1
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Jia X, Fang Z, Kim SC, Ding D, Zhou L, Szostak JW. Diaminopurine in Nonenzymatic RNA Template Copying. J Am Chem Soc 2024; 146:15897-15907. [PMID: 38818863 PMCID: PMC11177312 DOI: 10.1021/jacs.4c02560] [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: 02/20/2024] [Revised: 05/07/2024] [Accepted: 05/22/2024] [Indexed: 06/01/2024]
Abstract
In the RNA World before the emergence of an RNA polymerase, nonenzymatic template copying would have been essential for the transmission of genetic information. However, the products of chemical copying with the canonical nucleotides (A, U, C, and G) are heavily biased toward the incorporation of G and C, which form a more stable base pair than A and U. We therefore asked whether replacing adenine (A) with diaminopurine (D) might lead to more efficient and less biased nonenzymatic template copying by making a stronger version of the A:U pair. As expected, primer extension substrates containing D bound to U in the template more tightly than substrates containing A. However, primer extension with D exhibited elevated reaction rates on a C template, leading to concerns about fidelity. Our crystallographic studies revealed the nature of the D:C mismatch by showing that D can form a wobble-type base pair with C. We then asked whether competition with G would decrease the mismatched primer extension. We performed nonenzymatic primer extension with all four activated nucleotides on randomized RNA templates containing all four letters and used deep sequencing to analyze the products. We found that the DUCG genetic system exhibited a more even product distribution and a lower mismatch frequency than the canonical AUCG system. Furthermore, primer extension is greatly reduced following all mismatches, including the D:C mismatch. Our study suggests that D deserves further attention for its possible role in the RNA World and as a potentially useful component of artificial nonenzymatic RNA replication systems.
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Affiliation(s)
- Xiwen Jia
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
- Department
of Molecular Biology and Center for Computational and Integrative
Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Howard
Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Ziyuan Fang
- Howard
Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Seohyun Chris Kim
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
- Department
of Molecular Biology and Center for Computational and Integrative
Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
- Department
of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States
| | - Dian Ding
- Department
of Chemistry and Chemical Biology, Harvard
University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
- Department
of Molecular Biology and Center for Computational and Integrative
Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Lijun Zhou
- Department
of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn
Institute
for RNA Innovation, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Jack W. Szostak
- Howard
Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
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2
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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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3
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Meyer MO, Yamagami R, Choi S, Keating CD, Bevilacqua PC. RNA folding studies inside peptide-rich droplets reveal roles of modified nucleosides at the origin of life. SCIENCE ADVANCES 2023; 9:eadh5152. [PMID: 37729412 PMCID: PMC10511188 DOI: 10.1126/sciadv.adh5152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 08/16/2023] [Indexed: 09/22/2023]
Abstract
Compartmentalization of RNA in biopolymer-rich membraneless organelles is now understood to be pervasive and critical for the function of extant biology and has been proposed as a prebiotically plausible way to accumulate RNA. However, compartment-RNA interactions that drive encapsulation have the potential to influence RNA structure and function in compartment- and RNA sequence-dependent ways. Here, we detail next-generation sequencing (NGS) experiments performed in membraneless compartments called complex coacervates to characterize the fold of many different transfer RNAs (tRNAs) simultaneously under the potentially denaturing conditions of these compartments. Notably, we find that natural modifications favor the native fold of tRNAs in these compartments. This suggests that covalent RNA modifications could have played a critical role in metabolic processes at the origin of life.
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Affiliation(s)
- McCauley O. Meyer
- Department of Biochemistry, Microbiology, and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Ryota Yamagami
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Saehyun Choi
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Christine D. Keating
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Philip C. Bevilacqua
- Department of Biochemistry, Microbiology, and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
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4
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Meyer MO, Yamagami R, Choi S, Keating CD, Bevilacqua PC. RNA folding studies inside peptide-rich droplets reveal roles of modified nucleosides at the origin of life. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.27.530264. [PMID: 36909509 PMCID: PMC10002651 DOI: 10.1101/2023.02.27.530264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Compartmentalization of RNA in biopolymer-rich membraneless organelles is now understood to be pervasive and critical for the function of extant biology and has been proposed as a prebiotically-plausible way to accumulate RNA. However, compartment-RNA interactions that drive encapsulation have the potential to influence RNA structure and function in compartment- and RNA sequence-dependent ways. Herein, we detail Next-Generation Sequencing (NGS) experiments performed for the first time in membraneless compartments called complex coacervates to characterize the fold of many different transfer RNAs (tRNAs) simultaneously under the potentially denaturing conditions of these compartments. Strikingly, we find that natural modifications favor the native fold of tRNAs in these compartments. This suggests that covalent RNA modifications could have played a critical role in metabolic processes at the origin of life. One Sentence Summary We demonstrate that RNA folds into native secondary and tertiary structures in protocell models and that this is favored by covalent modifications, which is critical for the origins of life.
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5
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Cohen ZR, Todd ZR, Catling DC, Black RA, Keller SL. Prebiotic Vesicles Retain Solutes and Grow by Micelle Addition after Brief Cooling below the Membrane Melting Temperature. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:13407-13413. [PMID: 36278967 DOI: 10.1021/acs.langmuir.2c01842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Replication of RNA genomes within membrane vesicles may have been a critical step in the development of protocells on the early Earth. Cold temperatures near 0 °C improve the stability of RNA and allow efficient copying, while some climate models suggest a cold early Earth, so the first protocells may have arisen in cold-temperature environments. However, at cold temperatures, saturated fatty acids, which would have been available on the early Earth, form gel-phase membranes that are rigid and restrict mobility within the bilayer. Two primary roles of protocell membranes are to encapsulate solutes and to grow by incorporating additional fatty acids from the environment. We test here whether fatty acid membranes in the gel phase accomplish these roles. We find that gel-phase membranes of 10-carbon amphiphiles near 0 °C encapsulate aqueous dye molecules as efficiently as fluid-phase membranes do, but the contents are released if the aqueous solution is frozen at -20 °C. Gel-phase membranes do not grow measurably by micelle addition, but growth resumes when membranes are warmed above the gel-liquid transition temperature. We find that longer, 12-carbon amphiphiles do not retain encapsulated contents near 0 °C. Together, our results suggest that protocells could have developed within environments that experience temporary cooling below the membrane melting temperature, and that membranes composed of relatively short-chain fatty acids would encapsulate solutes more efficiently as temperatures approached 0 °C.
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6
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Benayad Z, Bova Saint-André M, Stirnemann G. Molecular Mechanisms of Phosphoester Bond Formation in Water Using Tight-Binding Ab Initio Molecular Dynamics. J Phys Chem B 2022; 126:8251-8265. [PMID: 36201374 DOI: 10.1021/acs.jpcb.2c04259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Phosphate groups are ubiquitous in biomolecules and are usually incorporated through phosphoester bonds between alcohol groups and orthophosphate. The formation of this bond is exceptionally difficult, with associated barriers of 30-45 kcal/mol in the absence of catalysts. In abiotic conditions, polymerizing nucleic acids without enzymes remains very challenging and is still a partly unsolved problem that severely questions the RNA World hypothesis for the origins of life. Offering a solution to this problem would involve a detailed knowledge of the reaction energetics and mechanisms, yet these remain not fully understood at a molecular level, especially because of the very slow reaction rates that represent a significant challenge for the experiments. The number of involved reaction coordinates and the possible role of the solvent in assisting the reaction are challenging for computational studies. Here, we use extensive ab initio molecular dynamics simulations using semiempirical tight-binding methods and enhanced sampling to address these issues. We first show that the choice of the tight-binding method is greatly limited by the instability of the water liquid phase for most DFTB generations and parameter sets that are widely available. We then focus on a model reaction involving methanol and orthophosphate, for which the two protonation states (mono- and dianionic) that are dominant around neutral pH are considered. We compare different proton coordinates that enable (or not) the participation of solvent water molecules. Our simulations suggest that in all cases, a dissociative associative mechanism, with an intermediate metaphosphate, is favored. The main difference between the two phosphate species is that reaction with the monoanion is assisted by the substrate, while that with the dianion involves solvent water molecules. Our results are in agreement with early experimental measurements, but the reaction barriers are underestimated in our framework. We believe that our approach provides an interesting perspective on how to sample the reaction phase space efficiently, but it calls for future studies using more accurate descriptions of chemical reactivity.
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Affiliation(s)
- Zakarya Benayad
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, PSL University, Université de Paris, 13 rue Pierre et Marie Curie, 75005Paris, France
| | - Matthias Bova Saint-André
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, PSL University, Université de Paris, 13 rue Pierre et Marie Curie, 75005Paris, France
| | - Guillaume Stirnemann
- CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, PSL University, Université de Paris, 13 rue Pierre et Marie Curie, 75005Paris, France
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7
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Mizuuchi R, Ichihashi N. Primitive Compartmentalization for the Sustainable Replication of Genetic Molecules. Life (Basel) 2021; 11:life11030191. [PMID: 33670881 PMCID: PMC7997230 DOI: 10.3390/life11030191] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/21/2021] [Accepted: 02/25/2021] [Indexed: 01/03/2023] Open
Abstract
Sustainable replication and evolution of genetic molecules such as RNA are likely requisites for the emergence of life; however, these processes are easily affected by the appearance of parasitic molecules that replicate by relying on the function of other molecules, while not contributing to their replication. A possible mechanism to repress parasite amplification is compartmentalization that segregates parasitic molecules and limits their access to functional genetic molecules. Although extent cells encapsulate genomes within lipid-based membranes, more primitive materials or simple geological processes could have provided compartmentalization on early Earth. In this review, we summarize the current understanding of the types and roles of primitive compartmentalization regarding sustainable replication of genetic molecules, especially from the perspective of the prevention of parasite replication. In addition, we also describe the ability of several environments to selectively accumulate longer genetic molecules, which could also have helped select functional genetic molecules rather than fast-replicating short parasitic molecules.
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Affiliation(s)
- Ryo Mizuuchi
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
- JST, PRESTO, Kawaguchi, Saitama 332-0012, Japan
- Correspondence: (R.M.); (N.I.)
| | - Norikazu Ichihashi
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
- Universal Biology Institute, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
- Correspondence: (R.M.); (N.I.)
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8
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Zhou L, Ding D, Szostak JW. The virtual circular genome model for primordial RNA replication. RNA (NEW YORK, N.Y.) 2021; 27:1-11. [PMID: 33028653 PMCID: PMC7749632 DOI: 10.1261/rna.077693.120] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 10/02/2020] [Indexed: 05/13/2023]
Abstract
We propose a model for the replication of primordial protocell genomes that builds upon recent advances in the nonenzymatic copying of RNA. We suggest that the original genomes consisted of collections of oligonucleotides beginning and ending at all possible positions on both strands of one or more virtual circular sequences. Replication is driven by feeding with activated monomers and by the activation of monomers and oligonucleotides in situ. A fraction of the annealed configurations of the protocellular oligonucleotides would allow for template-directed oligonucleotide growth by primer extension or ligation. Rearrangements of these annealed configurations, driven either by environmental fluctuations or occurring spontaneously, would allow for continued oligonucleotide elongation. Assuming that shorter oligonucleotides were more abundant than longer ones, replication of the entire genome could occur by the growth of all oligonucleotides by as little as one nucleotide on average. We consider possible scenarios that could have given rise to such protocell genomes, as well as potential routes to the emergence of catalytically active ribozymes and thus the more complex cells of the RNA World.
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Affiliation(s)
- Lijun Zhou
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Dian Ding
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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9
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He C, Lozoya-Colinas A, Gállego I, Grover MA, Hud NV. Solvent viscosity facilitates replication and ribozyme catalysis from an RNA duplex in a model prebiotic process. Nucleic Acids Res 2020; 47:6569-6577. [PMID: 31170298 PMCID: PMC6649698 DOI: 10.1093/nar/gkz496] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/22/2019] [Accepted: 05/24/2019] [Indexed: 11/24/2022] Open
Abstract
The RNA World hypothesis posits that RNA was once responsible for genetic information storage and catalysis. However, a prebiotic mechanism has yet to be reported for the replication of duplex RNA that could have operated before the emergence of polymerase ribozymes. Previously, we showed that a viscous solvent enables information transfer from one strand of long RNA duplex templates, overcoming ‘the strand inhibition problem'. Here, we demonstrate that the same approach allows simultaneous information transfer from both strands of long duplex templates. An additional challenge for the RNA World is that structured RNAs (like those with catalytic activity) function poorly as templates in model prebiotic RNA synthesis reactions, raising the question of how a single sequence could serve as both a catalyst and as a replication template. Here, we show that a viscous solvent also facilitates the transition of a newly synthesized hammerhead ribozyme sequence from its inactive, duplex state to its active, folded state. These results demonstrate how fluctuating environmental conditions can allow a ribozyme sequence to alternate between acting as a template for replication and functioning as a catalyst, and illustrate the potential for temporally changing environments to enable molecular processes necessary for the origin of life.
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Affiliation(s)
- Christine He
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332-0100, USA
| | - Adriana Lozoya-Colinas
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA
| | - Isaac Gállego
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA
| | - Martha A Grover
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332-0100, USA
| | - Nicholas V Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA
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10
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Abstract
Central to the “RNA world” hypothesis of the origin of life is the emergence of an RNA catalyst capable of RNA replication. However, possible replicase ribozymes are quite complex and were likely predated by simpler non-enzymatic replication reactions. The templated polymerisation of phosphorimidazolide (Imp) activated ribonucleotides currently appears as the most tractable route to both generate and replicate short RNA oligomer pools from which a replicase could emerge. Herein we demonstrate the rapid assembly of complex ribozymes from such Imp-activated RNA fragment pools. Specifically, we show assembly of a newly selected minimal RNA polymerase ribozyme variant (150 nt) by RNA templated ligation of 5’-2-methylimidazole-activated RNA oligomers <30 nucleotides long. Our results provide support for the possibility that complex RNA structures could have emerged from pools of activated RNA oligomers and outlines a path for the transition from non-enzymatic/chemical to enzymatic RNA replication.
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Affiliation(s)
- Falk Wachowius
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH (UK)
| | - Philipp Holliger
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH (UK)
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11
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Abstract
The emergence of functional cooperation between the three main classes of biomolecules - nucleic acids, peptides and lipids - defines life at the molecular level. However, how such mutually interdependent molecular systems emerged from prebiotic chemistry remains a mystery. A key hypothesis, formulated by Crick, Orgel and Woese over 40 year ago, posits that early life must have been simpler. Specifically, it proposed that an early primordial biology lacked proteins and DNA but instead relied on RNA as the key biopolymer responsible not just for genetic information storage and propagation, but also for catalysis, i.e. metabolism. Indeed, there is compelling evidence for such an 'RNA world', notably in the structure of the ribosome as a likely molecular fossil from that time. Nevertheless, one might justifiably ask whether RNA alone would be up to the task. From a purely chemical perspective, RNA is a molecule of rather uniform composition with all four bases comprising organic heterocycles of similar size and comparable polarity and pK a values. Thus, RNA molecules cover a much narrower range of steric, electronic and physicochemical properties than, e.g. the 20 amino acid side-chains of proteins. Herein we will examine the functional potential of RNA (and other nucleic acids) with respect to self-replication, catalysis and assembly into simple protocellular entities.
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12
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Akoopie A, Müller UF. Lower temperature optimum of a smaller, fragmented triphosphorylation ribozyme. Phys Chem Chem Phys 2018; 18:20118-25. [PMID: 27053323 DOI: 10.1039/c6cp00672h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The RNA world hypothesis describes a stage in the early evolution of life in which catalytic RNAs mediated the replication of RNA world organisms. One challenge to this hypothesis is that most existing ribozymes are much longer than what may be expected to originate from prebiotically plausible methods, or from the polymerization by currently existing polymerase ribozymes. We previously developed a 96-nucleotide long ribozyme, which generates a chemically activated 5'-phosphate (a 5'-triphosphate) from a prebiotically plausible molecule, trimetaphosphate, and an RNA 5'-hydroxyl group. Analogous ribozymes may have been important in the RNA world to access an energy source for the earliest life forms. Here we reduce the length of this ribozyme by fragmenting the ribozyme into multiple RNA strands, and by successively removing its longest double strand. The resulting ribozyme is composed of RNA fragments with none longer than 34 nucleotides. The temperature optimum was ∼20 °C, compared to ∼40 °C for the parent ribozyme. This shift in temperature dependence may be a more general phenomenon for fragmented ribozymes, and may have helped RNA world organisms to emerge at low temperature.
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Affiliation(s)
- Arvin Akoopie
- Department of Chemistry & Biochemistry, University of California, San Diego, USA.
| | - Ulrich F Müller
- Department of Chemistry & Biochemistry, University of California, San Diego, USA.
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13
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14
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Qiao H, Hu N, Bai J, Ren L, Liu Q, Fang L, Wang Z. Encapsulation of Nucleic Acids into Giant Unilamellar Vesicles by Freeze-Thaw: a Way Protocells May Form. ORIGINS LIFE EVOL B 2017; 47:499-510. [PMID: 27807660 DOI: 10.1007/s11084-016-9527-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 10/19/2016] [Indexed: 12/27/2022]
Abstract
Protocells are believed to consist of a lipid membrane and encapsulated nucleic acid. As the lipid membrane is impermeable to macromolecules like nucleic acids, the processes by which nucleic acids become encapsulated inside lipid membrane compartments are still unknown. In this paper, a freeze-thaw method was modified and applied to giant unilamellar vesicles (GUVs) and deoxyribonucleic acid (DNA) in mixed solution resulting in the efficient encapsulation of 6.4 kb plasmid DNA and similar length linear DNA into GUVs. The mechanism of encapsulation was followed by observing the effect of freeze-thaw temperatures on GUV morphological change, DNA encapsulation and ice crystal formation, and analyzing their correlation. Following ice crystal formation, the shape of spherical GUVs was altered and membrane integrity was damaged and this was found to be a necessary condition for encapsulation. Heating alone had no effects on DNA encapsulation, but was helpful for restoring the spherical shape and membrane integrity of GUVs damaged during freezing. These results suggested that freeze-thaw could promote the encapsulation of DNA into GUVs by a mechanism: the vesicle membrane was breached by ice crystal formation during freezing, DNA entered into damaged GUVs through these membrane gaps and was encapsulated after the membrane was resealed during the thawing process. The process described herein therefore describes a simple way for the encapsulation of nucleic acids and potentially other macromolecules into lipid vesicles, a process by which early protocells might have formed.
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Affiliation(s)
- Hai Qiao
- State Key Laboratory of Ultrasound Engineering in Medicine Co-Founed by Chongqing and the Ministry of Science and Technology, Chongqing Key Laboratory of Biomedical Engineering, College of Biomedical Engineering, Chongqing Medical University, P. O. Box 153, No.1 Yixueyuan Road, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Na Hu
- State Key Laboratory of Ultrasound Engineering in Medicine Co-Founed by Chongqing and the Ministry of Science and Technology, Chongqing Key Laboratory of Biomedical Engineering, College of Biomedical Engineering, Chongqing Medical University, P. O. Box 153, No.1 Yixueyuan Road, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Jin Bai
- State Key Laboratory of Ultrasound Engineering in Medicine Co-Founed by Chongqing and the Ministry of Science and Technology, Chongqing Key Laboratory of Biomedical Engineering, College of Biomedical Engineering, Chongqing Medical University, P. O. Box 153, No.1 Yixueyuan Road, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Lili Ren
- State Key Laboratory of Ultrasound Engineering in Medicine Co-Founed by Chongqing and the Ministry of Science and Technology, Chongqing Key Laboratory of Biomedical Engineering, College of Biomedical Engineering, Chongqing Medical University, P. O. Box 153, No.1 Yixueyuan Road, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Qing Liu
- State Key Laboratory of Ultrasound Engineering in Medicine Co-Founed by Chongqing and the Ministry of Science and Technology, Chongqing Key Laboratory of Biomedical Engineering, College of Biomedical Engineering, Chongqing Medical University, P. O. Box 153, No.1 Yixueyuan Road, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Liaoqiong Fang
- State Key Laboratory of Ultrasound Engineering in Medicine Co-Founed by Chongqing and the Ministry of Science and Technology, Chongqing Key Laboratory of Biomedical Engineering, College of Biomedical Engineering, Chongqing Medical University, P. O. Box 153, No.1 Yixueyuan Road, Yuzhong District, Chongqing, 400016, People's Republic of China.
| | - Zhibiao Wang
- State Key Laboratory of Ultrasound Engineering in Medicine Co-Founed by Chongqing and the Ministry of Science and Technology, Chongqing Key Laboratory of Biomedical Engineering, College of Biomedical Engineering, Chongqing Medical University, P. O. Box 153, No.1 Yixueyuan Road, Yuzhong District, Chongqing, 400016, People's Republic of China.
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15
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Taming Prebiotic Chemistry: The Role of Heterogeneous and Interfacial Catalysis in the Emergence of a Prebiotic Catalytic/Information Polymer System. Life (Basel) 2016; 6:life6040040. [PMID: 27827919 PMCID: PMC5198075 DOI: 10.3390/life6040040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/31/2016] [Accepted: 11/01/2016] [Indexed: 01/10/2023] Open
Abstract
Cellular life is based on interacting polymer networks that serve as catalysts, genetic information and structural molecules. The complexity of the DNA, RNA and protein biochemistry suggests that it must have been preceded by simpler systems. The RNA world hypothesis proposes RNA as the prime candidate for such a primal system. Even though this proposition has gained currency, its investigations have highlighted several challenges with respect to bulk aqueous media: (1) the synthesis of RNA monomers is difficult; (2) efficient pathways for monomer polymerization into functional RNAs and their subsequent, sequence-specific replication remain elusive; and (3) the evolution of the RNA function towards cellular metabolism in isolation is questionable in view of the chemical mixtures expected on the early Earth. This review will address the question of the possible roles of heterogeneous media and catalysis as drivers for the emergence of RNA-based polymer networks. We will show that this approach to non-enzymatic polymerizations of RNA from monomers and RNA evolution cannot only solve some issues encountered during reactions in bulk aqueous solutions, but may also explain the co-emergence of the various polymers indispensable for life in complex mixtures and their organization into primitive networks.
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He C, Gállego I, Laughlin B, Grover MA, Hud NV. A viscous solvent enables information transfer from gene-length nucleic acids in a model prebiotic replication cycle. Nat Chem 2016; 9:318-324. [PMID: 28338690 DOI: 10.1038/nchem.2628] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 08/23/2016] [Indexed: 11/09/2022]
Abstract
Many hypotheses concerning the nature of early life assume that genetic information was once transferred through the template-directed synthesis of RNA, before the emergence of coded enzymes. However, attempts to demonstrate enzyme-free, template-directed synthesis of nucleic acids have been limited by 'strand inhibition', whereby transferring information from a template strand in the presence of its complementary strand is inhibited by the stability of the template duplex. Here, we use solvent viscosity to circumvent strand inhibition, demonstrating information transfer from a gene-length template (>300 nt) within a longer (545 bp or 3 kb) duplex. These results suggest that viscous environments on the prebiotic Earth, generated periodically by water evaporation, could have facilitated nucleic acid replication-particularly of long, structured sequences such as ribozymes. Our approach works with DNA and RNA, suggesting that viscosity-mediated replication is possible for a range of genetic polymers, perhaps even for informational polymers that may have preceded RNA.
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Affiliation(s)
- Christine He
- School of Chemical &Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Isaac Gállego
- School of Chemistry &Biochemistry, Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Brandon Laughlin
- School of Chemistry &Biochemistry, Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Martha A Grover
- School of Chemical &Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Nicholas V Hud
- School of Chemistry &Biochemistry, Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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Jauker M, Griesser H, Richert C. Copying of RNA Sequences without Pre-Activation. Angew Chem Int Ed Engl 2015; 54:14559-63. [PMID: 26435291 PMCID: PMC4678514 DOI: 10.1002/anie.201506592] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 09/03/2015] [Indexed: 11/23/2022]
Abstract
Template-directed incorporation of nucleotides at the terminus of a growing complementary strand is the basis of replication. For RNA, this process can occur in the absence of enzymes, if the ribonucleotides are first converted to an active species with a leaving group. Thus far, the activation required a separate chemical step, complicating prebiotically plausible scenarios. Here we show that a combination of a carbodiimide and an organocatalyst induces near-quantitative incorporation of any of the four ribonucleotides. Upon in situ activation, adenosine monophosphate was found to also form oligomers in aqueous solution. So, both de novo strand formation and sequence-specific copying can occur without an artificial synthetic step.
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Affiliation(s)
- Mario Jauker
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart (Germany)
| | - Helmut Griesser
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart (Germany)
| | - Clemens Richert
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart (Germany).
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Jauker M, Griesser H, Richert C. Kopieren von RNA-Sequenzen ohne Voraktivierung. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506592] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Mutschler H, Wochner A, Holliger P. Freeze-thaw cycles as drivers of complex ribozyme assembly. Nat Chem 2015; 7:502-8. [PMID: 25991529 DOI: 10.1038/nchem.2251] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 03/25/2014] [Indexed: 12/22/2022]
Abstract
The emergence of an RNA catalyst capable of self-replication is considered a key transition in the origin of life. However, how such replicase ribozymes emerged from the pools of short RNA oligomers arising from prebiotic chemistry and non-enzymatic replication is unclear. Here we show that RNA polymerase ribozymes can assemble from simple catalytic networks of RNA oligomers no longer than 30 nucleotides. The entropically disfavoured assembly reaction is driven by iterative freeze-thaw cycles, even in the absence of external activation chemistry. The steep temperature and concentration gradients of such cycles result in an RNA chaperone effect that enhances the otherwise only partially realized catalytic potential of the RNA oligomer pool by an order of magnitude. Our work outlines how cyclic physicochemical processes could have driven an expansion of RNA compositional and phenotypic complexity from simple oligomer pools.
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Affiliation(s)
- Hannes Mutschler
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Aniela Wochner
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
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Ma W, Feng Y. Protocells: at the interface of life and non-life. Life (Basel) 2015; 5:447-58. [PMID: 25809963 PMCID: PMC4390862 DOI: 10.3390/life5010447] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 02/02/2015] [Indexed: 02/07/2023] Open
Abstract
The cellular form, manifesting as a membrane-bounded system (comprising various functional molecules), is essential to life. The ultimate reason for this is that, typically, one functional molecule can only adopt one “correct” structure to perform one special function (e.g., an enzyme), and thus molecular cooperation is inevitable. While this is particularly true for advanced life with complex functions, it should have already been true for life at its outset with only limited functions, which entailed some sort of primitive cellular form—“protocells”. At the very beginning, the protocells may have even been unable to intervene in the growth of their own membrane, which can be called “pseudo-protocells”. Then, the ability to synthesize membrane components (amphiphiles) may have emerged under selective pressure, leading to “true-protocells”. The emergence of a “chromosome” (with genes linked together)—thus avoiding “gene-loss” during the protocell division, was another key event in the evolution of protocells. Such “unitary-protocells”, containing a central genetic molecule, may have appeared as a milestone—in principle, since then life could evolve endlessly, “gaining” more and more functions by introducing new genes. To synthesize in laboratory these different types of protocells, which stand at the interface between life and non-life, would greatly enhance our understanding on the essence of life.
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Affiliation(s)
- Wentao Ma
- College of Life Sciences, Wuhan University, Wuhan 430072, China.
| | - Yu Feng
- College of Life Sciences, Wuhan University, Wuhan 430072, China.
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Cafferty BJ, Hud NV. Abiotic synthesis of RNA in water: a common goal of prebiotic chemistry and bottom-up synthetic biology. Curr Opin Chem Biol 2014; 22:146-57. [PMID: 25438801 DOI: 10.1016/j.cbpa.2014.09.015] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 09/13/2014] [Indexed: 01/01/2023]
Abstract
For more than half a century chemists have searched for a plausible prebiotic synthesis of RNA. The initial advances of the 1960s and 1970s were followed by decades of measured progress and a growing pessimism about overcoming remaining challenges. Fortunately, the past few years have provided a number of important advances, including new abiotic routes for the synthesis of nucleobases, nucleosides, and nucleotides. Recent discoveries also provide additional support for the hypothesis that RNA is the product of evolution, being preceded by ancestral genetic polymers, or pre-RNAs, that are synthesized more easily than RNA. In some cases, parallel searches for plausible prebiotic routes to RNA and pre-RNAs have provided more than one experimentally verified synthesis of RNA substructures and possible predecessors. Just as the synthesis of a contemporary biological molecule cannot be understood without knowledge of cellular metabolism, it is likely that an integrated approach that takes into account both plausible prebiotic reactions and plausible prebiotic environments will ultimately provide the most satisfactory and unifying chemical scenarios for the origin of nucleic acids. In this context, recent advances towards the abiotic synthesis of RNA and candidates for pre-RNAs are beginning to suggest that some molecules (e.g., urea) were multi-faceted contributors to the origin of nucleic acids, and the origin of life.
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Affiliation(s)
- Brian J Cafferty
- Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Nicholas V Hud
- Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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Mutschler H, Holliger P. Non-canonical 3'-5' extension of RNA with prebiotically plausible ribonucleoside 2',3'-cyclic phosphates. J Am Chem Soc 2014; 136:5193-6. [PMID: 24660752 PMCID: PMC4333585 DOI: 10.1021/ja4127714] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
![]()
Ribonucleoside
2′,3′-cyclic phosphates (N>p’s)
are generated by multiple prebiotically plausible processes and are
credible building blocks for the assembly of early RNA oligomers.
While N>p’s can be polymerized into short RNAs by non-enzymatic
processes with variable efficiency and regioselectivity, no enzymatic
route for RNA synthesis had been described. Here we report such a
non-canonical 3′-5′ nucleotidyl transferase activity.
We engineered a variant of the hairpin ribozyme to catalyze addition
of all four N>p’s (2′,3′-cyclic A-, G-, U-,
and
CMP) to the 5′-hydroxyl termini of RNA strands with 5′
nucleotide addition enhanced in all cases by eutectic ice phase formation
at −7 °C. We also observed 5′ addition of 2′,3′-cyclic
phosphate-activated β-nicotinamide adenine dinucleotide (NAD>p)
and ACA>p RNA trinucleotide, and multiple additions of GUCCA>p
RNA
pentamers. Our results establish a new mode of RNA 3′-5′
extension with implications for RNA oligomer synthesis from prebiotic
nucleotide pools.
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Affiliation(s)
- Hannes Mutschler
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus , Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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Sliding over the blocks in enzyme-free RNA copying--one-pot primer extension in ice. PLoS One 2013; 8:e75617. [PMID: 24058695 PMCID: PMC3776762 DOI: 10.1371/journal.pone.0075617] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 08/15/2013] [Indexed: 12/02/2022] Open
Abstract
Template-directed polymerization of RNA in the absence of enzymes is the basis for an information transfer in the ‘RNA-world’ hypothesis and in novel nucleic acid based technology. Previous investigations established that only cytidine rich strands are efficient templates in bulk aqueous solutions while a few specific sequences completely block the extension of hybridized primers. We show that a eutectic water/ice system can support Pb2+/Mg2+-ion catalyzed extension of a primer across such sequences, i.e. AA, AU and AG, in a one-pot synthesis. Using mixtures of imidazole activated nucleotide 5′-monophosphates, the two first “blocking” residues could be passed during template-directed polymerization, i.e., formation of triply extended products containing a high fraction of faithful copies was demonstrated. Across the AG sequence, a mismatch sequence was formed in similar amounts to the correct product due to U·G wobble pairing. Thus, the template-directed extension occurs both across pyrimidine and purine rich sequences and insertions of pyrimidines did not inhibit the subsequent insertions. Products were mainly formed with 2′-5′-phosphodiester linkages, however, the abundance of 3′–5′-linkages was higher than previously reported for pyrimidine insertions. When enzyme-free, template-directed RNA polymerization is performed in a eutectic water ice environment, various intrinsic reaction limitations observed in bulk solution can then be overcome.
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Cape JL, Edson JB, Spencer LP, DeClue MS, Ziock HJ, Maurer S, Rasmussen S, Monnard PA, Boncella JM. Phototriggered DNA phosphoramidate ligation in a tandem 5'-amine deprotection/3'-imidazole activated phosphate coupling reaction. Bioconjug Chem 2012; 23:2014-9. [PMID: 22985338 DOI: 10.1021/bc300093y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the preparation and use of an N-methyl picolinium carbamate protecting group for applications in a phototriggered nonenzymatic DNA phosphoramidate ligation reaction. Selective 5'-amino protection of a modified 13-mer oligonucleotide is achieved in aqueous solution by reaction with an N-methyl-4-picolinium carbonyl imidazole triflate protecting group precursor. Deprotection is carried out by photoinduced electron transfer from Ru(bpy)(3)(2+) using visible light photolysis and ascorbic acid as a sacrificial electron donor. Phototriggered 5'- amino oligonucleotide deprotection is used to initiate a nonenzymatic ligation of the 13-mer to an imidazole activated 3'-phospho-hairpin template to generate a ligated product with a phosphoramidate linkage. We demonstrate that this methodology offers a simple way to exert control over reaction initiation and rates in nonenzymatic DNA ligation for potential applications in the study of model protocellular systems and prebiotic nucleic acid synthesis.
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Affiliation(s)
- Jonathan L Cape
- Material, Physics and Applications Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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Menor-Salván C, Marín-Yaseli MR. Prebiotic chemistry in eutectic solutions at the water-ice matrix. Chem Soc Rev 2012; 41:5404-15. [PMID: 22660387 DOI: 10.1039/c2cs35060b] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A crystalline ice matrix at subzero temperatures can maintain a liquid phase where organic solutes and salts concentrate to form eutectic solutions. This concentration effect converts the confined reactant solutions in the ice matrix, sometimes making condensation and polymerisation reactions occur more favourably. These reactions occur at significantly high rates from a prebiotic chemistry standpoint, and the labile products can be protected from degradation. The experimental study of the synthesis of nitrogen heterocycles at the ice-water system showed the efficiency of this scenario and could explain the origin of nucleobases in the inner Solar System bodies, including meteorites and extra-terrestrial ices, and on the early Earth. The same conditions can also favour the condensation of monomers to form ribonucleic acid and peptides. Together with the synthesis of these monomers, the ice world (i.e., the chemical evolution in the range between the freezing point of water and the limit of stability of liquid brines, 273 to 210 K) is an under-explored experimental model in prebiotic chemistry.
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Affiliation(s)
- César Menor-Salván
- Centro de Astrobiología (INTA-CSIC), INTA, E-28850 Torrejón de Ardoz, Spain.
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Ma W, Hu J. Computer simulation on the cooperation of functional molecules during the early stages of evolution. PLoS One 2012; 7:e35454. [PMID: 22514745 PMCID: PMC3325964 DOI: 10.1371/journal.pone.0035454] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2011] [Accepted: 03/16/2012] [Indexed: 12/21/2022] Open
Abstract
It is very likely that life began with some RNA (or RNA-like) molecules, self-replicating by base-pairing and exhibiting enzyme-like functions that favored the self-replication. Different functional molecules may have emerged by favoring their own self-replication at different aspects. Then, a direct route towards complexity/efficiency may have been through the coexistence/cooperation of these molecules. However, the likelihood of this route remains quite unclear, especially because the molecules would be competing for limited common resources. By computer simulation using a Monte-Carlo model (with “micro-resolution” at the level of nucleotides and membrane components), we show that the coexistence/cooperation of these molecules can occur naturally, both in a naked form and in a protocell form. The results of the computer simulation also lead to quite a few deductions concerning the environment and history in the scenario. First, a naked stage (with functional molecules catalyzing template-replication and metabolism) may have occurred early in evolution but required high concentration and limited dispersal of the system (e.g., on some mineral surface); the emergence of protocells enabled a “habitat-shift” into bulk water. Second, the protocell stage started with a substage of “pseudo-protocells”, with functional molecules catalyzing template-replication and metabolism, but still missing the function involved in the synthesis of membrane components, the emergence of which would lead to a subsequent “true-protocell” substage. Third, the initial unstable membrane, composed of prebiotically available fatty acids, should have been superseded quite early by a more stable membrane (e.g., composed of phospholipids, like modern cells). Additionally, the membrane-takeover probably occurred at the transition of the two substages of the protocells. The scenario described in the present study should correspond to an episode in early evolution, after the emergence of single “genes”, but before the appearance of a “chromosome” with linked genes.
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Affiliation(s)
- Wentao Ma
- College of Life Sciences, Wuhan University, Wuhan, Hubei, China
- * E-mail:
| | - Jiming Hu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, China
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Mulkidjanian AY, Bychkov AY, Dibrova DV, Galperin MY, Koonin EV. Origin of first cells at terrestrial, anoxic geothermal fields. Proc Natl Acad Sci U S A 2012; 109:E821-30. [PMID: 22331915 PMCID: PMC3325685 DOI: 10.1073/pnas.1117774109] [Citation(s) in RCA: 216] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
All cells contain much more potassium, phosphate, and transition metals than modern (or reconstructed primeval) oceans, lakes, or rivers. Cells maintain ion gradients by using sophisticated, energy-dependent membrane enzymes (membrane pumps) that are embedded in elaborate ion-tight membranes. The first cells could possess neither ion-tight membranes nor membrane pumps, so the concentrations of small inorganic molecules and ions within protocells and in their environment would equilibrate. Hence, the ion composition of modern cells might reflect the inorganic ion composition of the habitats of protocells. We attempted to reconstruct the "hatcheries" of the first cells by combining geochemical analysis with phylogenomic scrutiny of the inorganic ion requirements of universal components of modern cells. These ubiquitous, and by inference primordial, proteins and functional systems show affinity to and functional requirement for K(+), Zn(2+), Mn(2+), and phosphate. Thus, protocells must have evolved in habitats with a high K(+)/Na(+) ratio and relatively high concentrations of Zn, Mn, and phosphorous compounds. Geochemical reconstruction shows that the ionic composition conducive to the origin of cells could not have existed in marine settings but is compatible with emissions of vapor-dominated zones of inland geothermal systems. Under the anoxic, CO(2)-dominated primordial atmosphere, the chemistry of basins at geothermal fields would resemble the internal milieu of modern cells. The precellular stages of evolution might have transpired in shallow ponds of condensed and cooled geothermal vapor that were lined with porous silicate minerals mixed with metal sulfides and enriched in K(+), Zn(2+), and phosphorous compounds.
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Affiliation(s)
- Armen Y. Mulkidjanian
- School of Physics, University of Osnabrück, D-49069 Osnabrück, Germany
- A. N. Belozersky Institute of Physico-Chemical Biology and Schools of
| | | | - Daria V. Dibrova
- School of Physics, University of Osnabrück, D-49069 Osnabrück, Germany
- Bioengineering and Bioinformatics, Moscow State University, Moscow 119992, Russia; and
| | - Michael Y. Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894
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Lehman N, Hayden EJ. Template-directed RNA polymerization: the taming of the milieu. Chembiochem 2011; 12:2727-8. [PMID: 22028272 DOI: 10.1002/cbic.201100611] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Indexed: 11/11/2022]
Abstract
No-bias binding: The abiotic template-directed synthesis of RNA could have been a key process in the origins of life on Earth. Recreating this process in the laboratory has been challenging, yet a combination of strategies has given rise to a synthesis that is both efficient and unbiased against any of the four nucleotides.
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Affiliation(s)
- Niles Lehman
- Department of Chemistry, Portland State University, P. O. Box 751, Portland, OR 97207, USA.
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Attwater J, Wochner A, Pinheiro VB, Coulson A, Holliger P. Ice as a protocellular medium for RNA replication. Nat Commun 2010; 1:76. [PMID: 20865803 DOI: 10.1038/ncomms1076] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Accepted: 08/23/2010] [Indexed: 11/09/2022] Open
Abstract
A crucial transition in the origin of life was the emergence of an informational polymer capable of self-replication and its compartmentalization within protocellular structures. We show that the physicochemical properties of ice, a simple medium widespread on a temperate early Earth, could have mediated this transition prior to the advent of membraneous protocells. Ice not only promotes the activity of an RNA polymerase ribozyme but also protects it from hydrolytic degradation, enabling the synthesis of exceptionally long replication products. Ice furthermore relieves the dependence of RNA replication on prebiotically implausible substrate concentrations, while providing quasicellular compartmentalization within the intricate microstructure of the eutectic phase. Eutectic ice phases had previously been shown to promote the de novo synthesis of nucleotide precursors, as well as the condensation of activated nucleotides into random RNA oligomers. Our results support a wider role for ice as a predisposed environment, promoting all the steps from prebiotic synthesis to the emergence of RNA self-replication and precellular Darwinian evolution.
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Affiliation(s)
- James Attwater
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
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Röthlingshöfer M, Richert C. Chemical primer extension at submillimolar concentration of deoxynucleotides. J Org Chem 2010; 75:3945-52. [PMID: 20364862 DOI: 10.1021/jo1002467] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Template-directed primer extension usually requires a polymerase, nucleoside triphosphates, and magnesium ions as cofactors. Enzyme-free, chemical primer extensions are known for preactivated nucleotides at millimolar concentrations. Based on a screen of carbodiimides, heterocyclic catalysts, and reactions conditions, we now show that near-quantitative primer conversion can be achieved at submillimolar concentration of any of the four deoxynucleotides (dAMP, dCMP, dGMP and dTMP). The new protocol relies on in situ activation with EDC and 1-methylimidazole and a magnesium-free buffer that was tested successfully for different sequence motifs. The method greatly simplifies chemical primer extension assays, further reduces the cost of such assays, and demonstrates the potential of the in situ activation approach.
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Affiliation(s)
- Manuel Röthlingshöfer
- Institute for Organic Chemistry, University of Karlsruhe/K.I.T., 76131 Karlsruhe, Germany
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Hansma HG. Possible origin of life between mica sheets. J Theor Biol 2010; 266:175-88. [PMID: 20558181 DOI: 10.1016/j.jtbi.2010.06.016] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2009] [Revised: 04/21/2010] [Accepted: 06/08/2010] [Indexed: 11/26/2022]
Abstract
The mica hypothesis is a new hypothesis about how life might have originated. The mica hypothesis provides simple solutions to many basic questions about the origins of life. In the mica hypothesis, the spaces between mica sheets functioned as the earliest cells. These 'cells' between mica sheets are filled with potassium ions, and they provide an environment in which: polymer entropy is low; cyclic wetting and drying can occur; molecules can evolve in isolated spaces and also migrate and ligate to form larger molecules. The mica hypothesis also proposes that mechanical energy (work) is a major energy source that could have been used on many length scales to form covalent bonds, to alter polymer conformations, and to bleb daughter cells off protocells. The mica hypothesis is consistent with many other origins hypotheses, including the RNA, lipid, and metabolic 'worlds'. Therefore the mica hypothesis has the potential to unify origins hypotheses, such that different molecular components and systems could simultaneously evolve in the spaces between mica sheets.
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Precambrian lunar volcanic protolife. Int J Mol Sci 2009; 10:2681-2721. [PMID: 19582224 PMCID: PMC2705511 DOI: 10.3390/ijms10062681] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2009] [Revised: 05/28/2009] [Accepted: 06/03/2009] [Indexed: 11/20/2022] Open
Abstract
Five representative terrestrial analogs of lunar craters are detailed relevant to Precambrian fumarolic activity. Fumarolic fluids contain the ingredients for protolife. Energy sources to derive formaldehyde, amino acids and related compounds could be by flow charging, charge separation and volcanic shock. With no photodecomposition in shadow, most fumarolic fluids at 40 K would persist over geologically long time periods. Relatively abundant tungsten would permit creation of critical enzymes, Fischer-Tropsch reactions could form polycyclic aromatic hydrocarbons and soluble volcanic polyphosphates would enable assembly of nucleic acids. Fumarolic stimuli factors are described. Orbital and lander sensors specific to protolife exploration including combined Raman/laser-induced breakdown spectrocsopy are evaluated.
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Briones C, Stich M, Manrubia SC. The dawn of the RNA World: toward functional complexity through ligation of random RNA oligomers. RNA (NEW YORK, N.Y.) 2009; 15:743-9. [PMID: 19318464 PMCID: PMC2673073 DOI: 10.1261/rna.1488609] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2008] [Accepted: 01/31/2009] [Indexed: 05/23/2023]
Abstract
A main unsolved problem in the RNA World scenario for the origin of life is how a template-dependent RNA polymerase ribozyme emerged from short RNA oligomers obtained by random polymerization on mineral surfaces. A number of computational studies have shown that the structural repertoire yielded by that process is dominated by topologically simple structures, notably hairpin-like ones. A fraction of these could display RNA ligase activity and catalyze the assembly of larger, eventually functional RNA molecules retaining their previous modular structure: molecular complexity increases but template replication is absent. This allows us to build up a stepwise model of ligation-based, modular evolution that could pave the way to the emergence of a ribozyme with RNA replicase activity, step at which information-driven Darwinian evolution would be triggered.
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Affiliation(s)
- Carlos Briones
- Centro de Astrobiología (CSIC-INTA), 28850 Torrejón de Ardoz, Madrid, Spain.
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Monnard PA, Ziock H. Eutectic Phase in Water-Ice: A Self-Assembled Environment Conducive to Metal-Catalyzed Non-Enzymatic RNA Polymerization. Chem Biodivers 2008; 5:1521-1539. [DOI: 10.1002/cbdv.200890141] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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