1
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Fu Y, Takeuchi N. Evolution of the division of labour between templates and catalysts in spatial replicator models. J Evol Biol 2024; 37:1158-1169. [PMID: 39120521 DOI: 10.1093/jeb/voae098] [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: 01/18/2024] [Revised: 05/29/2024] [Accepted: 08/02/2024] [Indexed: 08/10/2024]
Abstract
The central dogma of molecular biology can be conceptualised as the division of labour between templates and catalysts, where templates transmit genetic information, catalysts accelerate chemical reactions, and the information flows from templates to catalysts but not from catalysts to templates. How can template-catalyst division evolve in primordial replicating systems? A previous study has shown that even if the template-catalyst division does not provide an immediate fitness benefit, it can evolve through symmetry breaking between replicating molecules when the molecules are compartmentalised into protocells. However, cellular compartmentalisation may have been absent in primordial replicating systems. Here, we investigate whether cellular compartmentalisation is necessary for the evolution of the template-catalyst division via symmetry breaking using an individual-based model of replicators in a two-dimensional space. Our results show that replicators evolve the template-catalyst division via symmetry breaking when their diffusion constant is sufficiently high, a condition that results in low genetic relatedness between replicators. The evolution of the template-catalyst division reduces the risk of invasion by "cheaters," replicators that have no catalytic activities, encode no catalysts, but replicate to the detriment of local population growth. Our results suggest that the evolution of the template-catalyst division via symmetry breaking does not require cellular compartmentalization and is, instead, a general phenomenon in replicators with structured populations.
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Affiliation(s)
- Yao Fu
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Nobuto Takeuchi
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
- Research Center for Complex Systems Biology, Universal Biology Institute, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, Japan
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2
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Deamer D. Perspective: Protocells and the Path to Minimal Life. J Mol Evol 2024; 92:530-538. [PMID: 39230713 PMCID: PMC11458682 DOI: 10.1007/s00239-024-10197-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 08/20/2024] [Indexed: 09/05/2024]
Abstract
The path to minimal life involves a series of stages that can be understood in terms of incremental, stepwise additions of complexity ranging from simple solutions of organic compounds to systems of encapsulated polymers capable of capturing nutrients and energy to grow and reproduce. This brief review will describe the initial stages that lead to populations of protocells capable of undergoing selection and evolution. The stages incorporate knowledge of chemical and physical properties of organic compounds, self-assembly of membranous compartments, non-enzymatic polymerization of amino acids and nucleotides followed by encapsulation of polymers to produce protocell populations. The results are based on laboratory simulations related to cyclic hydrothermal conditions on the prebiotic Earth. The final portion of the review looks ahead to what remains to be discovered about this process in order to understand the evolutionary path to minimal life.
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Affiliation(s)
- David Deamer
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA.
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3
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DasGupta S, Weiss Z, Nisler C, Szostak JW. Evolution of the substrate specificity of an RNA ligase ribozyme from phosphorimidazole to triphosphate activation. Proc Natl Acad Sci U S A 2024; 121:e2407325121. [PMID: 39269776 PMCID: PMC11420214 DOI: 10.1073/pnas.2407325121] [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: 04/12/2024] [Accepted: 08/13/2024] [Indexed: 09/15/2024] Open
Abstract
The acquisition of new RNA functions through evolutionary processes was essential for the diversification of RNA-based primordial biology and its subsequent transition to modern biology. However, the mechanisms by which RNAs access new functions remain unclear. Do RNA enzymes need completely new folds to support new but related functions, or is reoptimization of the active site sufficient? What are the roles of neutral and adaptive mutations in evolutionary innovation? Here, we address these questions experimentally by focusing on the evolution of substrate specificity in RNA-catalyzed RNA assembly. We use directed in vitro evolution to show that a ligase ribozyme that uses prebiotically relevant 5'-phosphorimidazole-activated substrates can be evolved to catalyze ligation with substrates that are 5'-activated with the biologically relevant triphosphate group. Interestingly, despite catalyzing a related reaction, the new ribozyme folds into a completely new structure and exhibits promiscuity by catalyzing RNA ligation with both triphosphate and phosphorimidazole-activated substrates. Although distinct in sequence and structure, the parent phosphorimidazolide ligase and the evolved triphosphate ligase ribozymes can be connected by a series of point mutations where the intermediate sequences retain at least some ligase activity. The existence of a quasi-neutral pathway between these distinct ligase ribozymes suggests that neutral drift is sufficient to enable the acquisition of new substrate specificity, thereby providing opportunities for subsequent adaptive optimization. The transition from RNA-catalyzed RNA assembly using phosphorimidazole-activated substrates to triphosphate-activated substrates may have foreshadowed the later evolution of the protein enzymes that use monomeric triphosphates (nucleoside triphosphates, NTPs) for RNA synthesis.
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Affiliation(s)
- Saurja DasGupta
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA02114
- HHMI, Massachusetts General Hospital, Boston, MA02114
- Department of Genetics, Harvard Medical School, Boston, MA02115
| | - Zoe Weiss
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA02114
- HHMI, Massachusetts General Hospital, Boston, MA02114
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA02138
| | - Collin Nisler
- HHMI, The University of Chicago, Chicago, IL60637
- Department of Chemistry, The University of Chicago, Chicago, IL60637
| | - Jack W. Szostak
- Department of Molecular Biology, Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA02114
- HHMI, Massachusetts General Hospital, Boston, MA02114
- Department of Genetics, Harvard Medical School, Boston, MA02115
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4
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Kocher CD, Dill KA. The prebiotic emergence of biological evolution. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240431. [PMID: 39050718 PMCID: PMC11265915 DOI: 10.1098/rsos.240431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 05/10/2024] [Indexed: 07/27/2024]
Abstract
The origin of life must have been preceded by Darwin-like evolutionary dynamics that could propagate it. How did that adaptive dynamics arise? And from what prebiotic molecules? Using evolutionary invasion analysis, we develop a universal framework for describing any origin story for evolutionary dynamics. We find that cooperative autocatalysts, i.e. autocatalysts whose per-unit reproductive rate grows as their population increases, have the special property of being able to cross a barrier that separates their initial degradation-dominated state from a growth-dominated state with evolutionary dynamics. For some model parameters, this leap to persistent propagation is likely, not rare. We apply this analysis to the Foldcat Mechanism, wherein peptides fold and help catalyse the elongation of each other. Foldcats are found to have cooperative autocatalysis and be capable of emergent evolutionary dynamics.
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Affiliation(s)
- Charles D. Kocher
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794, USA
| | - Ken A. Dill
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794, USA
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5
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Hoog TG, Pawlak MR, Gaut NJ, Baxter GC, Bethel TA, Adamala KP, Engelhart AE. Emergent ribozyme behaviors in oxychlorine brines indicate a unique niche for molecular evolution on Mars. Nat Commun 2024; 15:3863. [PMID: 38769315 PMCID: PMC11106070 DOI: 10.1038/s41467-024-48037-2] [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: 11/29/2023] [Accepted: 04/19/2024] [Indexed: 05/22/2024] Open
Abstract
Mars is a particularly attractive candidate among known astronomical objects to potentially host life. Results from space exploration missions have provided insights into Martian geochemistry that indicate oxychlorine species, particularly perchlorate, are ubiquitous features of the Martian geochemical landscape. Perchlorate presents potential obstacles for known forms of life due to its toxicity. However, it can also provide potential benefits, such as producing brines by deliquescence, like those thought to exist on present-day Mars. Here we show perchlorate brines support folding and catalysis of functional RNAs, while inactivating representative protein enzymes. Additionally, we show perchlorate and other oxychlorine species enable ribozyme functions, including homeostasis-like regulatory behavior and ribozyme-catalyzed chlorination of organic molecules. We suggest nucleic acids are uniquely well-suited to hypersaline Martian environments. Furthermore, Martian near- or subsurface oxychlorine brines, and brines found in potential lifeforms, could provide a unique niche for biomolecular evolution.
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Affiliation(s)
- Tanner G Hoog
- Department of Genetics, Cell Biology, and Development, University of Minnesota, 6-160 Jackson Hall, 321 Church Street SE, Minneapolis, MN, 55455, USA
| | - Matthew R Pawlak
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN, 55455, USA
| | - Nathaniel J Gaut
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN, 55455, USA
| | - Gloria C Baxter
- Department of Genetics, Cell Biology, and Development, University of Minnesota, 6-160 Jackson Hall, 321 Church Street SE, Minneapolis, MN, 55455, USA
| | - Thomas A Bethel
- Department of Ecology, Evolution, and Behavior, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, St. Paul, MN, 55108, USA
| | - Katarzyna P Adamala
- Department of Genetics, Cell Biology, and Development, University of Minnesota, 6-160 Jackson Hall, 321 Church Street SE, Minneapolis, MN, 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN, 55455, USA
| | - Aaron E Engelhart
- Department of Genetics, Cell Biology, and Development, University of Minnesota, 6-160 Jackson Hall, 321 Church Street SE, Minneapolis, MN, 55455, USA.
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, MN, 55455, USA.
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6
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Humboldt A, Rami F, Topp FM, Arnold D, Göhringer D, Pallan PS, Egli M, Richert C. Prolinyl Phosphoramidates of Nucleotides with Increased Reactivity. Angew Chem Int Ed Engl 2024; 63:e202319958. [PMID: 38300702 DOI: 10.1002/anie.202319958] [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: 12/23/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/02/2024]
Abstract
Nucleoside monophosphates (NMPs) are the subunits of RNA. They are incorporated into growing complementary strands when sequences are copied in enzyme-free reactions using organic leaving groups at the phosphates. Amino acids are rarely considered as leaving groups, but proline can act as a leaving group when N-linked to NMPs, so that prolinyl NMPs hydrolyze in aqueous buffer at 37 °C, with half-life times as short as 2.4 h, and they act as monomers in enzyme-free primer extension. Still, their level of reactivity is insufficient for practical purposes, requiring months for some extensions. Herein we report the synthesis of eight substituted prolinyl AMPs together with seven related compounds and the results of a study of their reactivity. A δ-carboxy prolinyl NMP was found to be converted with a half-life time of just 11 min in magnesium-free buffer, and a δ-isopropyl prolinyl NMP was shown to react sevenfold faster than its prolinyl counterpart in enzyme-free genetic copying of RNA. Our results indicate that both anchimeric and steric effects can be employed to increase the reactivity of aminoacidyl nucleotides, i.e. compounds that combine two fundamental classes of biomolecules in one functional entity.
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Affiliation(s)
- Adrian Humboldt
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
| | - Fabian Rami
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
| | - Franka M Topp
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
| | - Dejana Arnold
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
| | - Daniela Göhringer
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
| | - Pradeep S Pallan
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, Tennessee, 37232, USA
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, Tennessee, 37232, USA
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
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7
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Shechner DM. Architecture of an RNA polymerase ribozyme illuminates the RNA World. Trends Genet 2024; 40:291-292. [PMID: 38485607 PMCID: PMC11003837 DOI: 10.1016/j.tig.2024.02.008] [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: 02/22/2024] [Accepted: 02/29/2024] [Indexed: 04/11/2024]
Abstract
'Ribo-organisms' of the primordial RNA World would have needed ribozymes that catalyze RNA replication. McRae, Wan, Kristoffersen et al. recently revealed how these RNA replicases might have functioned by solving the structure of an artificial polymerase ribozyme. This work illustrates how complex RNA structures evolve, with implications for the origins of life.
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Affiliation(s)
- David M Shechner
- Department of Pharmacology, University of Washington, Seattle, WA, USA; Institute for Stem Cell and Regenerative Medicine, Seattle, WA, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
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8
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Chen IA. RNA life on the edge of catastrophe. Proc Natl Acad Sci U S A 2024; 121:e2402649121. [PMID: 38478681 PMCID: PMC10990123 DOI: 10.1073/pnas.2402649121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024] Open
Affiliation(s)
- Irene A. Chen
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA90095
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
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9
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Papastavrou N, Horning DP, Joyce GF. RNA-catalyzed evolution of catalytic RNA. Proc Natl Acad Sci U S A 2024; 121:e2321592121. [PMID: 38437533 PMCID: PMC10945747 DOI: 10.1073/pnas.2321592121] [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: 12/07/2023] [Accepted: 01/25/2024] [Indexed: 03/06/2024] Open
Abstract
An RNA polymerase ribozyme that was obtained by directed evolution can propagate a functional RNA through repeated rounds of replication and selection, thereby enabling Darwinian evolution. Earlier versions of the polymerase did not have sufficient copying fidelity to propagate functional information, but a new variant with improved fidelity can replicate the hammerhead ribozyme through reciprocal synthesis of both the hammerhead and its complement, with the products then being selected for RNA-cleavage activity. Two evolutionary lineages were carried out in parallel, using either the prior low-fidelity or the newer high-fidelity polymerase. The former lineage quickly lost hammerhead functionality as the population diverged toward random sequences, whereas the latter evolved new hammerhead variants with improved fitness compared to the starting RNA. The increase in fitness was attributable to specific mutations that improved the replicability of the hammerhead, counterbalanced by a small decrease in hammerhead activity. Deep sequencing analysis was used to follow the course of evolution, revealing the emergence of a succession of variants that progressively diverged from the starting hammerhead as fitness increased. This study demonstrates the critical importance of replication fidelity for maintaining heritable information in an RNA-based evolving system, such as is thought to have existed during the early history of life on Earth. Attempts to recreate RNA-based life in the laboratory must achieve further improvements in replication fidelity to enable the fully autonomous Darwinian evolution of RNA enzymes as complex as the polymerase itself.
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10
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McRae EKS, Wan CJK, Kristoffersen EL, Hansen K, Gianni E, Gallego I, Curran JF, Attwater J, Holliger P, Andersen ES. Cryo-EM structure and functional landscape of an RNA polymerase ribozyme. Proc Natl Acad Sci U S A 2024; 121:e2313332121. [PMID: 38207080 PMCID: PMC10801858 DOI: 10.1073/pnas.2313332121] [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: 08/09/2023] [Accepted: 11/29/2023] [Indexed: 01/13/2024] Open
Abstract
The emergence of an RNA replicase capable of self-replication is considered an important stage in the origin of life. RNA polymerase ribozymes (PR) - including a variant that uses trinucleotide triphosphates (triplets) as substrates - have been created by in vitro evolution and are the closest functional analogues of the replicase, but the structural basis for their function is poorly understood. Here we use single-particle cryogenic electron microscopy (cryo-EM) and high-throughput mutation analysis to obtain the structure of a triplet polymerase ribozyme (TPR) apoenzyme and map its functional landscape. The cryo-EM structure at 5-Å resolution reveals the TPR as an RNA heterodimer comprising a catalytic subunit and a noncatalytic, auxiliary subunit, resembling the shape of a left hand with thumb and fingers at a 70° angle. The two subunits are connected by two distinct kissing-loop (KL) interactions that are essential for polymerase function. Our combined structural and functional data suggest a model for templated RNA synthesis by the TPR holoenzyme, whereby heterodimer formation and KL interactions preorganize the TPR for optimal primer-template duplex binding, triplet substrate discrimination, and templated RNA synthesis. These results provide a better understanding of TPR structure and function and should aid the engineering of more efficient PRs.
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Affiliation(s)
- Ewan K. S. McRae
- Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, Aarhus8000, Denmark
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council, Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Christopher J. K. Wan
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council, Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Emil L. Kristoffersen
- Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, Aarhus8000, Denmark
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council, Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Kalinka Hansen
- Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, Aarhus8000, Denmark
| | - Edoardo Gianni
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council, Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Isaac Gallego
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council, Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Joseph F. Curran
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council, Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - James Attwater
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council, Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Philipp Holliger
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council, Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Ebbe S. Andersen
- Interdisciplinary Nanoscience Center, Department of Molecular Biology and Genetics, Aarhus University, Aarhus8000, Denmark
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11
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Zorc SA, Roy RN. Origin & influence of autocatalytic reaction networks at the advent of the RNA world. RNA Biol 2024; 21:78-92. [PMID: 39358873 PMCID: PMC11451275 DOI: 10.1080/15476286.2024.2405757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 08/26/2024] [Accepted: 09/03/2024] [Indexed: 10/04/2024] Open
Abstract
Research on the origin of life investigates the transition from abiotic chemistry to the emergence of biology, with the 'RNA world hypothesis' as the leading theory. RNA's dual role in storage and catalysis suggests its importance in this narrative. The discovery of natural ribozymes emphasizes RNA's catalytic capabilities in prebiotic environments, supporting the plausibility of an RNA world and prompting exploration of precellular evolution. Collective autocatalytic sets (CASs) mark a crucial milestone in this transition, fostering complexity through autocatalysis. While modern biology emphasizes sequence-specific polymerases, remnants of CASs persist in primary metabolism highlighting their significance. Autocatalysis, driven by CASs, promotes complexity through mutually interdependent catalytic sets. Yet, the transition from ribonucleotides to complex RNA oligomers remains puzzling. Questions persist about the genesis of the first self-replicating RNA molecule, RNA's stability in prebiotic conditions, and the shift to complex molecular reproduction. This review delves into diverse facets of the RNA world's emergence, addressing critical bottlenecks and scientific advances. Integrating insights from simulation and in vitro evolution research, we illuminate the multistep biogenesis of catalytic RNA from the abiotic world. Through this exploration, we aim to elucidate the journey from the primordial soup to the dawn of life, emphasizing the interplay between chemistry and biology in understanding life's origins.
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Affiliation(s)
- Stephen A. Zorc
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, USA
| | - Raktim N. Roy
- Department of pathology and laboratory medicine, Indiana University School of Medicine, Indianapolis, IN, USA
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12
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Lu H, Blokhuis A, Turk-MacLeod R, Karuppusamy J, Franconi A, Woronoff G, Jeancolas C, Abrishamkar A, Loire E, Ferrage F, Pelupessy P, Jullien L, Szathmary E, Nghe P, Griffiths AD. Small-molecule autocatalysis drives compartment growth, competition and reproduction. Nat Chem 2024; 16:70-78. [PMID: 37550391 DOI: 10.1038/s41557-023-01276-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 06/16/2023] [Indexed: 08/09/2023]
Abstract
Sustained autocatalysis coupled to compartment growth and division is a key step in the origin of life, but an experimental demonstration of this phenomenon in an artificial system has previously proven elusive. We show that autocatalytic reactions within compartments-when autocatalysis, and reactant and solvent exchange outpace product exchange-drive osmosis and diffusion, resulting in compartment growth. We demonstrate, using the formose reaction compartmentalized in aqueous droplets in an emulsion, that compartment volume can more than double. Competition for a common reactant (formaldehyde) causes variation in droplet growth rate based on the composition of the surrounding droplets. These growth rate variations are partially transmitted after selective division of the largest droplets by shearing, which converts growth-rate differences into differences in droplet frequency. This shows how a combination of properties of living systems (growth, division, variation, competition, rudimentary heredity and selection) can arise from simple physical-chemical processes and may have paved the way for the emergence of evolution by natural selection.
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Affiliation(s)
- Heng Lu
- Laboratoire de Biochimie, Chimie Biologie et Innovation, ESPCI Paris, Université PSL, Paris, France
| | - Alex Blokhuis
- Laboratoire de Biochimie, Chimie Biologie et Innovation, ESPCI Paris, Université PSL, Paris, France
| | - Rebecca Turk-MacLeod
- Laboratoire de Biochimie, Chimie Biologie et Innovation, ESPCI Paris, Université PSL, Paris, France
| | - Jayaprakash Karuppusamy
- Laboratoire de Biochimie, Chimie Biologie et Innovation, ESPCI Paris, Université PSL, Paris, France
| | - Andrea Franconi
- Laboratoire de Biochimie, Chimie Biologie et Innovation, ESPCI Paris, Université PSL, Paris, France
| | - Gabrielle Woronoff
- Laboratoire de Biochimie, Chimie Biologie et Innovation, ESPCI Paris, Université PSL, Paris, France
| | - Cyrille Jeancolas
- Laboratoire de Biochimie, Chimie Biologie et Innovation, ESPCI Paris, Université PSL, Paris, France
| | - Afshin Abrishamkar
- Laboratoire de Biochimie, Chimie Biologie et Innovation, ESPCI Paris, Université PSL, Paris, France
| | - Estelle Loire
- Institut de Chimie Physique, Université Paris-Saclay, Orsay, France
| | - Fabien Ferrage
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, Université PSL, Sorbonne Université, CNRS, Paris, France
| | - Philippe Pelupessy
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, Université PSL, Sorbonne Université, CNRS, Paris, France
| | - Ludovic Jullien
- PASTEUR, Département de Chimie, École Normale Supérieure, Université PSL, Sorbonne Université, Paris, France
| | - Eörs Szathmary
- Centre for Ecological Research, Institute of Evolution, Budapest, Hungary.
- Department of Plant Systematics, Ecology and Theoretical Biology, Eötvös University, Budapest, Hungary.
- Parmenides Foundation, Center for the Conceptual Foundations of Science, Pöcking, Germany.
- Konrad Lorenz Institute for Evolution and Cognition Research, Klosterneuburg, Austria.
| | - Philippe Nghe
- Laboratoire de Biochimie, Chimie Biologie et Innovation, ESPCI Paris, Université PSL, Paris, France.
- Laboratoire Biophysique et Evolution, Chimie Biologie et Innovation, ESPCI Paris, Université PSL, Paris, France.
| | - Andrew D Griffiths
- Laboratoire de Biochimie, Chimie Biologie et Innovation, ESPCI Paris, Université PSL, Paris, France.
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13
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Luo Y, Liang M, Yu C, Ma W. Circular at the very beginning: on the initial genomes in the RNA world. RNA Biol 2024; 21:17-31. [PMID: 39016036 PMCID: PMC11259081 DOI: 10.1080/15476286.2024.2380130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2024] [Indexed: 07/18/2024] Open
Abstract
It is likely that an RNA world existed in early life, when RNA played both the roles of the genome and functional molecules, thereby undergoing Darwinian evolution. However, even with only one type of polymer, it seems quite necessary to introduce a labour division concerning these two roles because folding is required for functional molecules (ribozymes) but unfavourable for the genome (as a template in replication). Notably, while ribozymes tend to have adopted a linear form for folding without constraints, a circular form, which might have been topologically hindered in folding, seems more suitable for an RNA template. Another advantage of involving a circular genome could have been to resist RNA's end-degradation. Here, we explore the scenario of a circular RNA genome plus linear ribozyme(s) at the precellular stage of the RNA world through computer modelling. The results suggest that a one-gene scene could have been 'maintained', albeit with rather a low efficiency for the circular genome to produce the ribozyme, which required precise chain-break or chain-synthesis. This strict requirement may have been relieved by introducing a 'noncoding' sequence into the genome, which had the potential to derive a second gene through mutation. A two-gene scene may have 'run well' with the two corresponding ribozymes promoting the replication of the circular genome from different respects. Circular genomes with more genes might have arisen later in RNA-based protocells. Therefore, circular genomes, which are common in the modern living world, may have had their 'root' at the very beginning of life.
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Affiliation(s)
- Yufan Luo
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Minglun Liang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Chunwu Yu
- College of Computer Sciences, Wuhan University, Wuhan, China
| | - Wentao Ma
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
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14
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Borsley S, Gallagher JM, Leigh DA, Roberts BMW. Ratcheting synthesis. Nat Rev Chem 2024; 8:8-29. [PMID: 38102412 DOI: 10.1038/s41570-023-00558-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2023] [Indexed: 12/17/2023]
Abstract
Synthetic chemistry has traditionally relied on reactions between reactants of high chemical potential and transformations that proceed energetically downhill to either a global or local minimum (thermodynamic or kinetic control). Catalysts can be used to manipulate kinetic control, lowering activation energies to influence reaction outcomes. However, such chemistry is still constrained by the shape of one-dimensional reaction coordinates. Coupling synthesis to an orthogonal energy input can allow ratcheting of chemical reaction outcomes, reminiscent of the ways that molecular machines ratchet random thermal motion to bias conformational dynamics. This fundamentally distinct approach to synthesis allows multi-dimensional potential energy surfaces to be navigated, enabling reaction outcomes that cannot be achieved under conventional kinetic or thermodynamic control. In this Review, we discuss how ratcheted synthesis is ubiquitous throughout biology and consider how chemists might harness ratchet mechanisms to accelerate catalysis, drive chemical reactions uphill and programme complex reaction sequences.
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Affiliation(s)
- Stefan Borsley
- Department of Chemistry, University of Manchester, Manchester, UK
| | | | - David A Leigh
- Department of Chemistry, University of Manchester, Manchester, UK.
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15
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Toparlak Ö, Sebastianelli L, Egas Ortuno V, Karki M, Xing Y, Szostak JW, Krishnamurthy R, Mansy SS. Cyclophospholipids Enable a Protocellular Life Cycle. ACS NANO 2023; 17:23772-23783. [PMID: 38038709 PMCID: PMC10722605 DOI: 10.1021/acsnano.3c07706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 12/02/2023]
Abstract
There is currently no plausible path for the emergence of a self-replicating protocell, because prevalent formulations of model protocells are built with fatty acid vesicles that cannot withstand the concentrations of Mg2+ needed for the function and replication of nucleic acids. Although prebiotic chelates increase the survivability of fatty acid vesicles, the resulting model protocells are incapable of growth and division. Here, we show that protocells made of mixtures of cyclophospholipids and fatty acids can grow and divide in the presence of Mg2+-citrate. Importantly, these protocells retain encapsulated nucleic acids during growth and division, can acquire nucleotides from their surroundings, and are compatible with the nonenzymatic extension of an RNA oligonucleotide, chemistry needed for the replication of a primitive genome. Our work shows that prebiotically plausible mixtures of lipids form protocells that are active under the conditions necessary for the emergence of Darwinian evolution.
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Affiliation(s)
- Ö.
Duhan Toparlak
- Department
of Cellular, Computational and Integrative Biology, University of Trento, Via Sommarive 9, 38123 Povo, Trentino, Italy
| | - Lorenzo Sebastianelli
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton Alberta T6G 2G2, Canada
| | - Veronica Egas Ortuno
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Megha Karki
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yanfeng Xing
- Department
of Biochemistry and Molecular Biology, University
of Chicago, Chicago, Illinois 60637, United States
| | - Jack W. Szostak
- Howard
Hughes Medical Institute, Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Ramanarayanan Krishnamurthy
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Sheref S. Mansy
- Department
of Cellular, Computational and Integrative Biology, University of Trento, Via Sommarive 9, 38123 Povo, Trentino, Italy
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton Alberta T6G 2G2, Canada
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16
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Tozzi A, Mazzeo M. The First Nucleic Acid Strands May Have Grown on Peptides via Primeval Reverse Translation. Acta Biotheor 2023; 71:23. [PMID: 37947915 DOI: 10.1007/s10441-023-09474-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 10/25/2023] [Indexed: 11/12/2023]
Abstract
The central dogma of molecular biology dictates that, with only a few exceptions, information proceeds from DNA to protein through an RNA intermediate. Examining the enigmatic steps from prebiotic to biological chemistry, we take another road suggesting that primordial peptides acted as template for the self-assembly of the first nucleic acids polymers. Arguing in favour of a sort of archaic "reverse translation" from proteins to RNA, our basic premise is a Hadean Earth where key biomolecules such as amino acids, polypeptides, purines, pyrimidines, nucleosides and nucleotides were available under different prebiotically plausible conditions, including meteorites delivery, shallow ponds and hydrothermal vents scenarios. Supporting a protein-first scenario alternative to the RNA world hypothesis, we propose the primeval occurrence of short two-dimensional peptides termed "selective amino acid- and nucleotide-matching oligopeptides" (henceforward SANMAOs) that noncovalently bind at the same time the polymerized amino acids and the single nucleotides dispersed in the prebiotic milieu. In this theoretical paper, we describe the chemical features of this hypothetical oligopeptide, its biological plausibility and its virtues from an evolutionary perspective. We provide a theoretical example of SANMAO's selective pairing between amino acids and nucleosides, simulating a poly-Glycine peptide that acts as a template to build a purinic chain corresponding to the glycine's extant triplet codon GGG. Further, we discuss how SANMAO might have endorsed the formation of low-fidelity RNA's polymerized strains, well before the appearance of the accurate genetic material's transmission ensured by the current translation apparatus.
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Affiliation(s)
- Arturo Tozzi
- Center for Nonlinear Science, Department of Physics, University of North Texas, 1155 Union Circle, #311427, Denton, TX, 76203-5017, USA.
| | - Marco Mazzeo
- Erredibi Srl, Via Pazzigno 117, 80146, Naples, Italy
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17
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Tagami S. Why we are made of proteins and nucleic acids: Structural biology views on extraterrestrial life. Biophys Physicobiol 2023; 20:e200026. [PMID: 38496239 PMCID: PMC10941967 DOI: 10.2142/biophysico.bppb-v20.0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/29/2023] [Indexed: 03/19/2024] Open
Abstract
Is it a miracle that life exists on the Earth, or is it a common phenomenon in the universe? If extraterrestrial organisms exist, what are they like? To answer these questions, we must understand what kinds of molecules could evolve into life, or in other words, what properties are generally required to perform biological functions and store genetic information. This review summarizes recent findings on simple ancestral proteins, outlines the basic knowledge in textbooks, and discusses the generally required properties for biological molecules from structural biology viewpoints (e.g., restriction of shapes, and types of intra- and intermolecular interactions), leading to the conclusion that proteins and nucleic acids are at least one of the simplest (and perhaps very common) forms of catalytic and genetic biopolymers in the universe. This review article is an extended version of the Japanese article, On the Origin of Life: Coevolution between RNA and Peptide, published in SEIBUTSU BUTSURI Vol. 61, p. 232-235 (2021).
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Affiliation(s)
- Shunsuke Tagami
- RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa 230-0045, Japan
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18
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Kakoti A, Joyce GF. RNA Polymerase Ribozyme That Recognizes the Template-Primer Complex through Tertiary Interactions. Biochemistry 2023. [PMID: 37256719 DOI: 10.1021/acs.biochem.3c00091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
RNA enzymes (ribozymes) often rely on specific base-pairing interactions to engage RNA substrates, which limits the substrate sequence generality of these enzymes. An RNA polymerase ribozyme that was previously optimized by directed evolution to operate in a more efficient and sequence-general manner can now recognize the RNA template, RNA primer, and incoming nucleoside 5'-triphosphate (NTP) entirely through tertiary interactions. As with proteinaceous polymerases, these tertiary interactions are largely agnostic to the sequence of the template, which is an essential property for the unconstrained transmission of genetic information. The polymerase ribozyme exhibits Michaelis-Menten saturation kinetics, with a catalytic rate of 0.1-1 min-1 and a Km of 0.1-1 μM. Earlier forms of the polymerase did not exhibit a saturable substrate binding site, but this property emerged over the course of directed evolution as the ribozyme underwent a structural rearrangement of its catalytic center. The optimized polymerase makes tertiary contacts with both the template and primer, including a critical interaction at the C2' position of the template nucleotide that opposes the 3'-terminal nucleotide of the primer. UV cross-linking studies paint a picture of how several portions of the ribozyme, including regions that were remodeled by directed evolution, come together to position the template, primer, and NTP within the active site for RNA polymerization.
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Affiliation(s)
- Ankana Kakoti
- The Salk Institute, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Gerald F Joyce
- The Salk Institute, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
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19
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Gantz M, Neun S, Medcalf EJ, van Vliet LD, Hollfelder F. Ultrahigh-Throughput Enzyme Engineering and Discovery in In Vitro Compartments. Chem Rev 2023; 123:5571-5611. [PMID: 37126602 PMCID: PMC10176489 DOI: 10.1021/acs.chemrev.2c00910] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Indexed: 05/03/2023]
Abstract
Novel and improved biocatalysts are increasingly sourced from libraries via experimental screening. The success of such campaigns is crucially dependent on the number of candidates tested. Water-in-oil emulsion droplets can replace the classical test tube, to provide in vitro compartments as an alternative screening format, containing genotype and phenotype and enabling a readout of function. The scale-down to micrometer droplet diameters and picoliter volumes brings about a >107-fold volume reduction compared to 96-well-plate screening. Droplets made in automated microfluidic devices can be integrated into modular workflows to set up multistep screening protocols involving various detection modes to sort >107 variants a day with kHz frequencies. The repertoire of assays available for droplet screening covers all seven enzyme commission (EC) number classes, setting the stage for widespread use of droplet microfluidics in everyday biochemical experiments. We review the practicalities of adapting droplet screening for enzyme discovery and for detailed kinetic characterization. These new ways of working will not just accelerate discovery experiments currently limited by screening capacity but profoundly change the paradigms we can probe. By interfacing the results of ultrahigh-throughput droplet screening with next-generation sequencing and deep learning, strategies for directed evolution can be implemented, examined, and evaluated.
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Affiliation(s)
| | | | | | | | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K.
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20
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Ameta S, Kumar M, Chakraborty N, Matsubara YJ, S P, Gandavadi D, Thutupalli S. Multispecies autocatalytic RNA reaction networks in coacervates. Commun Chem 2023; 6:91. [PMID: 37156998 PMCID: PMC10167250 DOI: 10.1038/s42004-023-00887-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/19/2023] [Indexed: 05/10/2023] Open
Abstract
Robust localization of self-reproducing autocatalytic chemistries is a key step in the realization of heritable and evolvable chemical systems. While autocatalytic chemical reaction networks already possess attributes such as heritable self-reproduction and evolvability, localizing functional multispecies networks within complex primitive phases, such as coacervates, has remained unexplored. Here, we show the self-reproduction of the Azoarcus ribozyme system within charge-rich coacervates where catalytic ribozymes are produced by the autocatalytic assembly of constituent smaller RNA fragments. We systematically demonstrate the catalytic assembly of active ribozymes within phase-separated coacervates-both in micron-sized droplets as well as in a coalesced macrophase, underscoring the facility of the complex, charge-rich phase to support these reactions in multiple configurations. By constructing multispecies reaction networks, we show that these newly assembled molecules are active, participating both in self- and cross-catalysis within the coacervates. Finally, due to differential molecular transport, these phase-separated compartments endow robustness to the composition of the collectively autocatalytic networks against external perturbations. Altogether, our results establish the formation of multispecies self-reproducing reaction networks in phase-separated compartments which in turn render transient robustness to the network composition.
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Affiliation(s)
- Sandeep Ameta
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, Karnataka, India.
- Trivedi School of Biosciences, Ashoka University, Plot No. 2, Rajiv Gandhi Education City, P.O. Rai, Sonepat, Haryana, 131029, India.
| | - Manoj Kumar
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, Karnataka, India
| | - Nayan Chakraborty
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, Karnataka, India
| | - Yoshiya J Matsubara
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, Karnataka, India
| | - Prashanth S
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, Karnataka, India
| | - Dhanush Gandavadi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, Karnataka, India
| | - Shashi Thutupalli
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, Karnataka, India.
- International Centre for Theoretical Sciences, Tata Institute of Fundamental Research, Bengaluru, Karnataka, India.
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21
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Distinguishing Biotic vs. Abiotic Origins of ‘Bio’signatures: Clues from Messy Prebiotic Chemistry for Detection of Life in the Universe. Life (Basel) 2023; 13:life13030766. [PMID: 36983921 PMCID: PMC10058490 DOI: 10.3390/life13030766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/04/2023] [Accepted: 03/11/2023] [Indexed: 03/16/2023] Open
Abstract
It is not a stretch to say that the search for extraterrestrial life is possibly the biggest of the cosmic endeavors that humankind has embarked upon. With the continued discovery of several Earth-like exoplanets, the hope of detecting potential biosignatures is multiplying amongst researchers in the astrobiology community. However, to be able to discern these signatures as being truly of biological origin, we also need to consider their probable abiotic origin. The field of prebiotic chemistry, which is aimed at understanding enzyme-free chemical syntheses of biologically relevant molecules, could particularly aid in this regard. Specifically, certain peculiar characteristics of prebiotically pertinent messy chemical reactions, including diverse and racemic product yields and lower synthesis efficiencies, can be utilized in analyzing whether a perceived ‘signature of life’ could possibly have chemical origins. The knowledge gathered from understanding the transition from chemistry to biology during the origin of life could be used for creating a library of abiotically synthesized biologically relevant organic molecules. This can then be employed in designing, standardizing, and testing mission-specific instruments/analysis systems, while also enabling the effective targeting of exoplanets with potentially ‘ongoing’ molecular evolutionary processes for robust detection of life in future explorative endeavors.
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22
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Benner SA. Rethinking nucleic acids from their origins to their applications. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220027. [PMID: 36633284 PMCID: PMC9835595 DOI: 10.1098/rstb.2022.0027] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/17/2022] [Indexed: 01/13/2023] Open
Abstract
Reviewed are three decades of synthetic biology research in our laboratory that has generated alternatives to standard DNA and RNA as possible informational systems to support Darwinian evolution, and therefore life, and to understand their natural history, on Earth and throughout the cosmos. From this, we have learned that: • the core structure of nucleic acids appears to be a natural outcome of non-biological chemical processes probably in constrained, intermittently irrigated, sub-aerial aquifers on the surfaces of rocky planets like Earth and/or Mars approximately 4.36 ± 0.05 billion years ago; • however, this core is not unique. Synthetic biology has generated many different molecular systems able to support the evolution of molecular information; • these alternatives to standard DNA and RNA support biotechnology, including DNA synthesis, human diagnostics, biomedical research and medicine; • in particular, they support laboratory in vitro evolution (LIVE) with performance to generate catalysts at least 104-105 fold better than standard DNA libraries, enhancing access to receptors and catalysts on demand. Coupling nanostructures to the products of LIVE with expanded DNA offers new approaches for disease therapy; and • nevertheless, a polyelectrolyte structure and size regular building blocks are required for any informational polymer to support Darwinian evolution. These features serve as universal and agnostic biosignatures, useful for seeking life throughout the Solar System. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.
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Affiliation(s)
- Steven A. Benner
- Foundation for Applied Molecular Evolution, 13709 Progress Boulevard no. 7, Alachua, FL 32615, USA
- Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard no. 17, Alachua, FL 32615, USA
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23
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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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24
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Makhatadze GI, Chen CR, Khutsishvili I, Marky LA. The volume changes of unfolding of dsDNA. Biophys J 2022; 121:4892-4899. [PMID: 35962547 PMCID: PMC9811605 DOI: 10.1016/j.bpj.2022.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/23/2022] [Accepted: 08/08/2022] [Indexed: 01/07/2023] Open
Abstract
High hydrostatic pressure can have profound effects on the stability of biomacromolecules. The magnitude and direction (stabilizing or destabilizing) of this effect is defined by the volume changes in the system, ΔV. Positive volume changes will stabilize the starting native state, whereas negative volume changes will lead to the stabilization of the final unfolded state. For the DNA double helix, experimental data suggested that when the thermostability of dsDNA is below 50°C, increase in hydrostatic pressure will lead to destabilization; i.e., helix-to-coil transition has negative ΔV. In contrast, the dsDNA sequences with the thermostability above 50°C showed positive ΔV values and were stabilized by hydrostatic pressure. In order to get insight into this switch in the response of dsDNA to hydrostatic pressure as a function of temperature, first we further validated this trend using experimental measurements of ΔV for 10 different dsDNA sequences using pressure perturbation calorimetry. We also developed a computational protocol to calculate the expected volume changes of dsDNA unfolding, which was benchmarked against the experimental set of 50 ΔV values that included, in addition to our data, the values from the literature. Computation predicts well the experimental values of ΔV. Such agreement between computation and experiment lends credibility to the computation protocol and provides molecular level rational for the observed temperature dependence of ΔV that can be traced to the hydration. Difference in the ΔV value for A/T versus G/C basepairs is also discussed.
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Affiliation(s)
- George I Makhatadze
- Departments of Biological Sciences, Chemistry, and Chemical Biology, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York.
| | - Calvin R Chen
- Departments of Biological Sciences, Chemistry, and Chemical Biology, and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
| | - Irine Khutsishvili
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, Nebraska
| | - Luis A Marky
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, Nebraska
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25
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In vitro evolution of ribonucleases from expanded genetic alphabets. Proc Natl Acad Sci U S A 2022; 119:e2208261119. [PMID: 36279447 PMCID: PMC9636917 DOI: 10.1073/pnas.2208261119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ability of nucleic acids to catalyze reactions (as well as store and transmit information) is important for both basic and applied science, the first in the context of molecular evolution and the origin of life and the second for biomedical applications. However, the catalytic power of standard nucleic acids (NAs) assembled from just four nucleotide building blocks is limited when compared with that of proteins. Here, we assess the evolutionary potential of libraries of nucleic acids with six nucleotide building blocks as reservoirs for catalysis. We compare the outcomes of in vitro selection experiments toward RNA-cleavage activity of two nucleic acid libraries: one built from the standard four independently replicable nucleotides and the other from six, with the two added nucleotides coming from an artificially expanded genetic information system (AEGIS). Results from comparative experiments suggest that DNA libraries with increased chemical diversity, higher information density, and larger searchable sequence spaces are one order of magnitude richer reservoirs of molecules that catalyze the cleavage of a phosphodiester bond in RNA than DNA libraries built from a standard four-nucleotide alphabet. Evolved AEGISzymes with nitro-carrying nucleobase Z appear to exploit a general acid–base catalytic mechanism to cleave that bond, analogous to the mechanism of the ribonuclease A family of protein enzymes and heavily modified DNAzymes. The AEGISzyme described here represents a new type of catalysts evolved from libraries built from expanded genetic alphabets.
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26
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Hydrophobic-cationic peptides modulate RNA polymerase ribozyme activity by accretion. Nat Commun 2022; 13:3050. [PMID: 35665749 PMCID: PMC9166800 DOI: 10.1038/s41467-022-30590-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 05/04/2022] [Indexed: 11/09/2022] Open
Abstract
Accretion and the resulting increase in local concentration is a widespread mechanism in biology to enhance biomolecular functions (for example, in liquid-liquid demixing phases). Such macromolecular aggregation phases (e.g., coacervates, amyloids) may also have played a role in the origin of life. Here, we report that a hydrophobic-cationic RNA binding peptide selected by phage display (P43: AKKVWIIMGGS) forms insoluble amyloid-containing aggregates, which reversibly accrete RNA on their surfaces in an RNA-length and Mg2+-concentration dependent manner. The aggregates formed by P43 or its sequence-simplified version (K2V6: KKVVVVVV) inhibited RNA polymerase ribozyme (RPR) activity at 25 mM MgCl2, while enhancing it significantly at 400 mM MgCl2. Our work shows that such hydrophobic-cationic peptide aggregates can reversibly concentrate RNA and enhance the RPR activity, and suggests that they could have aided the emergence and evolution of longer and functional RNAs in the fluctuating environments of the prebiotic earth.
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27
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Mao D, Li Q, Li Q, Wang P, Mao C. A conformational study of the 10-23 DNAzyme via programmed DNA self-assembly. Chem Commun (Camb) 2022; 58:6188-6191. [PMID: 35521655 DOI: 10.1039/d2cc01144a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This communication measures the inter-helical angle of the 10-23 DNAzyme-substrate complex by atomic force microscopy (AFM). Herein, we have devised a strategy to assemble the DNAzyme-substrate complex into a periodic DNA 2D array, which allows reliable study of the conformation of the 10-23 DNAzyme by AFM imaging and fast Fourier transform (FFT). Specifically, the angle between the two flanking helical domains of the catalytic core has been determined via the repeating distance of the 2D array. We expect that the same strategy can generally be applicable for studying other nucleic acid structures.
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Affiliation(s)
- Dake Mao
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA.
| | - Qian Li
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA. .,College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Qian Li
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA.
| | - Pengfei Wang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Chengde Mao
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907, USA.
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28
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RNA World Modeling: A Comparison of Two Complementary Approaches. ENTROPY 2022; 24:e24040536. [PMID: 35455198 PMCID: PMC9027272 DOI: 10.3390/e24040536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/08/2022] [Accepted: 04/09/2022] [Indexed: 12/02/2022]
Abstract
Simple Summary Despite years of dedicated research, scientists are still not sure what the first ”living” cell would have looked like. One of the most well-known hypotheses is the RNA world hypothesis, which assumes that, in the beginning, life relied on RNA molecules instead of DNA as information carriers and primitive enzymes. The population of such RNAs is made up of self-replicating molecules (replicases) that could make copies of themselves and parasite molecules that could only be copied by replicases. In this study, we further investigated the interplay between these hypothetical prebiotic RNA species, since it plays a crucial role in generating diversity and complexity in prebiotic molecular evolution. We compared two approaches that are commonly used to investigate such simple prebiotic systems, representing different modeling and observation scales—namely, microscopic and macroscopic. In both cases, we were able to obtain consistent results. Abstract The origin of life remains one of the major scientific questions in modern biology. Among many hypotheses aiming to explain how life on Earth started, RNA world is probably the most extensively studied. It assumes that, in the very beginning, RNA molecules served as both enzymes and as genetic information carriers. However, even if this is true, there are many questions that still need to be answered—for example, whether the population of such molecules could achieve stability and retain genetic information for many generations, which is necessary in order for evolution to start. In this paper, we try to answer this question based on the parasite–replicase model (RP model), which divides RNA molecules into enzymes (RNA replicases) capable of catalyzing replication and parasites that do not possess replicase activity but can be replicated by RNA replicases. We describe the aforementioned system using partial differential equations and, based on the analysis of the simulation, surmise general rules governing its evolution. We also compare this approach with one where the RP system is modeled and implemented using a multi-agent modeling technique. We show that approaching the description and analysis of the RP system from different perspectives (microscopic represented by MAS and macroscopic depicted by PDE) provides consistent results. Therefore, applying MAS does not lead to erroneous results and allows us to study more complex situations where many cases are concerned, which would not be possible through the PDE model.
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Göppel T, Rosenberger JH, Altaner B, Gerland U. Thermodynamic and Kinetic Sequence Selection in Enzyme-Free Polymer Self-Assembly Inside a Non-Equilibrium RNA Reactor. Life (Basel) 2022; 12:life12040567. [PMID: 35455058 PMCID: PMC9032526 DOI: 10.3390/life12040567] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/03/2022] [Accepted: 04/06/2022] [Indexed: 11/18/2022] Open
Abstract
The RNA world is one of the principal hypotheses to explain the emergence of living systems on the prebiotic Earth. It posits that RNA oligonucleotides acted as both carriers of information as well as catalytic molecules, promoting their own replication. However, it does not explain the origin of the catalytic RNA molecules. How could the transition from a pre-RNA to an RNA world occur? A starting point to answer this question is to analyze the dynamics in sequence space on the lowest level, where mononucleotide and short oligonucleotides come together and collectively evolve into larger molecules. To this end, we study the sequence-dependent self-assembly of polymers from a random initial pool of short building blocks via templated ligation. Templated ligation requires two strands that are hybridized adjacently on a third strand. The thermodynamic stability of such a configuration crucially depends on the sequence context and, therefore, significantly influences the ligation probability. However, the sequence context also has a kinetic effect, since non-complementary nucleotide pairs in the vicinity of the ligation site stall the ligation reaction. These sequence-dependent thermodynamic and kinetic effects are explicitly included in our stochastic model. Using this model, we investigate the system-level dynamics inside a non-equilibrium ‘RNA reactor’ enabling a fast chemical activation of the termini of interacting oligomers. Moreover, the RNA reactor subjects the oligomer pool to periodic temperature changes inducing the reshuffling of the system. The binding stability of strands typically grows with the number of complementary nucleotides forming the hybridization site. While shorter strands unbind spontaneously during the cold phase, larger complexes only disassemble during the temperature peaks. Inside the RNA reactor, strand growth is balanced by cleavage via hydrolysis, such that the oligomer pool eventually reaches a non-equilibrium stationary state characterized by its length and sequence distribution. How do motif-dependent energy and stalling parameters affect the sequence composition of the pool of long strands? As a critical factor for self-enhancing sequence selection, we identify kinetic stalling due to non-complementary base pairs at the ligation site. Kinetic stalling enables cascades of self-amplification that result in a strong reduction of occupied states in sequence space. Moreover, we discuss the significance of the symmetry breaking for the transition from a pre-RNA to an RNA world.
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Seebacher F, Beaman J. Evolution of plasticity: metabolic compensation for fluctuating energy demands at the origin of life. J Exp Biol 2022; 225:274636. [PMID: 35254445 DOI: 10.1242/jeb.243214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Phenotypic plasticity of physiological functions enables rapid responses to changing environments and may thereby increase the resilience of organisms to environmental change. Here, we argue that the principal hallmarks of life itself, self-replication and maintenance, are contingent on the plasticity of metabolic processes ('metabolic plasticity'). It is likely that the Last Universal Common Ancestor (LUCA), 4 billion years ago, already possessed energy-sensing molecules that could adjust energy (ATP) production to meet demand. The earliest manifestation of metabolic plasticity, switching cells from growth and storage (anabolism) to breakdown and ATP production (catabolism), coincides with the advent of Darwinian evolution. Darwinian evolution depends on reliable translation of information from information-carrying molecules, and on cell genealogy where information is accurately passed between cell generations. Both of these processes create fluctuating energy demands that necessitate metabolic plasticity to facilitate replication of genetic material and (proto)cell division. We propose that LUCA possessed rudimentary forms of these capabilities. Since LUCA, metabolic networks have increased in complexity. Generalist founder enzymes formed the basis of many derived networks, and complexity arose partly by recruiting novel pathways from the untapped pool of reactions that are present in cells but do not have current physiological functions (the so-called 'underground metabolism'). Complexity may thereby be specific to environmental contexts and phylogenetic lineages. We suggest that a Boolean network analysis could be useful to model the transition of metabolic networks over evolutionary time. Network analyses can be effective in modelling phenotypic plasticity in metabolic functions for different phylogenetic groups because they incorporate actual biochemical regulators that can be updated as new empirical insights are gained.
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Affiliation(s)
- Frank Seebacher
- School of Life and Environmental Sciences, A08, University of Sydney, Sydney, NSW 2006, Australia
| | - Julian Beaman
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
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Charge-density reduction promotes ribozyme activity in RNA–peptide coacervates via RNA fluidization and magnesium partitioning. Nat Chem 2022; 14:407-416. [PMID: 35165426 PMCID: PMC8979813 DOI: 10.1038/s41557-022-00890-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 01/05/2022] [Indexed: 12/14/2022]
Abstract
It has long been proposed that phase-separated compartments can provide a basis for the formation of cellular precursors in prebiotic environments. However, we know very little about the properties of coacervates formed from simple peptides, their compatibility with ribozymes or their functional significance. Here we assess the conditions under which functional ribozymes form coacervates with simple peptides. We find coacervation to be most robust when transitioning from long homopeptides to shorter, more pre-biologically plausible heteropeptides. We mechanistically show that these RNA–peptide coacervates display peptide-dependent material properties and cofactor concentrations. We find that the interspacing of cationic and neutral amino acids increases RNA mobility, and we use isothermal calorimetry to reveal sequence-dependent Mg2+ partitioning, two critical factors that together enable ribozyme activity. Our results establish how peptides of limited length, homogeneity and charge density facilitate the compartmentalization of active ribozymes into non-gelating, magnesium-rich coacervates, a scenario that could be applicable to cellular precursors with peptide-dependent functional phenotypes. ![]()
Phase-separated compartments have long been proposed as precursors to cellular life. Now, it has been shown that RNA–peptide protocells are more robust when formed using shorter (rather than longer) peptides, and that peptide sequence determines the functional materials properties of these compartments.
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Wang F, Li P, Chu HC, Lo PK. Nucleic Acids and Their Analogues for Biomedical Applications. BIOSENSORS 2022; 12:93. [PMID: 35200353 PMCID: PMC8869748 DOI: 10.3390/bios12020093] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/20/2022] [Accepted: 01/25/2022] [Indexed: 05/07/2023]
Abstract
Nucleic acids are emerging as powerful and functional biomaterials due to their molecular recognition ability, programmability, and ease of synthesis and chemical modification. Various types of nucleic acids have been used as gene regulation tools or therapeutic agents for the treatment of human diseases with genetic disorders. Nucleic acids can also be used to develop sensing platforms for detecting ions, small molecules, proteins, and cells. Their performance can be improved through integration with other organic or inorganic nanomaterials. To further enhance their biological properties, various chemically modified nucleic acid analogues can be generated by modifying their phosphodiester backbone, sugar moiety, nucleobase, or combined sites. Alternatively, using nucleic acids as building blocks for self-assembly of highly ordered nanostructures would enhance their biological stability and cellular uptake efficiency. In this review, we will focus on the development and biomedical applications of structural and functional natural nucleic acids, as well as the chemically modified nucleic acid analogues over the past ten years. The recent progress in the development of functional nanomaterials based on self-assembled DNA-based platforms for gene regulation, biosensing, drug delivery, and therapy will also be presented. We will then summarize with a discussion on the advanced development of nucleic acid research, highlight some of the challenges faced and propose suggestions for further improvement.
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Affiliation(s)
- Fei Wang
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China; (F.W.); (P.L.); (H.C.C.)
| | - Pan Li
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China; (F.W.); (P.L.); (H.C.C.)
| | - Hoi Ching Chu
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China; (F.W.); (P.L.); (H.C.C.)
| | - Pik Kwan Lo
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China; (F.W.); (P.L.); (H.C.C.)
- Key Laboratory of Biochip Technology, Biotech and Health Care, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China
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Kondratyeva LG, Dyachkova MS, Galchenko AV. The Origin of Genetic Code and Translation in the Framework of Current Concepts on the Origin of Life. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:150-169. [PMID: 35508902 DOI: 10.1134/s0006297922020079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The origin of genetic code and translation system is probably the central and most difficult problem in the investigations on the origin of life and one of the most complex problems in the evolutionary biology in general. There are multiple hypotheses on the emergence and development of existing genetic systems that propose the mechanisms for the origin and early evolution of genetic code, as well as for the emergence of replication and translation. Here, we discuss the most well-known of these hypotheses, although none of them provides a description of the early evolution of genetic systems without gaps and assumptions. The RNA world hypothesis is a currently prevailing scientific idea on the early evolution of biological and pre-biological structures, the main advantage of which is the assumption that RNAs as the first living systems were self-sufficient, i.e., capable of functioning as both catalysts and templates. However, this hypothesis has also significant limitations. In particular, no ribozymes with processive polymerase activity have been yet discovered or synthesized. Taking into account the mutual need of proteins and nucleic acids in each other in the current world, many authors propose the early evolution scenarios based on the co-evolution of these two classes of organic molecules. They postulate that the emergence of translation was necessary for the replication of nucleic acids, in contrast to the RNA world hypothesis, according to which the emergence of translation was preceded by the era of self-replicating RNAs. Although such scenarios are less parsimonious from the evolutionary point of view, since they require simultaneous emergence and evolution of two classes of organic molecules, as well as the emergence of synchronized replication and translation, their major advantage is that they explain the development of processive and much more accurate protein-dependent replication.
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Affiliation(s)
- Liya G Kondratyeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | | | - Alexey V Galchenko
- Peoples' Friendship University of Russia (RUDN University), Moscow, 117198, Russia.
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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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35
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Furubayashi T, Ichihashi N. How evolution builds up complexity?: In vitro evolution approaches to witness complexification in artificial molecular replication systems. Biophys Physicobiol 2022; 19:1-10. [PMID: 35435608 PMCID: PMC8938154 DOI: 10.2142/biophysico.bppb-v19.0005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/10/2022] [Indexed: 12/01/2022] Open
Affiliation(s)
- Taro Furubayashi
- Department of Applied Chemistry, School of Engineering, The University of Tokyo
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36
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Kovalenko SP. On the Origin of Genetically Coded Protein Synthesis. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021060121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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37
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Genome Evolution from Random Ligation of RNAs of Autocatalytic Sets. Int J Mol Sci 2021; 22:ijms222413526. [PMID: 34948321 PMCID: PMC8707343 DOI: 10.3390/ijms222413526] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/08/2021] [Accepted: 12/15/2021] [Indexed: 11/16/2022] Open
Abstract
The evolutionary origin of the genome remains elusive. Here, I hypothesize that its first iteration, the protogenome, was a multi-ribozyme RNA. It evolved, likely within liposomes (the protocells) forming in dry-wet cycling environments, through the random fusion of ribozymes by a ligase and was amplified by a polymerase. The protogenome thereby linked, in one molecule, the information required to seed the protometabolism (a combination of RNA-based autocatalytic sets) in newly forming protocells. If this combination of autocatalytic sets was evolutionarily advantageous, the protogenome would have amplified in a population of multiplying protocells. It likely was a quasispecies with redundant information, e.g., multiple copies of one ribozyme. As such, new functionalities could evolve, including a genetic code. Once one or more components of the protometabolism were templated by the protogenome (e.g., when a ribozyme was replaced by a protein enzyme), and/or addiction modules evolved, the protometabolism became dependent on the protogenome. Along with increasing fidelity of the RNA polymerase, the protogenome could grow, e.g., by incorporating additional ribozyme domains. Finally, the protogenome could have evolved into a DNA genome with increased stability and storage capacity. I will provide suggestions for experiments to test some aspects of this hypothesis, such as evaluating the ability of ribozyme RNA polymerases to generate random ligation products and testing the catalytic activity of linked ribozyme domains.
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Akoopie A, Arriola JT, Magde D, Müller UF. A GTP-synthesizing ribozyme selected by metabolic coupling to an RNA polymerase ribozyme. SCIENCE ADVANCES 2021; 7:eabj7487. [PMID: 34613767 PMCID: PMC8494290 DOI: 10.1126/sciadv.abj7487] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
Synthesis of RNA in early life forms required chemically activated nucleotides, perhaps in the same form of nucleoside 5′-triphosphates (NTPs) as in the contemporary biosphere. We show the development of a catalytic RNA (ribozyme) that generates the nucleoside triphosphate guanosine 5′-triphosphate (GTP) from the nucleoside guanosine and the prebiotically plausible cyclic trimetaphosphate. Ribozymes were selected from 1.6 × 1014 different randomized sequences by metabolically coupling 6-thio GTP synthesis to primer extension by an RNA polymerase ribozyme within 1016 emulsion droplets. Several functional RNAs were identified, one of which was characterized in more detail. Under optimized reaction conditions, this ribozyme produced GTP at a rate 18,000-fold higher than the uncatalyzed rate, with a turnover of 1.7-fold, and supported the incorporation of GTP into RNA oligomers in tandem with an RNA polymerase ribozyme. These results are discussed in the context of early life forms.
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Affiliation(s)
- Arvin Akoopie
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Joshua T. Arriola
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Douglas Magde
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Ulrich F. Müller
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
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39
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Portillo X, Huang YT, Breaker RR, Horning DP, Joyce GF. Witnessing the structural evolution of an RNA enzyme. eLife 2021; 10:71557. [PMID: 34498588 PMCID: PMC8460264 DOI: 10.7554/elife.71557] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/08/2021] [Indexed: 11/17/2022] Open
Abstract
An RNA polymerase ribozyme that has been the subject of extensive directed evolution efforts has attained the ability to synthesize complex functional RNAs, including a full-length copy of its own evolutionary ancestor. During the course of evolution, the catalytic core of the ribozyme has undergone a major structural rearrangement, resulting in a novel tertiary structural element that lies in close proximity to the active site. Through a combination of site-directed mutagenesis, structural probing, and deep sequencing analysis, the trajectory of evolution was seen to involve the progressive stabilization of the new structure, which provides the basis for improved catalytic activity of the ribozyme. Multiple paths to the new structure were explored by the evolving population, converging upon a common solution. Tertiary structural remodeling of RNA is known to occur in nature, as evidenced by the phylogenetic analysis of extant organisms, but this type of structural innovation had not previously been observed in an experimental setting. Despite prior speculation that the catalytic core of the ribozyme had become trapped in a narrow local fitness optimum, the evolving population has broken through to a new fitness locale, raising the possibility that further improvement of polymerase activity may be achievable.
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Affiliation(s)
- Xavier Portillo
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States
| | | | - Ronald R Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, United States.,Howard Hughes Medical Institute, New Haven, United States
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Wilson TJ, Lilley DMJ. The potential versatility of RNA catalysis. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1651. [PMID: 33949113 DOI: 10.1002/wrna.1651] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 01/21/2023]
Abstract
It is commonly thought that in the early development of life on this planet RNA would have acted both as a store of genetic information and as a catalyst. While a number of RNA enzymes are known in contemporary cells, they are largely confined to phosphoryl transfer reactions, whereas an RNA based metabolism would have required a much greater chemical diversity of catalysis. Here we discuss how RNA might catalyze a wider variety of chemistries, and particularly how information gleaned from riboswitches could suggest how ribozymes might recruit coenzymes to expand their chemical range. We ask how we might seek such activities in modern biology. This article is categorized under: RNA-Based Catalysis > Miscellaneous RNA-Catalyzed Reactions Regulatory RNAs/RNAi/Riboswitches > Riboswitches RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry.
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Affiliation(s)
- Timothy J Wilson
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, UK
| | - David M J Lilley
- Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, UK
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41
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DasGupta S, Nykiel K, Piccirilli JA. The hammerhead self-cleaving motif as a precursor to complex endonucleolytic ribozymes. RNA (NEW YORK, N.Y.) 2021; 27:1017-1024. [PMID: 34131025 PMCID: PMC8370743 DOI: 10.1261/rna.078813.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 06/07/2021] [Indexed: 06/12/2023]
Abstract
Connections between distinct catalytic RNA motifs through networks of mutations that retain catalytic function (neutral networks) were likely central to the evolution of biocatalysis. Despite suggestions that functional RNAs collectively form an interconnected web of neutral networks, little evidence has emerged to demonstrate the existence of such intersecting networks in naturally occurring RNAs. Here we show that neutral networks of two naturally occurring, seemingly unrelated endonucleolytic ribozymes, the hammerhead (HH) and hairpin (HP), intersect. Sequences at the intersection of these networks exhibit catalytic functions corresponding to both ribozymes by potentially populating both catalytic folds and enable a smooth crossover between the two. Small and structurally simple endonucleolytic motifs like the HH ribozyme could, through mutational walks along their neutral networks, encounter novel catalytic phenotypes, and structurally flexible, bifunctional sequences at the intersection of these networks could have acted as nodes for evolutionary diversification in an RNA world. Considering the simplicity and small size of the HH ribozyme, we propose that this self-cleaving motif could have been a precursor to other more complex endonucleolytic ribozymes. More generally, our results suggest that RNAs that possess distinct sequences, structures, and catalytic functions, can potentially share evolutionary history through mutational connections in sequence space.
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Affiliation(s)
- Saurja DasGupta
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA
| | - Kamila Nykiel
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
| | - Joseph A Piccirilli
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, USA
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
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Magde D, Akoopie A, Magde MD, Müller UF. Water/Oil Emulsions with Controlled Droplet Sizes for In Vitro Selection Experiments. ACS OMEGA 2021; 6:21773-21783. [PMID: 34471779 PMCID: PMC8388082 DOI: 10.1021/acsomega.1c03445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
In the early history of life, RNA might have had many catalytic functions as ribozymes that do not exist today. To explore this possibility, catalytically active RNAs can be identified by in vitro selection experiments. Some of these experiments are best performed in nanodroplets to prevent diffusion between individual RNA sequences. In order to explore the suitability for the large-scale in emulsio selection of water-in-oil emulsions made by passing a mixture of mineral oil, the emulsifier ABIL-EM90, and a few percent of an aqueous phase through a microfluidizer, we used dynamic light scattering to characterize the size of aqueous droplets dispersed throughout the oil. We found that seven or more passes through the microfluidizer at 8000 psi with close to half molar inorganic salts and 10% polyethylene glycol produced droplets with sizes below 100 nm that were ideal for our purposes. We also identified conditions that would produce larger or smaller droplets, and we demonstrate that the emulsions are stable over weeks and months, which is desirable for different types of in vitro selection experiments.
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Affiliation(s)
- Douglas Magde
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Arvin Akoopie
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Michael D. Magde
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Ulrich F. Müller
- Department of Chemistry & Biochemistry, University of California San Diego, La Jolla, California 92093, United States
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Chizzolini F, Kent AD, Passalacqua LFM, Lupták A. Enzymatic RNA Production from NTPs Synthesized from Nucleosides and Trimetaphosphate*. Chembiochem 2021; 22:2098-2101. [PMID: 33798271 DOI: 10.1002/cbic.202100085] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/29/2021] [Indexed: 01/22/2023]
Abstract
A mechanism of nucleoside triphosphorylation would have been critical in an evolving "RNA world" to provide high-energy substrates for reactions such as RNA polymerization. However, synthetic approaches to produce ribonucleoside triphosphates (rNTPs) have suffered from conditions such as high temperatures or high pH that lead to increased RNA degradation, as well as substrate production that cannot sustain replication. Previous reports have demonstrated that cyclic trimetaphosphate (cTmp) can react with nucleosides to form rNTPs under prebiotically-relevant conditions, but their reaction rates were unknown and the influence of reaction conditions not well-characterized. Here we established a sensitive assay that allowed for the determination of second-order rate constants for all four rNTPs, ranging from 1.7×10-6 to 6.5×10-6 M-1 s-1 . The ATP reaction shows a linear dependence on pH and Mg2+ , and an enthalpy of activation of 88±4 kJ/mol. At millimolar nucleoside and cTmp concentrations, the rNTP production rate is sufficient to facilitate RNA synthesis by both T7 RNA polymerase and a polymerase ribozyme. We suggest that the optimized reaction of cTmp with nucleosides may provide a viable connection between prebiotic nucleotide synthesis and RNA replication.
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Affiliation(s)
- Fabio Chizzolini
- Department of Pharmaceutical Sciences, University of California at Irvine, Irvine, CA, 92617, USA
| | - Alexandra D Kent
- Department of Chemistry, University of California at Irvine, Irvine, CA, 92617, USA
| | - Luiz F M Passalacqua
- Department of Pharmaceutical Sciences, University of California at Irvine, Irvine, CA, 92617, USA
| | - Andrej Lupták
- Department of Pharmaceutical Sciences, University of California at Irvine, Irvine, CA, 92617, USA.,Department of Chemistry, University of California at Irvine, Irvine, CA, 92617, USA.,Department of Molecular Biology and Biochemistry, University of California at Irvine, Irvine, CA, 92617, USA
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Ameta S, Matsubara YJ, Chakraborty N, Krishna S, Thutupalli S. Self-Reproduction and Darwinian Evolution in Autocatalytic Chemical Reaction Systems. Life (Basel) 2021; 11:308. [PMID: 33916135 PMCID: PMC8066523 DOI: 10.3390/life11040308] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/25/2021] [Accepted: 03/27/2021] [Indexed: 11/18/2022] Open
Abstract
Understanding the emergence of life from (primitive) abiotic components has arguably been one of the deepest and yet one of the most elusive scientific questions. Notwithstanding the lack of a clear definition for a living system, it is widely argued that heredity (involving self-reproduction) along with compartmentalization and metabolism are key features that contrast living systems from their non-living counterparts. A minimal living system may be viewed as "a self-sustaining chemical system capable of Darwinian evolution". It has been proposed that autocatalytic sets of chemical reactions (ACSs) could serve as a mechanism to establish chemical compositional identity, heritable self-reproduction, and evolution in a minimal chemical system. Following years of theoretical work, autocatalytic chemical systems have been constructed experimentally using a wide variety of substrates, and most studies, thus far, have focused on the demonstration of chemical self-reproduction under specific conditions. While several recent experimental studies have raised the possibility of carrying out some aspects of experimental evolution using autocatalytic reaction networks, there remain many open challenges. In this review, we start by evaluating theoretical studies of ACSs specifically with a view to establish the conditions required for such chemical systems to exhibit self-reproduction and Darwinian evolution. Then, we follow with an extensive overview of experimental ACS systems and use the theoretically established conditions to critically evaluate these empirical systems for their potential to exhibit Darwinian evolution. We identify various technical and conceptual challenges limiting experimental progress and, finally, conclude with some remarks about open questions.
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Affiliation(s)
- Sandeep Ameta
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Yoshiya J. Matsubara
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Nayan Chakraborty
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Sandeep Krishna
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
| | - Shashi Thutupalli
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
- International Centre for Theoretical Sciences, Tata Institute of Fundamental Research, Bangalore 560089, India
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Cojocaru R, Unrau PJ. Processive RNA polymerization and promoter recognition in an RNA World. Science 2021; 371:1225-1232. [PMID: 33737482 DOI: 10.1126/science.abd9191] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 02/04/2021] [Indexed: 12/21/2022]
Abstract
Early life is thought to have required the self-replication of RNA by RNA replicases. However, how such replicases evolved and subsequently enabled gene expression remains largely unexplored. We engineered and selected a holopolymerase ribozyme that uses a sigma factor-like specificity primer to first recognize an RNA promoter sequence and then, in a second step, rearrange to a processive elongation form. Using its own sequence, the polymerase can also program itself to polymerize from certain RNA promoters and not others. This selective promoter-based polymerization could allow an RNA replicase ribozyme to define "self" from "nonself," an important development for the avoidance of replicative parasites. Moreover, the clamp-like mechanism of this polymerase could eventually enable strand invasion, a critical requirement for replication in the early evolution of life.
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Affiliation(s)
- Razvan Cojocaru
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6
| | - Peter J Unrau
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada V5A 1S6.
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Secondary Structure Libraries for Artificial Evolution Experiments. Molecules 2021; 26:molecules26061671. [PMID: 33802780 PMCID: PMC8002575 DOI: 10.3390/molecules26061671] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/07/2021] [Accepted: 03/08/2021] [Indexed: 12/20/2022] Open
Abstract
Methods of artificial evolution such as SELEX and in vitro selection have made it possible to isolate RNA and DNA motifs with a wide range of functions from large random sequence libraries. Once the primary sequence of a functional motif is known, the sequence space around it can be comprehensively explored using a combination of random mutagenesis and selection. However, methods to explore the sequence space of a secondary structure are not as well characterized. Here we address this question by describing a method to construct libraries in a single synthesis which are enriched for sequences with the potential to form a specific secondary structure, such as that of an aptamer, ribozyme, or deoxyribozyme. Although interactions such as base pairs cannot be encoded in a library using conventional DNA synthesizers, it is possible to modulate the probability that two positions will have the potential to pair by biasing the nucleotide composition at these positions. Here we show how to maximize this probability for each of the possible ways to encode a pair (in this study defined as A-U or U-A or C-G or G-C or G.U or U.G). We then use these optimized coding schemes to calculate the number of different variants of model stems and secondary structures expected to occur in a library for a series of structures in which the number of pairs and the extent of conservation of unpaired positions is systematically varied. Our calculations reveal a tradeoff between maximizing the probability of forming a pair and maximizing the number of possible variants of a desired secondary structure that can occur in the library. They also indicate that the optimal coding strategy for a library depends on the complexity of the motif being characterized. Because this approach provides a simple way to generate libraries enriched for sequences with the potential to form a specific secondary structure, we anticipate that it should be useful for the optimization and structural characterization of functional nucleic acid motifs.
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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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Ameta S, Arsène S, Foulon S, Saudemont B, Clifton BE, Griffiths AD, Nghe P. Darwinian properties and their trade-offs in autocatalytic RNA reaction networks. Nat Commun 2021; 12:842. [PMID: 33558542 PMCID: PMC7870898 DOI: 10.1038/s41467-021-21000-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 01/08/2021] [Indexed: 12/18/2022] Open
Abstract
Discovering autocatalytic chemistries that can evolve is a major goal in systems chemistry and a critical step towards understanding the origin of life. Autocatalytic networks have been discovered in various chemistries, but we lack a general understanding of how network topology controls the Darwinian properties of variation, differential reproduction, and heredity, which are mediated by the chemical composition. Using barcoded sequencing and droplet microfluidics, we establish a landscape of thousands of networks of RNAs that catalyze their own formation from fragments, and derive relationships between network topology and chemical composition. We find that strong variations arise from catalytic innovations perturbing weakly connected networks, and that growth increases with global connectivity. These rules imply trade-offs between reproduction and variation, and between compositional persistence and variation along trajectories of network complexification. Overall, connectivity in reaction networks provides a lever to balance variation (to explore chemical states) with reproduction and heredity (persistence being necessary for selection to act), as required for chemical evolution.
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Affiliation(s)
- Sandeep Ameta
- Laboratoire de Biochimie, ESPCI Paris, Université PSL, CNRS UMR 8231, 10 Rue Vauquelin, Paris, France
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences (TIFR), Bangalore, India
| | - Simon Arsène
- Laboratoire de Biochimie, ESPCI Paris, Université PSL, CNRS UMR 8231, 10 Rue Vauquelin, Paris, France
| | - Sophie Foulon
- Laboratoire de Biochimie, ESPCI Paris, Université PSL, CNRS UMR 8231, 10 Rue Vauquelin, Paris, France
| | - Baptiste Saudemont
- Laboratoire de Biochimie, ESPCI Paris, Université PSL, CNRS UMR 8231, 10 Rue Vauquelin, Paris, France
| | - Bryce E Clifton
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Andrew D Griffiths
- Laboratoire de Biochimie, ESPCI Paris, Université PSL, CNRS UMR 8231, 10 Rue Vauquelin, Paris, France.
| | - Philippe Nghe
- Laboratoire de Biochimie, ESPCI Paris, Université PSL, CNRS UMR 8231, 10 Rue Vauquelin, Paris, France.
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Catalytic promiscuity in the RNA World may have aided the evolution of prebiotic metabolism. PLoS Comput Biol 2021; 17:e1008634. [PMID: 33497378 PMCID: PMC7864428 DOI: 10.1371/journal.pcbi.1008634] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 02/05/2021] [Accepted: 12/14/2020] [Indexed: 11/19/2022] Open
Abstract
The Metabolically Coupled Replicator System (MCRS) model of early chemical evolution offers a plausible and efficient mechanism for the self-assembly and the maintenance of prebiotic RNA replicator communities, the likely predecessors of all life forms on Earth. The MCRS can keep different replicator species together due to their mandatory metabolic cooperation and limited mobility on mineral surfaces, catalysing reaction steps of a coherent reaction network that produces their own monomers from externally supplied compounds. The complexity of the MCRS chemical engine can be increased by assuming that each replicator species may catalyse more than a single reaction of metabolism, with different catalytic activities of the same RNA sequence being in a trade-off relation: one catalytic activity of a promiscuous ribozyme can increase only at the expense of the others on the same RNA strand. Using extensive spatially explicit computer simulations we have studied the possibility and the conditions of evolving ribozyme promiscuity in an initial community of single-activity replicators attached to a 2D surface, assuming an additional trade-off between replicability and catalytic activity. We conclude that our promiscuous replicators evolve under weak catalytic trade-off, relatively strong activity/replicability trade-off and low surface mobility of the replicators and the metabolites they produce, whereas catalytic specialists benefit from very strong catalytic trade-off, weak activity/replicability trade-off and high mobility. We argue that the combination of conditions for evolving promiscuity are more probable to occur for surface-bound RNA replicators, suggesting that catalytic promiscuity may have been a significant factor in the diversification of prebiotic metabolic reaction networks. Complex biochemical machineries responsible for maintaining the correct ratio of enzymes and genes were highly unlikely to exist at the wake of life. Individual genes must have been subject to competition for resources of replication leading to the competitive exclusion between them, and thus to the loss of genetic information. A feasible scenario that avoids competitive exclusion requires the assumption of mandatory cooperation between the enzymes. A potentially dynamically important but mostly neglected feature of RNA enzymes (ribozymes) is their capacity to catalyse more than a single reaction. Here, we analyse the possibility that this “promiscous” nature of prebiotic ribozymes could have helped the maintenance of early replicator communities cooperating in running a simple metabolism. To do so, we have implemented a spatially explicit computer model simulating the dynamics of replicating entities on a mineral surface–an extension of the Metabolically Coupled Replicator System including the possibility of multiple catalytic activities within the same replicator. Our results suggest that under realistic assumptions of replicator and metabolite mobility and feasible trade-off relations between different catalytic activities of the same RNA replicator molecule, catalytic promiscuity may have indeed helped booting up life through supporting the assembly of minimal metabolisms.
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Setterholm NA, Haratipour P, Kashemirov BA, McKenna CE, Joyce GF. Kinetic Effects of β,γ-Modified Deoxynucleoside 5'-Triphosphate Analogues on RNA-Catalyzed Polymerization of DNA. Biochemistry 2020; 60:1-5. [PMID: 33356161 DOI: 10.1021/acs.biochem.0c00779] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A recently described DNA polymerase ribozyme, obtained by in vitro evolution, provides the opportunity to investigate mechanistic features of RNA catalysis using methods that previously had only been applied to DNA polymerase proteins. Insight can be gained into the transition state of the DNA polymerization reaction by studying the behavior of various β,γ-bridging substituted methylene (CXY; X, Y = H, halo, methyl) or imido (NH) dNTP analogues that differ with regard to the pKa4 of the bisphosphonate or imidodiphosphate leaving group. The apparent rate constant (kpol) of the polymerase ribozyme was determined for analogues of dGTP and dCTP that span a broad range of acidities for the leaving group, ranging from 7.8 for the CF2-bisphosphonate to 11.6 for the CHCH3-bisphosphonate. A Brønsted plot of log(kpol) versus pKa4 of the leaving group demonstrates linear free energy relationships (LFERs) for dihalo-, monohalo-, and non-halogen-substituted analogues of the dNTPs, with negative slopes, as has been observed for DNA polymerase proteins. The unsubstituted dNTPs have a faster catalytic rate than would be predicted from consideration of the linear free energy relationship alone, presumably due to a relatively more favorable interaction of the β,γ-bridging oxygen within the active site. Although the DNA polymerase ribozyme is considerably slower than DNA polymerase proteins, it exhibits a similar LFER fingerprint, suggesting mechanistic commonality pertaining to the buildup of negative charge in the transition state, despite the very different chemical compositions of the two catalysts.
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Affiliation(s)
- Noah A Setterholm
- The Salk Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Pouya Haratipour
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts, and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Boris A Kashemirov
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts, and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Charles E McKenna
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts, and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Gerald F Joyce
- The Salk Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
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