51
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Bose T, Fridkin G, Davidovich C, Krupkin M, Dinger N, Falkovich A, Peleg Y, Agmon I, Bashan A, Yonath A. Origin of life: protoribosome forms peptide bonds and links RNA and protein dominated worlds. Nucleic Acids Res 2022; 50:1815-1828. [PMID: 35137169 PMCID: PMC8886871 DOI: 10.1093/nar/gkac052] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 12/13/2021] [Accepted: 01/25/2022] [Indexed: 12/15/2022] Open
Abstract
Although the mode of action of the ribosomes, the multi-component universal effective protein-synthesis organelles, has been thoroughly explored, their mere appearance remained elusive. Our earlier comparative structural studies suggested that a universal internal small RNA pocket-like segment called by us the protoribosome, which is still embedded in the contemporary ribosome, is a vestige of the primordial ribosome. Herein, after constructing such pockets, we show using the "fragment reaction" and its analyses by MALDI-TOF and LC-MS mass spectrometry techniques, that several protoribosome constructs are indeed capable of mediating peptide-bond formation. These findings present strong evidence supporting our hypothesis on origin of life and on ribosome's construction, thus suggesting that the protoribosome may be the missing link between the RNA dominated world and the contemporary nucleic acids/proteins life.
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Affiliation(s)
- Tanaya Bose
- Department of Chemical and Structural Biology, Weizmann Institute of Science 7610001 Rehovot, Israel
| | - Gil Fridkin
- Department of Chemical and Structural Biology, Weizmann Institute of Science 7610001 Rehovot, Israel,Department of Organic Chemistry, Israel Institute for Biological Research, P.O. Box 19, Ness Ziona 7410001, Israel
| | - Chen Davidovich
- Department of Chemical and Structural Biology, Weizmann Institute of Science 7610001 Rehovot, Israel
| | - Miri Krupkin
- Department of Chemical and Structural Biology, Weizmann Institute of Science 7610001 Rehovot, Israel
| | - Nikita Dinger
- Department of Chemical and Structural Biology, Weizmann Institute of Science 7610001 Rehovot, Israel
| | - Alla H Falkovich
- Department of Chemical and Structural Biology, Weizmann Institute of Science 7610001 Rehovot, Israel
| | - Yoav Peleg
- Department of Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot, Israel
| | - Ilana Agmon
- Institute for Advanced Studies in Theoretical Chemistry, Schulich Faculty of Chemistry-Technion-Israel Institute of Technology, Haifa 3200003, Israel,Fritz Haber Research Center for Molecular Dynamics, Hebrew University, Jerusalem 9190401, Israel
| | - Anat Bashan
- Department of Chemical and Structural Biology, Weizmann Institute of Science 7610001 Rehovot, Israel
| | - Ada Yonath
- To whom correspondence should be addressed. Tel : +972 89343028;
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52
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Cohen ZR, Kessenich BL, Hazra A, Nguyen J, Johnson RS, MacCoss MJ, Lalic G, Black RA, Keller SL. Prebiotic Membranes and Micelles Do Not Inhibit Peptide Formation During Dehydration. Chembiochem 2022; 23:e202100614. [PMID: 34881485 PMCID: PMC8957845 DOI: 10.1002/cbic.202100614] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/07/2021] [Indexed: 02/06/2023]
Abstract
Cycles of dehydration and rehydration could have enabled formation of peptides and RNA in otherwise unfavorable conditions on the early Earth. Development of the first protocells would have hinged upon colocalization of these biopolymers with fatty acid membranes. Using atomic force microscopy, we find that a prebiotic fatty acid (decanoic acid) forms stacks of membranes after dehydration. Using LC-MS-MS (liquid chromatography-tandem mass spectrometry) with isotope internal standards, we measure the rate of formation of serine dipeptides. We find that dipeptides form during dehydration at moderate temperatures (55 °C) at least as fast in the presence of decanoic acid membranes as in the absence of membranes. Our results are consistent with the hypothesis that protocells could have formed within evaporating environments on the early Earth.
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Affiliation(s)
- Zachary R. Cohen
- Department of Chemistry, University of Washington – Seattle, Seattle, Washington 98195-1700, USA, Astrobiology Program, University of Washington – Seattle, Seattle, Washington 98195, USA
| | - Brennan L. Kessenich
- Department of Chemistry, University of Washington – Seattle, Seattle, Washington 98195-1700, USA
| | - Avijit Hazra
- Department of Chemistry, University of Washington – Seattle, Seattle, Washington 98195-1700, USA
| | - Julia Nguyen
- Department of Chemistry, University of Washington – Seattle, Seattle, Washington 98195-1700, USA
| | - Richard S. Johnson
- Department of Genome Sciences, University of Washington – Seattle, Seattle, Washington 98195, USA
| | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington – Seattle, Seattle, Washington 98195, USA
| | - Gojko Lalic
- Department of Chemistry, University of Washington – Seattle, Seattle, Washington 98195-1700, USA
| | - Roy. A. Black
- Department of Chemistry, University of Washington – Seattle, Seattle, Washington 98195-1700, USA
| | - Sarah L. Keller
- Department of Chemistry, University of Washington – Seattle, Seattle, Washington 98195-1700, USA, Astrobiology Program, University of Washington – Seattle, Seattle, Washington 98195, USA
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53
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Cohen ZR, Cornell CE, Catling DC, Black RA, Keller SL. Prebiotic Protocell Membranes Retain Encapsulated Contents during Flocculation, and Phospholipids Preserve Encapsulation during Dehydration. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:1304-1310. [PMID: 35026114 DOI: 10.1021/acs.langmuir.1c03296] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The first cell membranes were likely composed of single-chain amphiphiles such as fatty acids. An open question is whether fatty acid membranes could have functioned within evaporative lakes on the early Earth, which have been hypothesized to concentrate prebiotic reactants. Evaporation also concentrates monovalent salts, which in turn cause fatty acid membrane vesicles to flocculate; significant loss of encapsulated contents during flocculation would have impeded early cell evolution. Here, we tested whether fatty acid vesicles retain encapsulated contents after flocculation and after drying. We found that vesicles composed of 2:1 decanoic acid:decanol encapsulate calcein dye throughout a process of flocculation in saturated salt solution and subsequent disaggregation of vesicles by dilution of the salt. However, 30 minutes of complete dehydration disrupted encapsulation by fatty acid vesicles. In contrast, phospholipid vesicles maintained encapsulation. Our results reveal a selective pressure for protocells to incorporate phospholipids: while fatty acid membranes can retain encapsulated contents during periods of dilute and saturating salt, phospholipids are necessary for encapsulation during dry periods. Our results are consistent with the hypothesis that evaporative lakes were productive sites for prebiotic chemistry and the origin of cells.
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Affiliation(s)
- Zachary R Cohen
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
- Astrobiology Program, University of Washington, Seattle, Washington 98195, United States
| | - Caitlin E Cornell
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - David C Catling
- Department of Earth and Space Sciences, University of Washington, Seattle, Washington 98195, United States
- Astrobiology Program, University of Washington, Seattle, Washington 98195, United States
| | - Roy A Black
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Sarah L Keller
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
- Astrobiology Program, University of Washington, Seattle, Washington 98195, United States
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54
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Deal AM, Frandsen BN, Vaida V. Lactic acid photochemistry following excitation of S
0
to S
1
at 220 to 250 nm. J PHYS ORG CHEM 2022. [DOI: 10.1002/poc.4316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Alexandra M. Deal
- Department of Chemistry and Cooperative Institute for Research in Environmental Sciences University of Colorado Boulder Boulder CO USA
| | - Benjamin N. Frandsen
- Department of Chemistry and Cooperative Institute for Research in Environmental Sciences University of Colorado Boulder Boulder CO USA
| | - Veronica Vaida
- Department of Chemistry and Cooperative Institute for Research in Environmental Sciences University of Colorado Boulder Boulder CO USA
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55
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Bocková J, Jones NC, Leyva V, Gaysinski M, Hoffmann SV, Meinert C. Concentration and pH effect on the electronic circular dichroism and anisotropy spectra of aqueous solutions of glyceric acid calcium salt. Chirality 2021; 34:245-252. [PMID: 34939233 DOI: 10.1002/chir.23407] [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: 07/29/2021] [Revised: 12/10/2021] [Accepted: 12/10/2021] [Indexed: 11/08/2022]
Abstract
Electronic circular dichroism (ECD) and anisotropy spectra carry information on differential absorption of left- and right-circularly polarized light (LCPL and RCPL) by optically active compounds. This makes them powerful tools for the rapid determination of enantiomeric excesses (ee) in asymmetric synthetic and pharmaceutical chemistry, as well as for predicting the ee inducible by ultraviolet (UV) CPL. The ECD response of a chiral molecule is, however, critically dependent on the properties of the surrounding medium. Here, we report on the first ECD/anisotropy spectra of aqueous solutions of the calcium salt dihydrate of glyceric acid. A systematic study of the effect of the salt concentration and pH on the chiroptical response revealed significant changes and the appearance of a new ECD band of opposite sign. Based on the literature, this can be rationalized by the increase in the relative proportion of free glyceric acid/glycerate to Ca2+ complexes with glycerate with decreasing salt concentration or pH. Glyceric acid can be readily produced under astrophysical conditions. The anisotropy spectra of the solution containing prevalently the free form of this dihydroxy carboxylic acid resemble the ones of previously investigated aliphatic chain hydroxycarboxylic acids and proteinogenic amino acids. This indicates possible common handedness of stellar CPL-induced asymmetry in the potential comonomers of primitive proto-peptides.
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Affiliation(s)
- Jana Bocková
- Institut de Chimie de Nice, CNRS UMR 7272, Université Côte d'Azur, Nice, France
| | - Nykola C Jones
- ISA, Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
| | - Vanessa Leyva
- Institut de Chimie de Nice, CNRS UMR 7272, Université Côte d'Azur, Nice, France
| | - Marc Gaysinski
- Institut de Chimie de Nice, CNRS UMR 7272, Université Côte d'Azur, Nice, France
| | - Søren V Hoffmann
- ISA, Department of Physics and Astronomy, Aarhus University, Aarhus, Denmark
| | - Cornelia Meinert
- Institut de Chimie de Nice, CNRS UMR 7272, Université Côte d'Azur, Nice, France
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56
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Jia TZ, Kuruma Y. Increasing complexity of primitive compartments. Biophys Physicobiol 2021; 18:269-273. [PMID: 34909364 PMCID: PMC8639197 DOI: 10.2142/biophysico.bppb-v18.032] [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: 11/05/2021] [Accepted: 11/15/2021] [Indexed: 12/01/2022] Open
Affiliation(s)
- Tony Z Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan.,Blue Marble Space Institute of Science, Seattle, Washington 98154, USA
| | - Yutetsu Kuruma
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan.,Extra-cutting-edge Science and Technology Avant-garde Research Program, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa 237-0061, Japan.,Japan Science and Technology Agency, PRESTO, Kawaguchi, Saitama 332-0012, Japan
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57
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Tsai YT, Huang CW, Yu SS. The effect of temperature on the kinetics of enhanced amide bond formation from lactic acid and valine driven by deep eutectic solvents. Phys Chem Chem Phys 2021; 23:27498-27507. [PMID: 34874376 DOI: 10.1039/d1cp03243g] [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
Deep eutectic solvents have been found to facilitate the copolymerization of hydroxy acids and amino acids through an ester-amide exchange reaction, and to drive the formation of amino acid-enriched oligomers with peptide backbones. The complexity of oligomer distribution is significantly reduced in deep eutectic solvents and amide-linked oligomers can be selectively produced. In the present study, we investigated the kinetics of amide bond formation in deep eutectic solvents to understand how the solvents regulate the pathways of complex copolymerization. A mathematical model successfully simulated the reaction of a lactic acid/valine mixture in deep eutectic solvents at different temperatures and provided insight into the activation energy of each step. Our findings indicated that the esterification and the evaporation of hydroxy acids were greatly suppressed in deep eutectic solvents because of the strong interaction between the quaternary ammonium salts and the hydroxy acids. In contrast, the ester-amide exchange reaction in deep eutectic solvents was significantly enhanced by lowering the activation entropies. The synergic effect of reduced esterification and increased exchange leads to amino acid-enriched oligomers with high yield and high selectivity. Furthermore, the reduced evaporation of hydroxy acids in deep eutectic solvents may preserve limited reactants in the prebiotic scenario. These results reveal deep eutectic solvents as sustainable media for the simple synthesis of amide bonds.
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Affiliation(s)
- Yi-Ting Tsai
- Department of Chemical Engineering, National Cheng Kung University, Tainan, 70101, Taiwan.
| | - Cong-Wei Huang
- Department of Chemical Engineering, National Cheng Kung University, Tainan, 70101, Taiwan.
| | - Sheng-Sheng Yu
- Department of Chemical Engineering, National Cheng Kung University, Tainan, 70101, Taiwan. .,Core Facility Center, National Cheng Kung University, Tainan, 70101, Taiwan
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58
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Le Vay K, Song EY, Ghosh B, Tang TD, Mutschler H. Enhanced Ribozyme‐Catalyzed Recombination and Oligonucleotide Assembly in Peptide‐RNA Condensates. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202109267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Kristian Le Vay
- Biomimetic Systems Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
- Department of Chemistry and Chemical Biology TU Dortmund University Otto-Hahn-Str. 4a 44227 Dortmund Germany
| | - Emilie Yeonwha Song
- Biomimetic Systems Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
- Department of Chemistry and Chemical Biology TU Dortmund University Otto-Hahn-Str. 4a 44227 Dortmund Germany
| | - Basusree Ghosh
- Max-Planck Institute of Molecular Cell Biology and Genetics Pfotenhauerstraße 108 01307 Dresden Germany
| | - T.‐Y. Dora Tang
- Max-Planck Institute of Molecular Cell Biology and Genetics Pfotenhauerstraße 108 01307 Dresden Germany
| | - Hannes Mutschler
- Department of Chemistry and Chemical Biology TU Dortmund University Otto-Hahn-Str. 4a 44227 Dortmund Germany
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59
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Havig JR, Kuether JE, Gangidine AJ, Schroeder S, Hamilton TL. Hot Spring Microbial Community Elemental Composition: Hot Spring and Soil Inputs, and the Transition from Biocumulus to Siliceous Sinter. ASTROBIOLOGY 2021; 21:1526-1546. [PMID: 34889663 DOI: 10.1089/ast.2019.2086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Hydrothermal systems host microbial communities that include some of the most deeply branching members of the tree of life, and recent work has suggested that terrestrial hot springs may have provided ideal conditions for the origin of life. Hydrothermal microbial communities are a potential source for biosignatures, and the presence of terrestrial hot spring deposits in 3.48 Ga rocks as well as on the surface of Mars lends weight to a need to better understand the preservation of biosignatures in these systems. Although there are general patterns of elemental enrichment in hydrothermal water dependent on physical and geochemical conditions, the elemental composition of bulk hydrothermal microbial communities (here termed biocumulus, including cellular biomass and accumulated non-cellular material) is largely unexplored. However, recent work has suggested both bulk and spatial trace element enrichment as a potential biosignature in hot spring deposits. To elucidate the elemental composition of hot spring biocumulus samples and explore the sources of those elements, we analyzed a suite of 16 elements in hot spring water samples and corresponding biocumulus from 60 hot springs sinter samples, and rock samples from 8 hydrothermal areas across Yellowstone National Park. We combined these data with values reported in literature to assess the patterns of elemental uptake into biocumulus and retention in associated siliceous sinter. Hot spring biocumuli are of biological origin, but organic carbon comprises a minor percentage of the total mass of both thermophilic chemotrophic and phototrophic biocumulus. Instead, the majority of hot spring biocumulus is inorganic material-largely silica-and the distribution of major and trace elements mimics that of surrounding rock and soil rather than the hot spring fluids. Analyses indicate a systematic loss of biologically associated elements during diagenetic transformation of biocumulus to siliceous sinter, suggesting a potential for silica sinter to preserve a trace element biosignature.
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Affiliation(s)
- Jeff R Havig
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, Minnesota, USA
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, USA
| | - Joshua E Kuether
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, Minnesota, USA
| | | | - Sarah Schroeder
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, Minnesota, USA
| | - Trinity L Hamilton
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, USA
- BioTechnology Institute, University of Minnesota, Saint Paul, Minnesota, USA
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60
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Roy S, Sengupta S. Evolution towards increasing complexity through functional diversification in a protocell model of the RNA world. Proc Biol Sci 2021; 288:20212098. [PMID: 34784760 PMCID: PMC8596018 DOI: 10.1098/rspb.2021.2098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 10/21/2021] [Indexed: 11/12/2022] Open
Abstract
The encapsulation of genetic material inside compartments together with the creation and sustenance of functionally diverse internal components are likely to have been key steps in the formation of 'live', replicating protocells in an RNA world. Several experiments have shown that RNA encapsulated inside lipid vesicles can lead to vesicular growth and division through physical processes alone. Replication of RNA inside such vesicles can produce a large number of RNA strands. Yet, the impact of such replication processes on the emergence of the first ribozymes inside such protocells and on the subsequent evolution of the protocell population remains an open question. In this paper, we present a model for the evolution of protocells with functionally diverse ribozymes. Distinct ribozymes can be created with small probabilities during the error-prone RNA replication process via the rolling circle mechanism. We identify the conditions that can synergistically enhance the number of different ribozymes inside a protocell and allow functionally diverse protocells containing multiple ribozymes to dominate the population. Our work demonstrates the existence of an effective pathway towards increasing complexity of protocells that might have eventually led to the origin of life in an RNA world.
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Affiliation(s)
- Suvam Roy
- Department of Physical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India
| | - Supratim Sengupta
- Department of Physical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India
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61
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Lozoya-Colinas A, Clifton BE, Grover MA, Hud NV. Urea and Acetamide Rich Solutions Circumvent the Strand Inhibition Problem to Allow Multiple Rounds of DNA and RNA Copying. Chembiochem 2021; 23:e202100495. [PMID: 34797020 DOI: 10.1002/cbic.202100495] [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: 09/18/2021] [Revised: 11/18/2021] [Indexed: 11/08/2022]
Abstract
For decades prebiotic chemists have attempted to achieve replication of RNA under prebiotic conditions with only limited success. One of the long-recognized impediments to achieving true replication of a duplex (copying of both strands) is the so-called strand inhibition problem. Specifically, while the two strands of an RNA (or DNA) duplex can be separated by heating, upon cooling the strands of a duplex will reanneal before mononucleotide or oligonucleotide substrates can bind to the individual strands. Here we demonstrate that a class of plausible prebiotic solvents, when coupled with thermal cycling and varying levels of hydration, circumvents the strand inhibition problem, and allows multiple rounds of information transfer from both strands of a duplex (replication). Replication was achieved by simultaneous ligation of oligomers that bind to their templates with the aid of the solvents. The solvents used consisted of concentrated solutions of urea and acetamide in water (UAcW), components that were likely abundant on the early Earth. The UAcW solvent system favors the annealing of shorter strands over the re-annealing of long strands, thereby circumventing strand inhibition. We observed an improvement of DNA and RNA replication yields by a factor of 100× over aqueous buffer. Information transfer in the UAcW solvent system is robust, being achieved for a range of solvent component ratios, various drying conditions, and in the absence or presence of added salts.
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Affiliation(s)
- Adriana Lozoya-Colinas
- NSF/NASA Center for Chemical Evolution, GA 30332, Atlanta, USA.,School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, GA 30332, Atlanta, USA
| | - Bryce E Clifton
- NSF/NASA Center for Chemical Evolution, GA 30332, Atlanta, USA.,School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, GA 30332, Atlanta, USA
| | - Martha A Grover
- NSF/NASA Center for Chemical Evolution, GA 30332, Atlanta, USA.,School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst Drive NW, GA 30332, Atlanta, USA
| | - Nicholas V Hud
- NSF/NASA Center for Chemical Evolution, GA 30332, Atlanta, USA.,School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, GA 30332, Atlanta, USA
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62
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Was There Land on the Early Earth? Life (Basel) 2021; 11:life11111142. [PMID: 34833018 PMCID: PMC8623345 DOI: 10.3390/life11111142] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 10/22/2021] [Accepted: 10/25/2021] [Indexed: 11/17/2022] Open
Abstract
The presence of exposed land on the early Earth is a prerequisite for a certain type of prebiotic chemical evolution in which the oscillating activity of water, driven by short-term, day–night, and seasonal cycles, facilitates the synthesis of proto-biopolymers. Exposed land is, however, not guaranteed to exist on the early Earth, which is likely to have been drastically different from the modern Earth. This mini-review attempts to provide an up-to-date account on the possibility of exposed land on the early Earth by integrating recent geological and geophysical findings. Owing to the competing effects of the growing ocean and continents in the Hadean, a substantial expanse of the Earth’s surface (∼20% or more) could have been covered by exposed continents in the mid-Hadean. In contrast, exposed land may have been limited to isolated ocean islands in the late Hadean and early Archean. The importance of exposed land during the origins of life remains an open question.
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63
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Thermodynamics of Potential CHO Metabolites in a Reducing Environment. Life (Basel) 2021; 11:life11101025. [PMID: 34685396 PMCID: PMC8537574 DOI: 10.3390/life11101025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/24/2021] [Accepted: 09/28/2021] [Indexed: 11/17/2022] Open
Abstract
How did metabolism arise and evolve? What chemical compounds might be suitable to support and sustain a proto-metabolism before the advent of more complex co-factors? We explore these questions by using first-principles quantum chemistry to calculate the free energies of CHO compounds in aqueous solution, allowing us to probe the thermodynamics of core extant cycles and their closely related chemical cousins. By framing our analysis in terms of the simplest feasible cycle and its permutations, we analyze potentially favorable thermodynamic cycles for CO2 fixation with H2 as a reductant. We find that paying attention to redox states illuminates which reactions are endergonic or exergonic. Our results highlight the role of acetate in proto-metabolic cycles, and its connection to other prebiotic molecules such as glyoxalate, glycolaldehyde, and glycolic acid.
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64
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Le Vay K, Song EY, Ghosh B, Tang TYD, Mutschler H. Enhanced Ribozyme-Catalyzed Recombination and Oligonucleotide Assembly in Peptide-RNA Condensates. Angew Chem Int Ed Engl 2021; 60:26096-26104. [PMID: 34569680 PMCID: PMC9299051 DOI: 10.1002/anie.202109267] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Indexed: 11/17/2022]
Abstract
The ability of RNA to catalyze RNA ligation is critical to its central role in many prebiotic model scenarios, in particular the copying of information during self‐replication. Prebiotically plausible ribozymes formed from short oligonucleotides can catalyze reversible RNA cleavage and ligation reactions, but harsh conditions or unusual scenarios are often required to promote folding and drive the reaction equilibrium towards ligation. Here, we demonstrate that ribozyme activity is greatly enhanced by charge‐mediated phase separation with poly‐L‐lysine, which shifts the reaction equilibrium from cleavage in solution to ligation in peptide‐RNA coaggregates and coacervates. This compartmentalization enables robust isothermal RNA assembly over a broad range of conditions, which can be leveraged to assemble long and complex RNAs from short fragments under mild conditions in the absence of exogenous activation chemistry, bridging the gap between pools of short oligomers and functional RNAs.
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Affiliation(s)
- Kristian Le Vay
- Biomimetic Systems, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.,Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Emilie Yeonwha Song
- Biomimetic Systems, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.,Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
| | - Basusree Ghosh
- Max-Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307, Dresden, Germany
| | - T-Y Dora Tang
- Max-Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307, Dresden, Germany
| | - Hannes Mutschler
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
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65
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Freire MÁ. Short non-coded peptides interacting with cofactors facilitated the integration of early chemical networks. Biosystems 2021; 211:104547. [PMID: 34547425 DOI: 10.1016/j.biosystems.2021.104547] [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: 05/31/2021] [Revised: 08/28/2021] [Accepted: 09/15/2021] [Indexed: 11/02/2022]
Abstract
Independently developed iron-sulphur/thioester- and phosphate-driven chemical reactions would have set up two distinct reaction networks prior to coupling in a proto-metabolic system supporting a minimal organisation closure. Each chemical system assisted initially by simple catalysts and then by more complex cofactors would have provided the precursors of the small metabolites and monomer units along with their respective polymers through dehydrating template-independent assemblies. For example, acylation reactions mediated by activated thioester groups produced peptides, fatty acids and polyhydroxyalkanoates, while phosphorylation reactions by phosphorylating agents allowed the synthesis of polysaccharides, polyribonucleotides and polyphosphates. Here, we address how these independent chemical systems might fit together and shaped a proto-metabolic system, focusing specifically on cofactors as molecular fossils of metabolism. As a result, the proposed overview suggests that non-coded peptides capable of binding a variety of ligands, but in particular with a redox active versatility and/or group transfer potential could have facilitated the chemical connections that led to a minimal closure with a proto-metabolism. Later developments would have made it possible to establish a cellular organisation with more complex and interdependent metabolic pathways.
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Affiliation(s)
- Miguel Ángel Freire
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET, Universidad Nacional de Córdoba (UNC). Facultad de Ciencias Exactas, Físicas y Naturales. Av. Vélez Sarsfield 299, CC 495, 5000, Córdoba, Argentina.
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Maguire OR, Smokers IBA, Huck WTS. A physicochemical orthophosphate cycle via a kinetically stable thermodynamically activated intermediate enables mild prebiotic phosphorylations. Nat Commun 2021; 12:5517. [PMID: 34535651 PMCID: PMC8448844 DOI: 10.1038/s41467-021-25555-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 08/18/2021] [Indexed: 12/02/2022] Open
Abstract
The incorporation of orthophosphate from scarce geochemical sources into the organic compounds essential for life under mild conditions is a fundamental challenge for prebiotic chemistry. Here we report a prebiotic system capable of overcoming this challenge by taking inspiration from extant life's recycling of orthophosphate via its conversion into kinetically stable thermodynamically activated (KSTA) nucleotide triphosphates (e.g. ATP). We separate the activation of orthophosphate from its transfer to organic compounds by, crucially, first accumulating a KSTA phosphoramidate. We use cyanate to activate orthophosphate in aqueous solution under mild conditions and then react it with imidazole to accumulate the KSTA imidazole phosphate. In a paste, imidazole phosphate phosphorylates all the essential building blocks of life. Integration of this chemistry into a wet/dry cycle enables the continuous recycling of orthophosphate and the accretion of phosphorylated compounds. This system functions even at low reagent concentrations due to solutes concentrating during evaporation. Our system demonstrates a general strategy for how to maximise the usage of scarce resources based upon cycles which accumulate and then release activated intermediates.
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Affiliation(s)
- Oliver R Maguire
- Institute for Molecules and Materials, Radboud University Nijmegen, 6525, AJ, Nijmegen, The Netherlands
| | - Iris B A Smokers
- Institute for Molecules and Materials, Radboud University Nijmegen, 6525, AJ, Nijmegen, The Netherlands
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University Nijmegen, 6525, AJ, Nijmegen, The Netherlands.
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Fialho DM, Karunakaran SC, Greeson KW, Martínez I, Schuster GB, Krishnamurthy R, Hud NV. Depsipeptide Nucleic Acids: Prebiotic Formation, Oligomerization, and Self-Assembly of a New Proto-Nucleic Acid Candidate. J Am Chem Soc 2021; 143:13525-13537. [PMID: 34398608 DOI: 10.1021/jacs.1c02287] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The mechanism by which informational polymers first formed on the early earth is currently unknown. The RNA world hypothesis implies that RNA oligomers were produced prebiotically, before the emergence of enzymes, but the demonstration of such a process remains challenging. Alternatively, RNA may have been preceded by an earlier ancestral polymer, or proto-RNA, that had a greater propensity for self-assembly than RNA, with the eventual transition to functionally superior RNA being the result of chemical or biological evolution. We report a new class of nucleic acid analog, depsipeptide nucleic acid (DepsiPNA), which displays several properties that are attractive as a candidate for proto-RNA. The monomers of depsipeptide nucleic acids can form under plausibly prebiotic conditions. These monomers oligomerize spontaneously when dried from aqueous solutions to form nucleobase-functionalized depsipeptides. Once formed, these DepsiPNA oligomers are capable of complementary self-assembly and are resistant to hydrolysis in the assembled state. These results suggest that the initial formation of primitive, self-assembling, informational polymers on the early earth may have been relatively facile if the constraints of an RNA-first scenario are relaxed.
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Affiliation(s)
- David M Fialho
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Suneesh C Karunakaran
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Katherine W Greeson
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Isaac Martínez
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Gary B Schuster
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Ramanarayanan Krishnamurthy
- NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States.,Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Nicholas V Hud
- School of Chemistry and Biochemistry and Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
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68
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Primitive selection of the fittest emerging through functional synergy in nucleopeptide networks. Proc Natl Acad Sci U S A 2021; 118:2015285118. [PMID: 33622789 DOI: 10.1073/pnas.2015285118] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Many fundamental cellular and viral functions, including replication and translation, involve complex ensembles hosting synergistic activity between nucleic acids and proteins/peptides. There is ample evidence indicating that the chemical precursors of both nucleic acids and peptides could be efficiently formed in the prebiotic environment. Yet, studies on nonenzymatic replication, a central mechanism driving early chemical evolution, have focused largely on the activity of each class of these molecules separately. We show here that short nucleopeptide chimeras can replicate through autocatalytic and cross-catalytic processes, governed synergistically by the hybridization of the nucleobase motifs and the assembly propensity of the peptide segments. Unequal assembly-dependent replication induces clear selectivity toward the formation of a certain species within small networks of complementary nucleopeptides. The selectivity pattern may be influenced and indeed maximized to the point of almost extinction of the weakest replicator when the system is studied far from equilibrium and manipulated through changes in the physical (flow) and chemical (template and inhibition) conditions. We postulate that similar processes may have led to the emergence of the first functional nucleic-acid-peptide assemblies prior to the origin of life. Furthermore, spontaneous formation of related replicating complexes could potentially mark the initiation point for information transfer and rapid progression in complexity within primitive environments, which would have facilitated the development of a variety of functions found in extant biological assemblies.
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Ying J, Ding R, Liu Y, Zhao Y. Prebiotic Chemistry in Aqueous Environment: A Review of Peptide Synthesis and Its Relationship with Genetic Code. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202100120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jianxi Ying
- Institute of Drug Discovery Technology Ningbo University, No.818 Fenghua Road, Ningbo Zhejiang 315211 China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences Ningbo University No.818 Fenghua Road, Ningbo Zhejiang 315211 China
| | - Ruiwen Ding
- Institute of Drug Discovery Technology Ningbo University, No.818 Fenghua Road, Ningbo Zhejiang 315211 China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences Ningbo University No.818 Fenghua Road, Ningbo Zhejiang 315211 China
| | - Yan Liu
- College of Chemistry and Chemical Engineering Xiamen University, No. 422, Siming South Road Xiamen Fujian 361005 China
| | - Yufen Zhao
- Institute of Drug Discovery Technology Ningbo University, No.818 Fenghua Road, Ningbo Zhejiang 315211 China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences Ningbo University No.818 Fenghua Road, Ningbo Zhejiang 315211 China
- College of Chemistry and Chemical Engineering Xiamen University, No. 422, Siming South Road Xiamen Fujian 361005 China
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Xue M, Black RA, Cohen ZR, Roehrich A, Drobny GP, Keller SL. Binding of Dipeptides to Fatty Acid Membranes Explains Their Colocalization in Protocells but Does Not Select for Them Relative to Unjoined Amino Acids. J Phys Chem B 2021; 125:7933-7939. [PMID: 34283913 DOI: 10.1021/acs.jpcb.1c01485] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dipeptides, which consist of two amino acids joined by a peptide bond, have been shown to have catalytic functions. This observation leads to fundamental questions relevant to the origin of life. How could peptides have become colocalized with the first protocells? Which structural features would have determined the association of amino acids and peptides with membranes? Could the association of dipeptides with protocell membranes have driven molecular evolution, favoring dipeptides over individual amino acids? Using pulsed-field gradient nuclear magnetic resonance, we find that several prebiotic amino acids and dipeptides bind to prebiotic membranes. For amino acids, the side chains and carboxylate contribute to the interaction. For dipeptides, the extent of binding is generally less than that of the constituent amino acids, implying that other mechanisms would be necessary to drive molecular evolution. Nevertheless, our results are consistent with a scheme in which the building blocks of the biological polymers colocalized with protocells prior to the emergence of RNA and proteins.
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Affiliation(s)
- Mengjun Xue
- Department of Chemistry, University of Washington, Seattle, Washington 98195 United States
| | - Roy A Black
- Department of Chemistry, University of Washington, Seattle, Washington 98195 United States
| | - Zachary R Cohen
- Department of Chemistry, University of Washington, Seattle, Washington 98195 United States
| | - Adrienne Roehrich
- Department of Chemistry, University of Washington, Seattle, Washington 98195 United States
| | - Gary P Drobny
- Department of Chemistry, University of Washington, Seattle, Washington 98195 United States
| | - Sarah L Keller
- Department of Chemistry, University of Washington, Seattle, Washington 98195 United States
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72
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Wang W, Qiao L, He J, Ju Y, Yu K, Kan G, Guo C, Zhang H, Jiang J. Water Microdroplets Allow Spontaneously Abiotic Production of Peptides. J Phys Chem Lett 2021; 12:5774-5780. [PMID: 34134488 DOI: 10.1021/acs.jpclett.1c01083] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The chemistry of abiotic synthesis of peptides in the context of their prebiotic origins is a continuing challenge that arises from thermodynamic and kinetic constraints in aqueous media. Here we reported a strategy of microdroplets' mass spectrometry for peptide bonds formed from pure amino acids or a mixture in the presence of phosphoric acids in aqueous microdroplets. In contrast to bulk experiments, the condensation reactions proceed spontaneously under ambient conditions. The microdroplet gave a negative free-energy change (ΔG ∼ -1.1 kcal/mol), and product yields of ∼75% were obtained at the scale of a few milliseconds. Experiments in which nebulization gas pressure and external charge were varied established dependence of peptide production on the droplet size that has a high surface-to-volume ratio. It is concluded that the condensation reactions occurred at or near the air-water interfaces of microdroplets. This aqueous microdroplets approach also provides a route for chemistry synthesis in the prebiotic era.
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Affiliation(s)
- Wenxin Wang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, China
| | - Lina Qiao
- Marine College, Shandong University (Weihai), Weihai, Shandong 264209, China
| | - Jing He
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, China
| | - Yun Ju
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, China
| | - Kai Yu
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, China
| | - Guangfeng Kan
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, China
| | - Changlu Guo
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, China
| | - Hong Zhang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, China
| | - Jie Jiang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, Shandong 264209, China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, Heilongjiang 150090, China
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Bocková J, Jones NC, Meierhenrich UJ, Hoffmann SV, Meinert C. Chiroptical activity of hydroxycarboxylic acids with implications for the origin of biological homochirality. Commun Chem 2021; 4:86. [PMID: 36697718 PMCID: PMC9814692 DOI: 10.1038/s42004-021-00524-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/14/2021] [Indexed: 02/05/2023] Open
Abstract
Circularly polarised light (CPL) interacting with interstellar organic molecules might have imparted chiral bias and hence preluded prebiotic evolution of biomolecular homochirality. The L-enrichment of extra-terrestrial amino acids in meteorites, as opposed to no detectable excess in monocarboxylic acids and amines, has previously been attributed to their intrinsic interaction with stellar CPL revealed by substantial differences in their chiroptical signals. Recent analyses of meteoritic hydroxycarboxylic acids (HCAs) - potential co-building blocks of ancestral proto-peptides - indicated a chiral bias toward the L-enantiomer of lactic acid. Here we report on novel anisotropy spectra of several HCAs using a synchrotron radiation electronic circular dichroism spectrophotometer to support the re-evaluation of chiral biomarkers of extra-terrestrial origin in the context of absolute photochirogenesis. We found that irradiation by CPL which would yield L-excess in amino acids would also yield L-excess in aliphatic chain HCAs, including lactic acid and mandelic acid, in the examined conditions. Only tartaric acid would show "unnatural" D-enrichment, which makes it a suitable target compound for further assessing the relevance of the CPL scenario.
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Affiliation(s)
- Jana Bocková
- grid.460782.f0000 0004 4910 6551University Côte d’Azur, CNRS, Institute de Chimie de Nice, UMR 7272, Nice, France
| | - Nykola C. Jones
- grid.7048.b0000 0001 1956 2722ISA, Department of Physics and Astronomy, Aarhus University, Aarhus C, Denmark
| | - Uwe J. Meierhenrich
- grid.460782.f0000 0004 4910 6551University Côte d’Azur, CNRS, Institute de Chimie de Nice, UMR 7272, Nice, France
| | - Søren V. Hoffmann
- grid.7048.b0000 0001 1956 2722ISA, Department of Physics and Astronomy, Aarhus University, Aarhus C, Denmark
| | - Cornelia Meinert
- grid.460782.f0000 0004 4910 6551University Côte d’Azur, CNRS, Institute de Chimie de Nice, UMR 7272, Nice, France
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de Azambuja F, Loosen A, Conic D, van den Besselaar M, Harvey JN, Parac-Vogt TN. En Route to a Heterogeneous Catalytic Direct Peptide Bond Formation by Zr-Based Metal–Organic Framework Catalysts. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01782] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Alexandra Loosen
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Dragan Conic
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | | | - Jeremy N. Harvey
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
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Russell MJ. The "Water Problem"( sic), the Illusory Pond and Life's Submarine Emergence-A Review. Life (Basel) 2021; 11:429. [PMID: 34068713 PMCID: PMC8151828 DOI: 10.3390/life11050429] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 04/30/2021] [Accepted: 05/01/2021] [Indexed: 01/10/2023] Open
Abstract
The assumption that there was a "water problem" at the emergence of life-that the Hadean Ocean was simply too wet and salty for life to have emerged in it-is here subjected to geological and experimental reality checks. The "warm little pond" that would take the place of the submarine alkaline vent theory (AVT), as recently extolled in the journal Nature, flies in the face of decades of geological, microbiological and evolutionary research and reasoning. To the present author, the evidence refuting the warm little pond scheme is overwhelming given the facts that (i) the early Earth was a water world, (ii) its all-enveloping ocean was never less than 4 km deep, (iii) there were no figurative "Icelands" or "Hawaiis", nor even an "Ontong Java" then because (iv) the solidifying magma ocean beneath was still too mushy to support such salient loadings on the oceanic crust. In place of the supposed warm little pond, we offer a well-protected mineral mound precipitated at a submarine alkaline vent as life's womb: in place of lipid membranes, we suggest peptides; we replace poisonous cyanide with ammonium and hydrazine; instead of deleterious radiation we have the appropriate life-giving redox and pH disequilibria; and in place of messy chemistry we offer the potential for life's emergence from the simplest of geochemically available molecules and ions focused at a submarine alkaline vent in the Hadean-specifically within the nano-confined flexible and redox active interlayer walls of the mixed-valent double layer oxyhydroxide mineral, fougerite/green rust comprising much of that mound.
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Affiliation(s)
- Michael J Russell
- Dipartimento di Chimica, Università degli Studi di Torino, via P. Giuria 7, 10125 Turin, Italy
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76
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Sarkar S, Dagar S, Rajamani S. Influence of Wet–Dry Cycling on the Self‐Assembly and Physicochemical Properties of Model Protocellular Membrane Systems. CHEMSYSTEMSCHEM 2021. [DOI: 10.1002/syst.202100014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Susovan Sarkar
- Department of Biology Indian Institute of Science Education and Research Pune 411008 India
| | - Shikha Dagar
- Department of Biology Indian Institute of Science Education and Research Pune 411008 India
| | - Sudha Rajamani
- Department of Biology Indian Institute of Science Education and Research Pune 411008 India
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77
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Stolar T, Grubešić S, Cindro N, Meštrović E, Užarević K, Hernández JG. Mechanochemical Prebiotic Peptide Bond Formation*. Angew Chem Int Ed Engl 2021; 60:12727-12731. [PMID: 33769680 DOI: 10.1002/anie.202100806] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/11/2021] [Indexed: 12/15/2022]
Abstract
The presence of amino acids on the prebiotic Earth, either stemming from endogenous chemical routes or delivered by meteorites, is consensually accepted. Prebiotically plausible pathways to peptides from inactivated amino acids are still unclear as most oligomerization approaches rely on thermodynamically disfavored reactions in solution. Now, a combination of prebiotically plausible minerals and mechanochemical activation enables the oligomerization of glycine at ambient temperature in the absence of water. Raising the reaction temperature increases the degree of oligomerization concomitantly with the formation of a commonly unwanted cyclic glycine dimer (DKP). However, DKP is a productive intermediate in the mechanochemical oligomerization of glycine. The findings of this research show that mechanochemical peptide bond formation is a dynamic process that provides alternative routes towards oligopeptides and establishes new synthetic approaches for prebiotic chemistry.
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Affiliation(s)
- Tomislav Stolar
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000, Zagreb, Croatia
| | - Saša Grubešić
- Xellia Pharmaceuticals, Slavonska avenija 24/6, 10000, Zagreb, Croatia
| | - Nikola Cindro
- Department of Organic Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000, Zagreb, Croatia
| | - Ernest Meštrović
- Xellia Pharmaceuticals, Slavonska avenija 24/6, 10000, Zagreb, Croatia
| | - Krunoslav Užarević
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000, Zagreb, Croatia
| | - José G Hernández
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000, Zagreb, Croatia
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78
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Stolar T, Grubešić S, Cindro N, Meštrović E, Užarević K, Hernández JG. Mechanochemical Prebiotic Peptide Bond Formation**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100806] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Tomislav Stolar
- Division of Physical Chemistry Ruđer Bošković Institute Bijenička c. 54 10000 Zagreb Croatia
| | - Saša Grubešić
- Xellia Pharmaceuticals Slavonska avenija 24/6 10000 Zagreb Croatia
| | - Nikola Cindro
- Department of Organic Chemistry Faculty of Science University of Zagreb Horvatovac 102a 10000 Zagreb Croatia
| | - Ernest Meštrović
- Xellia Pharmaceuticals Slavonska avenija 24/6 10000 Zagreb Croatia
| | - Krunoslav Užarević
- Division of Physical Chemistry Ruđer Bošković Institute Bijenička c. 54 10000 Zagreb Croatia
| | - José G. Hernández
- Division of Physical Chemistry Ruđer Bošković Institute Bijenička c. 54 10000 Zagreb Croatia
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79
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Seaton KM, Cable ML, Stockton AM. Analytical Chemistry in Astrobiology. Anal Chem 2021; 93:5981-5997. [PMID: 33835785 DOI: 10.1021/acs.analchem.0c04271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This Feature introduces and discusses the findings of key analytical techniques used to study planetary bodies in our solar system in the search for life beyond Earth, future missions planned for high-priority astrobiology targets in our solar system, and the challenges we face in performing these investigations.
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Affiliation(s)
- Kenneth Marshall Seaton
- School of Chemistry & Biochemistry, Georgia Institute of Technology, North Avenue NW, Atlanta, Georgia 30332, United States
| | - Morgan Leigh Cable
- Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California 91109, United States
| | - Amanda Michelle Stockton
- School of Chemistry & Biochemistry, Georgia Institute of Technology, North Avenue NW, Atlanta, Georgia 30332, United States
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Abstract
The evolution of coenzymes, or their impact on the origin of life, is fundamental for understanding our own existence. Having established reasonable hypotheses about the emergence of prebiotic chemical building blocks, which were probably created under palaeogeochemical conditions, and surmising that these smaller compounds must have become integrated to afford complex macromolecules such as RNA, the question of coenzyme origin and its relation to the evolution of functional biochemistry should gain new impetus. Many coenzymes have a simple chemical structure and are often nucleotide-derived, which suggests that they may have coexisted with the emergence of RNA and may have played a pivotal role in early metabolism. Based on current theories of prebiotic evolution, which attempt to explain the emergence of privileged organic building blocks, this Review discusses plausible hypotheses on the prebiotic formation of key elements within selected extant coenzymes. In combination with prebiotic RNA, coenzymes may have dramatically broadened early protometabolic networks and the catalytic scope of RNA during the evolution of life.
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Affiliation(s)
- Andreas Kirschning
- Institut für Organische Chemie und Biomolekulares Wirkstoffzentrum (BMWZ)Leibniz Universität HannoverSchneiderberg 1B30167HannoverGermany
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81
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The Theory of Chemical Symbiosis: A Margulian View for the Emergence of Biological Systems (Origin of Life). Acta Biotheor 2021; 69:67-78. [PMID: 32783083 DOI: 10.1007/s10441-020-09388-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 08/04/2020] [Indexed: 10/23/2022]
Abstract
The theory of chemical symbiosis (TCS) suggests that biological systems started with the collaboration of two polymeric molecules existing in early Earth: nucleic acids and peptides. Chemical symbiosis emerged when RNA-like nucleic acid polymers happened to fold into 3D structures capable to bind amino acids together, forming a proto peptidyl-transferase center. This folding catalyzed the formation of quasi-random small peptides, some of them capable to bind this ribozyme structure back and starting to form an initial layer that would produce the larger subunit of the ribosome by accretion. TCS suggests that there is no chicken-and-egg problem into the emergence of biological systems as RNAs and peptides were of equal importance to the origin of life. Life has initially emerged when these two macromolecules started to interact in molecular symbiosis. Further, we suggest that life evolved into progenotes and cells due to the emergence of new layers of symbiosis. Mutualism is the strongest force in biology, capable to create novelties by emergent principles; on which the whole is bigger than the sum of the parts. TCS aims to apply the Margulian view of biology into the origins of life field.
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82
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Sibilska-Kaminski IK, Yin J. Toward Molecular Cooperation by De Novo Peptides. ORIGINS LIFE EVOL B 2021; 51:71-82. [PMID: 33566281 PMCID: PMC8212187 DOI: 10.1007/s11084-021-09603-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 01/08/2021] [Indexed: 10/22/2022]
Abstract
Theoretical models of the chemical origins of life depend on self-replication or autocatalysis, processes that arise from molecular interactions, recruitment, and cooperation. Such models often lack details about the molecules and reactions involved, giving little guidance to those seeking to detect signs of interaction, recruitment, or cooperation in the laboratory. Here, we develop minimal mathematical models of reactions involving specific chemical entities: amino acids and their condensation reactions to form de novo peptides. Reactions between two amino acids form a dipeptide product, which enriches linearly in time; subsequent recruitment of such products to form longer peptides exhibit super-linear growth. Such recruitment can be reciprocated: a peptide contributes to and benefits from the formation of one or more other peptides; in this manner, peptides can cooperate and thereby exhibit autocatalytic or exponential growth. We have started to test these predictions by quantitative analysis of de novo peptide synthesis conducted by wet-dry cycling of a five-amino acid mixture over 21 days. Using high-performance liquid chromatography, we tracked abundance changes for >60 unique peptide species. Some species were highly transient, with the emergence of up to 17 new species and the extinction of nine species between samplings, while other species persisted across many cycles. Of the persisting species, most exhibited super-linear growth, a sign of recruitment anticipated by our models. This work shows how mathematical modeling and quantitative analysis of kinetic data can guide the search for prebiotic chemistries that have the potential to cooperate and replicate.
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Affiliation(s)
- Izabela K Sibilska-Kaminski
- Department of Chemical and Biological Engineering, Wisconsin Institute for Discovery , University of Wisconsin-Madison, 330 N. Orchard Street, Madison, WI, 53715, USA
| | - John Yin
- Department of Chemical and Biological Engineering, Wisconsin Institute for Discovery , University of Wisconsin-Madison, 330 N. Orchard Street, Madison, WI, 53715, USA.
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83
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Jia TZ, Caudan M, Mamajanov I. Origin of Species before Origin of Life: The Role of Speciation in Chemical Evolution. Life (Basel) 2021; 11:154. [PMID: 33671365 PMCID: PMC7922636 DOI: 10.3390/life11020154] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/11/2021] [Accepted: 02/15/2021] [Indexed: 11/17/2022] Open
Abstract
Speciation, an evolutionary process by which new species form, is ultimately responsible for the incredible biodiversity that we observe on Earth every day. Such biodiversity is one of the critical features which contributes to the survivability of biospheres and modern life. While speciation and biodiversity have been amply studied in organismic evolution and modern life, it has not yet been applied to a great extent to understanding the evolutionary dynamics of primitive life. In particular, one unanswered question is at what point in the history of life did speciation as a phenomenon emerge in the first place. Here, we discuss the mechanisms by which speciation could have occurred before the origins of life in the context of chemical evolution. Specifically, we discuss that primitive compartments formed before the emergence of the last universal common ancestor (LUCA) could have provided a mechanism by which primitive chemical systems underwent speciation. In particular, we introduce a variety of primitive compartment structures, and associated functions, that may have plausibly been present on early Earth, followed by examples of both discriminate and indiscriminate speciation affected by primitive modes of compartmentalization. Finally, we discuss modern technologies, in particular, droplet microfluidics, that can be applied to studying speciation phenomena in the laboratory over short timescales. We hope that this discussion highlights the current areas of need in further studies on primitive speciation phenomena while simultaneously proposing directions as important areas of study to the origins of life.
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Affiliation(s)
- Tony Z. Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan;
- Blue Marble Space Institute of Science, 1001 4th Ave., Suite 3201, Seattle, WA 98154, USA
| | - Melina Caudan
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan;
| | - Irena Mamajanov
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan;
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84
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Frenkel-Pinter M, Rajaei V, Glass JB, Hud NV, Williams LD. Water and Life: The Medium is the Message. J Mol Evol 2021; 89:2-11. [PMID: 33427903 PMCID: PMC7884305 DOI: 10.1007/s00239-020-09978-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 11/21/2020] [Indexed: 02/06/2023]
Abstract
Water, the most abundant compound on the surface of the Earth and probably in the universe, is the medium of biology, but is much more than that. Water is the most frequent actor in the chemistry of metabolism. Our quantitation here reveals that water accounts for 99.4% of metabolites in Escherichia coli by molar concentration. Between a third and a half of known biochemical reactions involve consumption or production of water. We calculated the chemical flux of water and observed that in the life of a cell, a given water molecule frequently and repeatedly serves as a reaction substrate, intermediate, cofactor, and product. Our results show that as an E. coli cell replicates in the presence of molecular oxygen, an average in vivo water molecule is chemically transformed or is mechanistically involved in catalysis ~ 3.7 times. We conclude that, for biological water, there is no distinction between medium and chemical participant. Chemical transformations of water provide a basis for understanding not only extant biochemistry, but the origins of life. Because the chemistry of water dominates metabolism and also drives biological synthesis and degradation, it seems likely that metabolism co-evolved with biopolymers, which helps to reconcile polymer-first versus metabolism-first theories for the origins of life.
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Affiliation(s)
- Moran Frenkel-Pinter
- NASA Center for the Origins of Life, Atlanta, GA, USA
- NSF-NASA Center of Chemical Evolution, Atlanta, GA, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 315 Ferst Drive NW, Atlanta, GA, 30332-0400, USA
| | - Vahab Rajaei
- NASA Center for the Origins of Life, Atlanta, GA, USA
- NSF-NASA Center of Chemical Evolution, Atlanta, GA, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 315 Ferst Drive NW, Atlanta, GA, 30332-0400, USA
| | - Jennifer B Glass
- NASA Center for the Origins of Life, Atlanta, GA, USA
- School of Earth and Atmospheric Science, Georgia Institute of Technology, 311 Ferst Drive NW, Atlanta, GA, 30332-0340, USA
| | - Nicholas V Hud
- NASA Center for the Origins of Life, Atlanta, GA, USA
- NSF-NASA Center of Chemical Evolution, Atlanta, GA, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 315 Ferst Drive NW, Atlanta, GA, 30332-0400, USA
| | - Loren Dean Williams
- NASA Center for the Origins of Life, Atlanta, GA, USA.
- NSF-NASA Center of Chemical Evolution, Atlanta, GA, USA.
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 315 Ferst Drive NW, Atlanta, GA, 30332-0400, USA.
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85
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Namani T, Snyder S, Eagan JM, Bevilacqua PC, Wesdemiotis C, Sahai N. Amino Acid Specific Nonenzymatic Montmorillonite‐Promoted RNA Polymerization. CHEMSYSTEMSCHEM 2021. [DOI: 10.1002/syst.202000060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Trishool Namani
- School of Polymer Science and Polymer Engineering The University of Akron Akron OH 44325 USA
| | - Savannah Snyder
- Department of Chemistry The University of Akron Akron OH 44325 USA
| | - James M. Eagan
- School of Polymer Science and Polymer Engineering The University of Akron Akron OH 44325 USA
| | - Philip C. Bevilacqua
- Department of Chemistry and Biochemistry Department of Microbiology and Molecular Biology Center for RNA Molecular Biology Pennsylvania State University University Park Pennsylvania PA 16802 USA
| | | | - Nita Sahai
- School of Polymer Science and Polymer Engineering The University of Akron Akron OH 44325 USA
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86
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Frenkel-Pinter M, Sargon AB, Glass JB, Hud NV, Williams LD. Transition metals enhance prebiotic depsipeptide oligomerization reactions involving histidine. RSC Adv 2021; 11:3534-3538. [PMID: 35424306 PMCID: PMC8694183 DOI: 10.1039/d0ra07965k] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/08/2020] [Indexed: 11/30/2022] Open
Abstract
Biochemistry exhibits an intense dependence on metals. Here we show that during dry-down reactions, zinc and a few other transition metals increase the yield of long histidine-containing depsipeptides, which contain both ester and amide linkages. Our results suggest that interactions of proto-peptides with metal ions influenced early chemical evolution. Transition metals enhance prebiotic proto-peptide oligomerization reactions through direct association with histidine.![]()
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Affiliation(s)
- Moran Frenkel-Pinter
- NSF/NASA Center for Chemical Evolution USA .,School of Chemistry & Biochemistry, Georgia Institute of Technology Atlanta GA 30332 USA.,NASA Center for the Origins of Life, Georgia Institute of Technology Atlanta GA 30332 USA
| | - Alyssa B Sargon
- NSF/NASA Center for Chemical Evolution USA .,School of Chemistry & Biochemistry, Georgia Institute of Technology Atlanta GA 30332 USA
| | - Jennifer B Glass
- NASA Center for the Origins of Life, Georgia Institute of Technology Atlanta GA 30332 USA.,School of Earth and Atmospheric Science, Georgia Institute of Technology Atlanta GA 30332 USA
| | - Nicholas V Hud
- NSF/NASA Center for Chemical Evolution USA .,School of Chemistry & Biochemistry, Georgia Institute of Technology Atlanta GA 30332 USA.,NASA Center for the Origins of Life, Georgia Institute of Technology Atlanta GA 30332 USA
| | - Loren Dean Williams
- NSF/NASA Center for Chemical Evolution USA .,School of Chemistry & Biochemistry, Georgia Institute of Technology Atlanta GA 30332 USA.,NASA Center for the Origins of Life, Georgia Institute of Technology Atlanta GA 30332 USA
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87
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Navrotsky A, Hervig R, Lyons J, Seo DK, Shock E, Voskanyan A. Cooperative formation of porous silica and peptides on the prebiotic Earth. Proc Natl Acad Sci U S A 2021; 118:e2021117118. [PMID: 33376204 PMCID: PMC7812765 DOI: 10.1073/pnas.2021117118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Modern technology has perfected the synthesis of catalysts such as zeolites and mesoporous silicas using organic structure directing agents (SDA) and their industrial use to catalyze a large variety of organic reactions within their pores. We suggest that early in prebiotic evolution, synergistic interplay arose between organic species in aqueous solution and silica formed from rocks by dynamic dissolution-recrystallization. The natural organics, for example, amino acids, small peptides, and fatty acids, acted as SDA for assembly of functional porous silica structures that induced further polymerization of amino acids and peptides, as well as other organic reactions. Positive feedback between synthesis and catalysis in the silica-organic system may have accelerated the early stages of abiotic evolution by increasing the formation of polymerized species.
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Affiliation(s)
- Alexandra Navrotsky
- Center for Materials of the Universe, Arizona State University, Tempe, AZ 85287;
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287
- School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287
| | - Richard Hervig
- Center for Materials of the Universe, Arizona State University, Tempe, AZ 85287
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ 85287
| | - James Lyons
- Center for Materials of the Universe, Arizona State University, Tempe, AZ 85287
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ 85287
| | - Dong-Kyun Seo
- Center for Materials of the Universe, Arizona State University, Tempe, AZ 85287
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287
| | - Everett Shock
- Center for Materials of the Universe, Arizona State University, Tempe, AZ 85287
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ 85287
| | - Albert Voskanyan
- Center for Materials of the Universe, Arizona State University, Tempe, AZ 85287
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287
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88
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Wu LF, Liu Z, Sutherland JD. pH-Dependent peptide bond formation by the selective coupling of α-amino acids in water. Chem Commun (Camb) 2021; 57:73-76. [PMID: 33242043 PMCID: PMC7808311 DOI: 10.1039/d0cc06042a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 11/20/2020] [Indexed: 12/21/2022]
Abstract
A novel mechanism enabling selective peptide elongation by coupling α-amino acids over other potentially competing prebiotic amines under acidic aqueous condition is suggested. It proceeds via the generation of a carboxylic acid anhydride intermediate with subsequent intramolecular formation of the amide bond.
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Affiliation(s)
- Long-Fei Wu
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK.
| | - Ziwei Liu
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK.
| | - John D Sutherland
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK.
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89
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Van Kranendonk MJ, Baumgartner R, Djokic T, Ota T, Steller L, Garbe U, Nakamura E. Elements for the Origin of Life on Land: A Deep-Time Perspective from the Pilbara Craton of Western Australia. ASTROBIOLOGY 2021; 21:39-59. [PMID: 33404294 DOI: 10.1089/ast.2019.2107] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
For decades, deep sea hydrothermal vents have been a preferred setting for the Origin of Life, but "The Water Problem" as relates to polymerization of organic molecules, together with a propensity to dilute critical prebiotic elements as well as a number of other crucial factors, suggests that a terrestrial hot spring field with the capacity for wet-dry cycling and element concentration may represent a more likely candidate. Here, we investigate a 3.5 billion-year-old, anoxic hot spring setting from the Pilbara Craton (Australia) and show that its hydrothermal veins and compositionally varied pools and springs concentrated all of the essential elements required for prebiotic chemistry (including B, Zn, Mn, and K, in addition to C, H, N, O, P, and S). Temporal variability (seasonal to decadal), together with the known propensity of hot springs for wet-dry cycling and information exchange, would lead to innovation pools with peaks of fitness for developing molecules. An inference from the chemical complexity of the Pilbara analogue is that life could perhaps get started quickly on planets with volcanoes, silicate rocks, an exposed land surface, and water, ingredients that should form the backbone in the search for life in the Universe.
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Affiliation(s)
- Martin J Van Kranendonk
- Australian Centre for Astrobiology, School of Biological Earth and Environmental Sciences, University of New South Wales Sydney, Kensington, Australia
- Pheasant Memorial Laboratory, Institute for Planetary Materials, Okayama University, Misasa, Japan
| | - Raphael Baumgartner
- Australian Centre for Astrobiology, School of Biological Earth and Environmental Sciences, University of New South Wales Sydney, Kensington, Australia
| | - Tara Djokic
- Australian Centre for Astrobiology, School of Biological Earth and Environmental Sciences, University of New South Wales Sydney, Kensington, Australia
| | - Tsutomu Ota
- Pheasant Memorial Laboratory, Institute for Planetary Materials, Okayama University, Misasa, Japan
| | - Luke Steller
- Australian Centre for Astrobiology, School of Biological Earth and Environmental Sciences, University of New South Wales Sydney, Kensington, Australia
| | - Ulf Garbe
- Australian Nuclear Science and Technology Organisation, Kirrawee, Australia
| | - Eizo Nakamura
- Pheasant Memorial Laboratory, Institute for Planetary Materials, Okayama University, Misasa, Japan
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90
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Jia TZ, Wang PH, Niwa T, Mamajanov I. Connecting primitive phase separation to biotechnology, synthetic biology, and engineering. J Biosci 2021; 46:79. [PMID: 34373367 PMCID: PMC8342986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
One aspect of the study of the origins of life focuses on how primitive chemistries assembled into the first cells on Earth and how these primitive cells evolved into modern cells. Membraneless droplets generated from liquid-liquid phase separation (LLPS) are one potential primitive cell-like compartment; current research in origins of life includes study of the structure, function, and evolution of such systems. However, the goal of primitive LLPS research is not simply curiosity or striving to understand one of life's biggest unanswered questions, but also the possibility to discover functions or structures useful for application in the modern day. Many applicational fields, including biotechnology, synthetic biology, and engineering, utilize similar phaseseparated structures to accomplish specific functions afforded by LLPS. Here, we briefly review LLPS applied to primitive compartment research and then present some examples of LLPS applied to biomolecule purification, drug delivery, artificial cell construction, waste and pollution management, and flavor encapsulation. Due to a significant focus on similar functions and structures, there appears to be much for origins of life researchers to learn from those working on LLPS in applicational fields, and vice versa, and we hope that such researchers can start meaningful cross-disciplinary collaborations in the future.
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Affiliation(s)
- Tony Z Jia
- grid.32197.3e0000 0001 2179 2105Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550 Japan ,grid.482804.2Blue Marble Space Institute of Science, 1001 4th Ave., Suite 3201, Seattle, Washington 98154 USA
| | - Po-Hsiang Wang
- grid.32197.3e0000 0001 2179 2105Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550 Japan ,grid.37589.300000 0004 0532 3167Graduate Institute of Environmental Engineering, National Central University, Zhongli Dist, 300 Zhongda Rd, Taoyuan City, 32001 Taiwan
| | - Tatsuya Niwa
- grid.32197.3e0000 0001 2179 2105Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, 226-8503 Japan
| | - Irena Mamajanov
- grid.32197.3e0000 0001 2179 2105Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550 Japan
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91
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Tran QP, Adam ZR, Fahrenbach AC. Prebiotic Reaction Networks in Water. Life (Basel) 2020; 10:E352. [PMID: 33339192 PMCID: PMC7765580 DOI: 10.3390/life10120352] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/05/2020] [Accepted: 12/06/2020] [Indexed: 02/07/2023] Open
Abstract
A prevailing strategy in origins of life studies is to explore how chemistry constrained by hypothetical prebiotic conditions could have led to molecules and system level processes proposed to be important for life's beginnings. This strategy has yielded model prebiotic reaction networks that elucidate pathways by which relevant compounds can be generated, in some cases, autocatalytically. These prebiotic reaction networks provide a rich platform for further understanding and development of emergent "life-like" behaviours. In this review, recent advances in experimental and analytical procedures associated with classical prebiotic reaction networks, like formose and Miller-Urey, as well as more recent ones are highlighted. Instead of polymeric networks, i.e., those based on nucleic acids or peptides, the focus is on small molecules. The future of prebiotic chemistry lies in better understanding the genuine complexity that can result from reaction networks and the construction of a centralised database of reactions useful for predicting potential network evolution is emphasised.
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Affiliation(s)
| | - Zachary R. Adam
- Department of Planetary Sciences, University of Arizona, Tucson, AZ 85721, USA;
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92
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Prebiotic chemistry and origins of life research with atomistic computer simulations. Phys Life Rev 2020; 34-35:105-135. [DOI: 10.1016/j.plrev.2018.09.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 09/10/2018] [Indexed: 02/02/2023]
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93
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AFM Images of Viroid-Sized Rings That Self-Assemble from Mononucleotides through Wet-Dry Cycling: Implications for the Origin of Life. Life (Basel) 2020; 10:life10120321. [PMID: 33266191 PMCID: PMC7760185 DOI: 10.3390/life10120321] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 11/25/2020] [Accepted: 11/26/2020] [Indexed: 11/17/2022] Open
Abstract
It is possible that early life relied on RNA polymers that served as ribozyme-like catalysts and for storing genetic information. The source of such polymers is uncertain, but previous investigations reported that wet–dry cycles simulating prebiotic hot springs provide sufficient energy to drive condensation reactions of mononucleotides to form oligomers. The aim of the study reported here was to visualize the products by atomic force microscopy. In addition to globular oligomers, ring-like structures ranging from 10–200 nm in diameter, with an average around 30–40 nm, were abundant, particularly when nucleotides capable of base pairing were present. The thickness of the rings was consistent with single stranded products, but some had thicknesses indicating base pair stacking. Others had more complex structures in the form of short polymer attachments and pairing of rings. These observations suggest the possibility that base-pairing may promote polymerization during wet–dry cycling followed by solvation of the rings. We conclude that RNA-like rings and structures could have been synthesized non-enzymatically on the prebiotic Earth, with sizes sufficient to fold into ribozymes and genetic molecules required for life to begin.
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94
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Fares HM, Marras AE, Ting JM, Tirrell MV, Keating CD. Impact of wet-dry cycling on the phase behavior and compartmentalization properties of complex coacervates. Nat Commun 2020; 11:5423. [PMID: 33110067 PMCID: PMC7592044 DOI: 10.1038/s41467-020-19184-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 10/02/2020] [Indexed: 11/16/2022] Open
Abstract
Wet-dry cycling on the early Earth is thought to have facilitated production of molecular building blocks of life, but its impact on self-assembly and compartmentalization remains largely unexplored. Here, we investigate dehydration/rehydration of complex coacervates, which are membraneless compartments formed by phase separation of polyelectrolyte solutions. Solution compositions are identified for which tenfold water loss results in maintenance, disappearance, or appearance of coacervate droplets. Systems maintaining coacervates throughout the dehydration process are further evaluated to understand how their compartmentalization properties change with drying. Although added total RNA concentrations increase tenfold, RNA concentration within coacervates remains steady. Exterior RNA concentrations rise, and exchange rates for encapsulated versus free RNAs increase with dehydration. We explain these results in light of the phase diagram, with dehydration-driven ionic strength increase being particularly important in determining coacervate properties. This work shows that wet-dry cycling can alter the phase behavior and protocell-relevant functions of complex coacervates. Wet-dry cycling is thought to have enabled the production of molecular building blocks of life. Here, the authors investigate the impact of dehydration/rehydration on RNA-containing complex coacervates, which are membraneless compartments formed by phase separation of polyelectrolyte solutions.
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Affiliation(s)
- Hadi M Fares
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA.,NASA Postdoctoral Program, Universities Space Research Association, Columbia, MD, 21046, USA
| | - Alexander E Marras
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA.,Center for Molecular Engineering and Materials Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Jeffrey M Ting
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA.,Center for Molecular Engineering and Materials Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA.,3M Company, 3M Center, Saint Paul, MN, 55144, USA
| | - Matthew V Tirrell
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA.,Center for Molecular Engineering and Materials Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Christine D Keating
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA.
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95
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Liquid Crystal Peptide/DNA Coacervates in the Context of Prebiotic Molecular Evolution. CRYSTALS 2020. [DOI: 10.3390/cryst10110964] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Liquid–liquid phase separation (LLPS) phenomena are ubiquitous in biological systems, as various cellular LLPS structures control important biological processes. Due to their ease of in vitro assembly into membraneless compartments and their presence within modern cells, LLPS systems have been postulated to be one potential form that the first cells on Earth took on. Recently, liquid crystal (LC)-coacervate droplets assembled from aqueous solutions of short double-stranded DNA (s-dsDNA) and poly-L-lysine (PLL) have been reported. Such LC-coacervates conjugate the advantages of an associative LLPS with the relevant long-range ordering and fluidity properties typical of LC, which reflect and propagate the physico-chemical properties of their molecular constituents. Here, we investigate the structure, assembly, and function of DNA LC-coacervates in the context of prebiotic molecular evolution and the emergence of functional protocells on early Earth. We observe through polarization microscopy that LC-coacervate systems can be dynamically assembled and disassembled based on prebiotically available environmental factors including temperature, salinity, and dehydration/rehydration cycles. Based on these observations, we discuss how LC-coacervates can in principle provide selective pressures effecting and sustaining chemical evolution within partially ordered compartments. Finally, we speculate about the potential for LC-coacervates to perform various biologically relevant properties, such as segregation and concentration of biomolecules, catalysis, and scaffolding, potentially providing additional structural complexity, such as linearization of nucleic acids and peptides within the LC ordered matrix, that could have promoted more efficient polymerization. While there are still a number of remaining open questions regarding coacervates, as protocell models, including how modern biologies acquired such membraneless organelles, further elucidation of the structure and function of different LLPS systems in the context of origins of life and prebiotic chemistry could provide new insights for understanding new pathways of molecular evolution possibly leading to the emergence of the first cells on Earth.
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96
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Affiliation(s)
- Andreas Kirschning
- Institut für Organische Chemie und Biomolekulares Wirkstoffzentrum (BMWZ) Leibniz Universität Hannover Schneiderberg 1B 30167 Hannover Deutschland
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97
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Chandru K, Jia TZ, Mamajanov I, Bapat N, Cleaves HJ. Prebiotic oligomerization and self-assembly of structurally diverse xenobiological monomers. Sci Rep 2020; 10:17560. [PMID: 33067516 PMCID: PMC7567815 DOI: 10.1038/s41598-020-74223-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 09/22/2020] [Indexed: 02/07/2023] Open
Abstract
Prebiotic chemists often study how modern biopolymers, e.g., peptides and nucleic acids, could have originated in the primitive environment, though most contemporary biomonomers don't spontaneously oligomerize under mild conditions without activation or catalysis. However, life may not have originated using the same monomeric components that it does presently. There may be numerous non-biological (or "xenobiological") monomer types that were prebiotically abundant and capable of facile oligomerization and self-assembly. Many modern biopolymers degrade abiotically preferentially via processes which produce thermodynamically stable ring structures, e.g. diketopiperazines in the case of proteins and 2', 3'-cyclic nucleotide monophosphates in the case of RNA. This weakness is overcome in modern biological systems by kinetic control, but this need not have been the case for primitive systems. We explored here the oligomerization of a structurally diverse set of prebiotically plausible xenobiological monomers, which can hydrolytically interconvert between cyclic and acyclic forms, alone or in the presence of glycine under moderate temperature drying conditions. These monomers included various lactones, lactams and a thiolactone, which varied markedly in their stability, propensity to oligomerize and apparent modes of initiation, and the oligomeric products of some of these formed self-organized microscopic structures which may be relevant to protocell formation.
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Affiliation(s)
- Kuhan Chandru
- Space Science Center (ANGKASA), Institute of Climate Change, Level 3, Research Complex, National University of Malaysia, UKM, 43600, Bangi, Selangor, Malaysia.
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technicka 5, 16628, Prague 6-Dejvice, Czech Republic.
| | - Tony Z Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
- Blue Marble Space Institute for Science, 1001 4th Ave, Suite 3201, Seattle, WA, 98154, USA
| | - Irena Mamajanov
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Niraja Bapat
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, Maharashtra, 411 008, India
| | - H James Cleaves
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
- Blue Marble Space Institute for Science, 1001 4th Ave, Suite 3201, Seattle, WA, 98154, USA
- Institute for Advanced Study, 1 Einstein Drive, Princeton, NJ, 08540, USA
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98
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Chien CY, Yu SS. Ester-mediated peptide formation promoted by deep eutectic solvents: a facile pathway to proto-peptides. Chem Commun (Camb) 2020; 56:11949-11952. [PMID: 32929424 DOI: 10.1039/d0cc03319g] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The ester-amide exchange reaction enables spontaneous formation of prebiotic proto-peptides under mild conditions. However, this reaction also leads to oligomers with a vast sequence diversity of ester and amide linkages. Here, we demonstrate using deep eutectic solvents as a universal strategy to regulate the reaction pathways and promote the formation of amino acid-enriched oligomers with peptide backbones.
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Affiliation(s)
- Chen-Yu Chien
- Department of Chemical Engineering, National Cheng Kung University, No. 1 University Road, Tainan City, 70101, Taiwan, Republic of China.
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99
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Kovalenko SP. Physicochemical Processes That Probably Originated Life. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162020040093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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100
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Parker ET, Karki M, Glavin DP, Dworkin JP, Krishnamurthy R. A sensitive quantitative analysis of abiotically synthesized short homopeptides using ultraperformance liquid chromatography and time-of-flight mass spectrometry. J Chromatogr A 2020; 1630:461509. [PMID: 32927393 DOI: 10.1016/j.chroma.2020.461509] [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: 06/05/2020] [Revised: 08/04/2020] [Accepted: 08/22/2020] [Indexed: 10/23/2022]
Abstract
In the origins of life field understanding the abiotic polymerization of simple organic monomers (e.g., amino acids) into larger biomolecules (e.g., oligopeptides), remains a seminal challenge. Recently, preliminary observations showed a limited set of peptides formed in the presence of the plausible prebiotic phosphorylating agent, diamidophosphate (DAP), highlighting the need for an analytical tool to critically evaluate the ability of DAP to induce oligomerization of simple organics under aqueous conditions. However, performing accurate and precise, targeted analyses of short oligopeptides remains a distinct challenge in the analytical chemistry field. Here, we developed a new technique to detect and quantitate amino acids and their homopeptides in a single run using ultraperformance liquid chromatography-fluorescence detection/time of flight mass spectrometry. Over an 8-minute retention time window, 18 target analytes were identified and quantitated, 16 of which were chromatographically separated at, or near baseline resolution. Compound identity was confirmed by accurate mass analysis using a 10 ppm mass tolerance window. This method featured limits of detection < 5 nM (< 1 fmol on column) and limits of quantitation (LOQs) <15 nM (< 3 fmol on column). The LODs and LOQs were upwards of ∼28x and ∼788x lower, respectively, than previous methods for the same analytes, highlighting the quantifiable advantages of this new method. Both detectors provided good quantitative linearity (R2 > 0.985) for all analytes spanning concentration ranges ∼3 - 4 orders of magnitude. We performed a series of laboratory experiments to investigate DAP-mediated oligomerization of amino acids and peptides and analyzed experimental products with the new method. DAP readily polymerized amino acids and peptides under a range of simulated environmental conditions. This research underscores the potential of DAP to have generated oligopeptides on the primordial Earth, enhancing prebiotic chemical diversity and complexity at or near the origin of life.
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Affiliation(s)
- Eric T Parker
- NASA Goddard Space Flight Center, Solar System Exploration Division, 8800 Greenbelt Road, Greenbelt, MD 20771, United States
| | - Megha Karki
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Daniel P Glavin
- NASA Goddard Space Flight Center, Solar System Exploration Division, 8800 Greenbelt Road, Greenbelt, MD 20771, United States
| | - Jason P Dworkin
- NASA Goddard Space Flight Center, Solar System Exploration Division, 8800 Greenbelt Road, Greenbelt, MD 20771, United States.
| | - Ramanarayanan Krishnamurthy
- Department of Chemistry, Scripps Research, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States.
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