambridge Street, Boston, Massachusetts 02114, United States.,Department of Genetics, Harvard Medical School , 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Albert C Fahrenbach
- 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.,Earth-Life Science Institute, Tokyo Institute of Technology , 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Wen Zhang
- 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
| | - Travis Walton
- 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.,Program of Biological and Biomedical Sciences, Harvard Medical School , 25 Shattuck Street, Gordon Hall, 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 Chemistry and Chemical Biology, Harvard University , 12 Oxford Street, Cambridge, Massachusetts 02138, United States.,Department of Genetics, Harvard Medical School , 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.,Earth-Life Science Institute, Tokyo Institute of Technology , 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
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