1
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Seitz C, Geisberger T, West AR, Fertl J, Eisenreich W, Huber C. From Zero to Hero: The Cyanide-Free Formation of Amino Acids and Amides from Acetylene, Ammonia and Carbon Monoxide in Aqueous Environments in a Simulated Hadean Scenario. Life (Basel) 2024; 14:719. [PMID: 38929702 PMCID: PMC11204499 DOI: 10.3390/life14060719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
Amino acids are one of the most important building blocks of life. During the biochemical process of translation, cells sequentially connect amino acids via amide bonds to synthesize proteins, using the genetic information in messenger RNA (mRNA) as a template. From a prebiotic perspective (i.e., without enzymatic catalysis), joining amino acids to peptides via amide bonds is difficult due to the highly endergonic nature of the condensation reaction. We show here that amides can be formed in reactions catalyzed by the transition metal sulfides from acetylene, carbon monoxide and ammonia under aqueous conditions. Some α- and β-amino acids were also formed under the same conditions, demonstrating an alternative cyanide-free path for the formation of amino acids in prebiotic environments. Experiments performed with stable isotope labeled precursors, like 15NH4Cl and 13C-acetylene, enabled the accurate mass spectroscopic identification of the products formed from the starting materials and their composition. Reactions catalyzed using the transition metal sulfides seem to offer a promising alternative pathway for the formation of amides and amino acids in prebiotic environments, bypassing the challenges posed by the highly endergonic condensation reaction. These findings shed light on the potential mechanisms by which the building blocks of life could have originated on early Earth.
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Affiliation(s)
| | | | | | | | | | - Claudia Huber
- Bayerisches NMR Zentrum, Strukturelle Membranbiochemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany; (C.S.); (T.G.); (A.R.W.); (J.F.); (W.E.)
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2
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Li F, Weng K, Tanaka T, He J, Zheng H, Noda D, Irifune S, Sato H. Fabrication of Waterborne Silicone-Modified Polyurethane Nanofibers for Nonfluorine Elastic Waterproof and Breathable Membranes. Polymers (Basel) 2024; 16:1505. [PMID: 38891452 PMCID: PMC11174452 DOI: 10.3390/polym16111505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024] Open
Abstract
Waterproof and breathable membranes have a huge market demand in areas, such as textiles and medical protection. However, existing fluorinated nanofibrous membranes, while possessing good waterproof and breathable properties, pose health and environmental hazards. Consequently, fabricating fluorine-free, eco-friendly waterborne membranes by integrating outstanding waterproofing, breathability, and robust mechanical performance remains a significant challenge. Herein, we successfully prepared waterborne silicone-modified polyurethane nanofibrous membranes with excellent elasticity, waterproofing, and breathability properties through waterborne electrospinning, using a small quantity of poly(ethylene oxide) as a template polymer and in situ doping of the poly(carbodiimide) crosslinking agent, followed by a simple hot-pressing treatment. The silicone imparted the nanofibrous membrane with high hydrophobicity, and the crosslinking agent enabled its stable porous structure. The hot-pressing treatment (120 °C) further reduced the pore size and improved the water resistance. This environmentally friendly nanofibrous membrane showed a high elongation at break of 428%, an ultra-high elasticity of 67.5% (160 cycles under 400% tensile strain), an air transmission of 13.2 mm s-1, a water vapor transmission rate of 5476 g m-2 d-1, a hydrostatic pressure of 51.5 kPa, and a static water contact angle of 137.9°. The successful fabrication of these environmentally friendly, highly elastic membranes provides an important reference for applications in healthcare, protective textiles, and water purification.
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Affiliation(s)
- Fang Li
- Interdisciplinary Graduate School of Science and Technology, Shinshu University, 3-15-1, Tokida, Ueda-shi 386-8567, Nagano, Japan; (F.L.); (K.W.)
| | - Kai Weng
- Interdisciplinary Graduate School of Science and Technology, Shinshu University, 3-15-1, Tokida, Ueda-shi 386-8567, Nagano, Japan; (F.L.); (K.W.)
| | - Toshihisa Tanaka
- Interdisciplinary Graduate School of Science and Technology, Shinshu University, 3-15-1, Tokida, Ueda-shi 386-8567, Nagano, Japan; (F.L.); (K.W.)
| | - Jianxin He
- International Joint Laboratory of New Textile Materials and Textiles of Henan Province, Zhongyuan University of Technology, Zhengzhou 450007, China
| | - Haimin Zheng
- International Joint Laboratory of New Textile Materials and Textiles of Henan Province, Zhongyuan University of Technology, Zhengzhou 450007, China
| | - Daisuke Noda
- Silicone-Electronics Materials Research Center, Shin-Etsu Chemical Co., Ltd., 1-10, Hitomi, Matsuida-Machi, Annaka-shi 379-0224, Gunma, Japan
| | - Shinji Irifune
- Silicone-Electronics Materials Research Center, Shin-Etsu Chemical Co., Ltd., 1-10, Hitomi, Matsuida-Machi, Annaka-shi 379-0224, Gunma, Japan
| | - Hiromasa Sato
- Dainichiseika Color & Chemicals Mfg. Co., Ltd., 2087-4, Ohta, Sakura-shi 285-0808, Chiba, Japan
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3
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David R, Tuñón I, Laage D. Competing Reaction Mechanisms of Peptide Bond Formation in Water Revealed by Deep Potential Molecular Dynamics and Path Sampling. J Am Chem Soc 2024; 146:14213-14224. [PMID: 38739765 DOI: 10.1021/jacs.4c03445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The formation of an amide bond is an essential step in the synthesis of materials and drugs, and in the assembly of amino acids to form peptides. The mechanism of this reaction has been studied extensively, in particular to understand how it can be catalyzed, but a representation capable of explaining all the experimental data is still lacking. Numerical simulation should provide the necessary molecular description, but the solvent involvement poses a number of challenges. Here, we combine the efficiency and accuracy of neural network potential-based reactive molecular dynamics with the extensive and unbiased exploration of reaction pathways provided by transition path sampling. Using microsecond-scale simulations at the density functional theory level, we show that this method reveals the presence of two competing distinct mechanisms for peptide bond formation between alanine esters in aqueous solution. We describe how both reaction pathways, via a general base catalysis mechanism and via direct cleavage of the tetrahedral intermediate respectively, change with pH. This result contrasts with the conventional mechanism involving a single pathway in which only the barrier heights are affected by pH. We show that this new proposal involving two competing mechanisms is consistent with the experimental data, and we discuss the implications for peptide bond formation under prebiotic conditions and in the ribosome. Our work shows that integrating deep potential molecular dynamics with path sampling provides a powerful approach for exploring complex chemical mechanisms.
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Affiliation(s)
- Rolf David
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Iñaki Tuñón
- Departamento de Química Física, Universitat de Valencia, Burjassot, 46100 Valencia, Spain
| | - Damien Laage
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
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4
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Rezaeerod K, Heinzmann H, Torrence AV, Patel J, Forsythe JG. Qualitative Monitoring of Proto-Peptide Condensation by Differential FTIR Spectroscopy. ACS EARTH & SPACE CHEMISTRY 2024; 8:937-944. [PMID: 38774359 PMCID: PMC11103710 DOI: 10.1021/acsearthspacechem.3c00257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/24/2024]
Abstract
Condensation processes such as wet-dry cycling are thought to have played significant roles in the emergence of proto-peptides. Here, we describe a simple and low-cost method, differential Fourier transform infrared (FTIR) spectroscopy, for qualitative analysis of peptide condensation products in model primordial reactions. We optimize differential FTIR for depsipeptides and apply this method to investigate their polymerization in the presence of extraterrestrial dust simulants.
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Affiliation(s)
- Keon Rezaeerod
- Department
of Chemistry and Biochemistry, College of
Charleston, Charleston, South Carolina 29424, United States
| | - Hanna Heinzmann
- Department
of Chemistry and Biochemistry, College of
Charleston, Charleston, South Carolina 29424, United States
- Analytical
and Bioanalytical Chemistry, Aalen University, 73430 Aalen, Germany
| | - Alexis V. Torrence
- Department
of Chemistry and Biochemistry, College of
Charleston, Charleston, South Carolina 29424, United States
| | - Jui Patel
- Department
of Chemistry and Biochemistry, College of
Charleston, Charleston, South Carolina 29424, United States
| | - Jay G. Forsythe
- Department
of Chemistry and Biochemistry, College of
Charleston, Charleston, South Carolina 29424, United States
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5
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Samrout OE, Berlier G, Lambert JF. Amino Acid Polymerization on Silica Surfaces. Chempluschem 2024; 89:e202300642. [PMID: 38226922 DOI: 10.1002/cplu.202300642] [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: 11/11/2023] [Revised: 01/05/2024] [Accepted: 01/15/2024] [Indexed: 01/17/2024]
Abstract
The polymerization of unactivated amino acids (AAs) is an important topic because of its applications in various fields including industrial medicinal chemistry and prebiotic chemistry. Silica as a promoter for this reaction, is of great interest owing to its large abundance and low cost. The amide/peptide bond synthesis on silica has been largely demonstrated but suffers from a lack of knowledge regarding its reaction mechanism, the key parameters, and surface features that influence AA adsorption and reactivity, the selectivity of the reaction product, the role of water in the reaction, etc. The present review addresses these problems by summarizing experimental and modeling results from the literature and attempts to rationalize some apparent divergences in published results. After briefly presenting the main types of silica surface sites and other relevant macroscopic features, we discuss the different deposition procedures of AAs, whose importance is often neglected. We address the possible AA adsorption mechanisms including covalent grafting and H-bonding and show that they are highly dependent on silanol types and density. We then consider how the adsorption mechanisms determine the occurrence and outcome of AA condensation (formation of cyclic dimers or of long linear chains), and outline some recent results that suggest significant polymerization selectivity in systems containing several AAs, as well as the formation of specific elements of secondary structure in the growing polypeptide chains.
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Affiliation(s)
- Ola El Samrout
- Department of Chemistry, University of Torino, Via P. Giuria 7, 10125, Torino, Italy
| | - Gloria Berlier
- Department of Chemistry, University of Torino, Via P. Giuria 7, 10125, Torino, Italy
| | - Jean-François Lambert
- Laboratoire de Réactivité de Surface, LRS, Sorbonne Université Place Jussieu, 75005, Paris, France
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6
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Zhang L, Ying J. Amino acid analogues provide multiple plausible pathways to prebiotic peptides. J R Soc Interface 2024; 21:20240014. [PMID: 38715323 PMCID: PMC11077012 DOI: 10.1098/rsif.2024.0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/18/2024] [Indexed: 05/12/2024] Open
Abstract
Prebiotic peptide synthesis has consistently been a prominent topic within the field of the origin of life. While research predominantly centres on the 20 classical amino acids, the synthesis process encounters significant thermodynamic barriers. Consequently, amino acid analogues are being explored as potential building blocks for prebiotic peptide synthesis. This review delves into the pathway of polypeptide formation, identifying specific amino acid analogues that might have existed on early Earth, potentially participating in peptide synthesis and chemical evolution. Moreover, considering the complexity and variability of the environment on early Earth, we propose the plausibility of coevolution between amino acids and their analogues.
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Affiliation(s)
- Li Zhang
- Institute of Drug Discovery Technology, Ningbo University, No. 818 Fenghua Road, Ningbo, Zhejiang 315211, People's Republic of China
| | - Jianxi Ying
- Institute of Drug Discovery Technology, Ningbo University, No. 818 Fenghua Road, Ningbo, Zhejiang 315211, People's Republic of China
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7
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Cohen ZR, Todd ZR, Maibaum L, Catling DC, Black RA. Stabilization of Prebiotic Vesicles by Peptides Depends on Sequence and Chirality: A Mechanism for Selection of Protocell-Associated Peptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:8971-8980. [PMID: 38629792 DOI: 10.1021/acs.langmuir.4c00150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Cells require oligonucleotides and polypeptides with specific, homochiral sequences to perform essential functions, but it is unclear how such oligomers were selected from random sequences at the origin of life. Cells were probably preceded by simple compartments such as fatty acid vesicles, and oligomers that increased the stability, growth, or division of vesicles could have thereby increased in frequency. We therefore tested whether prebiotic peptides alter the stability or growth of vesicles composed of a prebiotic fatty acid. We find that three of 15 dipeptides tested reduce salt-induced flocculation of vesicles. All three contain leucine, and increasing their length increases the efficacy. Also, leucine-leucine but not alanine-alanine increases the size of vesicles grown by multiple additions of micelles. In a molecular simulation, leucine-leucine docks to the membrane, with the side chains inserted into the hydrophobic core of the bilayer, while alanine-alanine fails to dock. Finally, the heterochiral forms of leucine-leucine, at a high concentration, rapidly shrink the vesicles and make them leakier and less stable to high pH than the homochiral forms do. Thus, prebiotic peptide-membrane interactions influence the flocculation, growth, size, leakiness, and pH stability of prebiotic vesicles, with differential effects due to sequence, length, and chirality. These differences could lead to a population of vesicles enriched for peptides with beneficial sequence and chirality, beginning selection for the functional oligomers that underpin life.
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Affiliation(s)
- Zachary R Cohen
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Zoe R Todd
- Department of Earth and Space Science, University of Washington, Seattle, Washington 98195, United States
| | - Lutz Maibaum
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - David C Catling
- Department of Earth and Space Science, University of Washington, Seattle, Washington 98195, United States
| | - Roy A Black
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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8
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Verma A, Mateo T, Quintero Botero J, Mohankumar N, Fraccia TP. Microfluidics-Based Drying-Wetting Cycles to Investigate Phase Transitions of Small Molecules Solutions. Life (Basel) 2024; 14:472. [PMID: 38672743 PMCID: PMC11050796 DOI: 10.3390/life14040472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/24/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
Drying-wetting cycles play a crucial role in the investigation of the origin of life as processes that both concentrate and induce the supramolecular assembly and polymerization of biomolecular building blocks, such as nucleotides and amino acids. Here, we test different microfluidic devices to study the dehydration-hydration cycles of the aqueous solutions of small molecules, and to observe, by optical microscopy, the insurgence of phase transitions driven by self-assembly, exploiting water pervaporation through polydimethylsiloxane (PDMS). As a testbed, we investigate solutions of the chromonic dye Sunset Yellow (SSY), which self-assembles into face-to-face columnar aggregates and produces nematic and columnar liquid crystal (LC) phases as a function of concentration. We show that the LC temperature-concentration phase diagram of SSY can be obtained with a fair agreement with previous reports, that droplet hydration-dehydration can be reversibly controlled and automated, and that the simultaneous incubation of samples with different final water contents, corresponding to different phases, can be implemented. These methods can be further extended to study the assembly of diverse prebiotically relevant small molecules and to characterize their phase transitions.
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Affiliation(s)
- Ajay Verma
- IPGG, CBI UMR 8231—CNRS—ESPCI Paris, PSL Research University, 75005 Paris, France
| | - Tiphaine Mateo
- IPGG, CBI UMR 8231—CNRS—ESPCI Paris, PSL Research University, 75005 Paris, France
| | | | - Nishanth Mohankumar
- IPGG, CBI UMR 8231—CNRS—ESPCI Paris, PSL Research University, 75005 Paris, France
| | - Tommaso P. Fraccia
- IPGG, CBI UMR 8231—CNRS—ESPCI Paris, PSL Research University, 75005 Paris, France
- Department of Pharmacological and Biomolecular Sciences, University of Milan, 20133 Milan, Italy
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9
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Maguire OR, Smokers IBA, Oosterom BG, Zheliezniak A, Huck WTS. A Prebiotic Precursor to Life's Phosphate Transfer System with an ATP Analog and Histidyl Peptide Organocatalysts. J Am Chem Soc 2024; 146:7839-7849. [PMID: 38448161 PMCID: PMC10958518 DOI: 10.1021/jacs.4c01156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 03/08/2024]
Abstract
Biochemistry is dependent upon enzyme catalysts accelerating key reactions. At the origin of life, prebiotic chemistry must have incorporated catalytic reactions. While this would have yielded much needed amplification of certain reaction products, it would come at the possible cost of rapidly depleting the high energy molecules that acted as chemical fuels. Biochemistry solves this problem by combining kinetically stable and thermodynamically activated molecules (e.g., ATP) with enzyme catalysts. Here, we demonstrate a prebiotic phosphate transfer system involving an ATP analog (imidazole phosphate) and histidyl peptides, which function as organocatalytic enzyme analogs. We demonstrate that histidyl peptides catalyze phosphorylations via a phosphorylated histidyl intermediate. We integrate these histidyl-catalyzed phosphorylations into a complete prebiotic scenario whereby inorganic phosphate is incorporated into organic compounds though physicochemical wet-dry cycles. Our work demonstrates a plausible system for the catalyzed production of phosphorylated compounds on the early Earth and how organocatalytic peptides, as enzyme precursors, could have played an important role in this.
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Affiliation(s)
- Oliver R. Maguire
- Institute for Molecules and
Materials, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen AJ 6525, The Netherlands
| | - Iris B. A. Smokers
- Institute for Molecules and
Materials, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen AJ 6525, The Netherlands
| | - Bob G. Oosterom
- Institute for Molecules and
Materials, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen AJ 6525, The Netherlands
| | - Alla Zheliezniak
- Institute for Molecules and
Materials, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen AJ 6525, The Netherlands
| | - Wilhelm T. S. Huck
- Institute for Molecules and
Materials, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen AJ 6525, The Netherlands
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10
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Rodriguez LE, Altair T, Hermis NY, Jia TZ, Roche TP, Steller LH, Weber JM. Chapter 4: A Geological and Chemical Context for the Origins of Life on Early Earth. ASTROBIOLOGY 2024; 24:S76-S106. [PMID: 38498817 DOI: 10.1089/ast.2021.0139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Within the first billion years of Earth's history, the planet transformed from a hot, barren, and inhospitable landscape to an environment conducive to the emergence and persistence of life. This chapter will review the state of knowledge concerning early Earth's (Hadean/Eoarchean) geochemical environment, including the origin and composition of the planet's moon, crust, oceans, atmosphere, and organic content. It will also discuss abiotic geochemical cycling of the CHONPS elements and how these species could have been converted to biologically relevant building blocks, polymers, and chemical networks. Proposed environments for abiogenesis events are also described and evaluated. An understanding of the geochemical processes under which life may have emerged can better inform our assessment of the habitability of other worlds, the potential complexity that abiotic chemistry can achieve (which has implications for putative biosignatures), and the possibility for biochemistries that are vastly different from those on Earth.
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Affiliation(s)
- Laura E Rodriguez
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- Lunar and Planetary Institute, Universities Space Research Association, Houston, Texas, USA. (Current)
| | - Thiago Altair
- Institute of Chemistry of São Carlos, Universidade de São Paulo, São Carlos, Brazil
- Department of Chemistry, College of the Atlantic, Bar Harbor, Maine, USA. (Current)
| | - Ninos Y Hermis
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- Department of Physics and Space Sciences, University of Granada, Granada Spain. (Current)
| | - Tony Z Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo, Japan
- Blue Marble Space Institute of Science, Seattle, Washington, USA
| | - Tyler P Roche
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Luke H Steller
- Australian Centre for Astrobiology, and School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, Australia
| | - Jessica M Weber
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
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11
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Haugerud IS, Jaiswal P, Weber CA. Nonequilibrium Wet-Dry Cycling Acts as a Catalyst for Chemical Reactions. J Phys Chem B 2024; 128:1724-1736. [PMID: 38335971 PMCID: PMC10895654 DOI: 10.1021/acs.jpcb.3c05824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Abstract
Recent experimental studies suggest that wet-dry cycles and coexisting phases can each strongly alter chemical processes. The mechanisms of why and to what degree chemical processes are altered when subjected to evaporation and condensation are unclear. To close this gap, we developed a theoretical framework for nondilute chemical reactions subject to nonequilibrium conditions of evaporation and condensation. We find that such conditions can change the half-time of the product's yield by more than an order of magnitude, depending on the substrate-solvent interaction. We show that the cycle frequency strongly affects the chemical turnover when the system is maintained out of equilibrium by wet-dry cycles. There exists a resonance behavior in the cycle frequency where the turnover is maximal. This resonance behavior enables wet-dry cycles to select specific chemical reactions, suggesting a potential mechanism for chemical evolution in prebiotic soups at early Earth.
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Affiliation(s)
- Ivar Svalheim Haugerud
- Faculty of Mathematics, Natural Sciences, and Materials Engineering: Institute of Physics, University of Augsburg, Universitätsstraße 1, Augsburg 86159, Germany
| | - Pranay Jaiswal
- Faculty of Mathematics, Natural Sciences, and Materials Engineering: Institute of Physics, University of Augsburg, Universitätsstraße 1, Augsburg 86159, Germany
| | - Christoph A Weber
- Faculty of Mathematics, Natural Sciences, and Materials Engineering: Institute of Physics, University of Augsburg, Universitätsstraße 1, Augsburg 86159, Germany
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12
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Qiu L, Cooks RG. Oxazolone mediated peptide chain extension and homochirality in aqueous microdroplets. Proc Natl Acad Sci U S A 2024; 121:e2309360120. [PMID: 38165938 PMCID: PMC10786291 DOI: 10.1073/pnas.2309360120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 11/20/2023] [Indexed: 01/04/2024] Open
Abstract
Peptide formation from amino acids is thermodynamically unfavorable but a recent study provided evidence that the reaction occurs at the air/solution interfaces of aqueous microdroplets. Here, we show that i) the suggested amino acid complex in microdroplets undergoes dehydration to form oxazolone; ii) addition of water to oxazolone forms the dipeptide; and iii) reaction of oxazolone with other amino acids forms tripeptides. Furthermore, the chirality of the reacting amino acids is preserved in the oxazolone product, and strong chiral selectivity is observed when converting the oxazolone to tripeptide. This last fact ensures that optically impure amino acids will undergo chain extension to generate pure homochiral peptides. Peptide formation in bulk by wet-dry cycling shares a common pathway with the microdroplet reaction, both involving the oxazolone intermediate.
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Affiliation(s)
- Lingqi Qiu
- Department of Chemistry, Purdue University, West Lafayette, IN47907
| | - R. Graham Cooks
- Department of Chemistry, Purdue University, West Lafayette, IN47907
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13
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Toparlak Ö, Sebastianelli L, Egas Ortuno V, Karki M, Xing Y, Szostak JW, Krishnamurthy R, Mansy SS. Cyclophospholipids Enable a Protocellular Life Cycle. ACS NANO 2023; 17:23772-23783. [PMID: 38038709 PMCID: PMC10722605 DOI: 10.1021/acsnano.3c07706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 12/02/2023]
Abstract
There is currently no plausible path for the emergence of a self-replicating protocell, because prevalent formulations of model protocells are built with fatty acid vesicles that cannot withstand the concentrations of Mg2+ needed for the function and replication of nucleic acids. Although prebiotic chelates increase the survivability of fatty acid vesicles, the resulting model protocells are incapable of growth and division. Here, we show that protocells made of mixtures of cyclophospholipids and fatty acids can grow and divide in the presence of Mg2+-citrate. Importantly, these protocells retain encapsulated nucleic acids during growth and division, can acquire nucleotides from their surroundings, and are compatible with the nonenzymatic extension of an RNA oligonucleotide, chemistry needed for the replication of a primitive genome. Our work shows that prebiotically plausible mixtures of lipids form protocells that are active under the conditions necessary for the emergence of Darwinian evolution.
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Affiliation(s)
- Ö.
Duhan Toparlak
- Department
of Cellular, Computational and Integrative Biology, University of Trento, Via Sommarive 9, 38123 Povo, Trentino, Italy
| | - Lorenzo Sebastianelli
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton Alberta T6G 2G2, Canada
| | - Veronica Egas Ortuno
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Megha Karki
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Yanfeng Xing
- Department
of Biochemistry and Molecular Biology, University
of Chicago, Chicago, Illinois 60637, United States
| | - Jack W. Szostak
- Howard
Hughes Medical Institute, Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Ramanarayanan Krishnamurthy
- Department
of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Sheref S. Mansy
- Department
of Cellular, Computational and Integrative Biology, University of Trento, Via Sommarive 9, 38123 Povo, Trentino, Italy
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton Alberta T6G 2G2, Canada
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14
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Chen C, Yi R, Igisu M, Sakaguchi C, Afrin R, Potiszil C, Kunihiro T, Kobayashi K, Nakamura E, Ueno Y, Antunes A, Wang A, Chandru K, Hao J, Jia TZ. Spectroscopic and Biophysical Methods to Determine Differential Salt-Uptake by Primitive Membraneless Polyester Microdroplets. SMALL METHODS 2023; 7:e2300119. [PMID: 37203261 DOI: 10.1002/smtd.202300119] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 04/23/2023] [Indexed: 05/20/2023]
Abstract
α-Hydroxy acids are prebiotic monomers that undergo dehydration synthesis to form polyester gels, which assemble into membraneless microdroplets upon aqueous rehydration. These microdroplets are proposed as protocells that can segregate and compartmentalize primitive molecules/reactions. Different primitive aqueous environments with a variety of salts could have hosted chemistries that formed polyester microdroplets. These salts could be essential cofactors of compartmentalized prebiotic reactions or even directly affect protocell structure. However, fully understanding polyester-salt interactions remains elusive, partially due to technical challenges of quantitative measurements in condensed phases. Here, spectroscopic and biophysical methods are applied to analyze salt uptake by polyester microdroplets. Inductively coupled plasma mass spectrometry is applied to measure the cation concentration within polyester microdroplets after addition of chloride salts. Combined with methods to determine the effects of salt uptake on droplet turbidity, size, surface potential and internal water distribution, it was observed that polyester microdroplets can selectively partition salt cations, leading to differential microdroplet coalescence due to ionic screening effects reducing electrostatic repulsion forces between microdroplets. Through applying existing techniques to novel analyses related to primitive compartment chemistry and biophysics, this study suggests that even minor differences in analyte uptake can lead to significant protocellular structural change.
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Affiliation(s)
- Chen Chen
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Ruiqin Yi
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Motoko Igisu
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan
| | - Chie Sakaguchi
- The Pheasant Memorial Laboratory for Geochemistry and Cosmochemistry, Institute for Planetary Materials, Okayama University, Misasa, Tottori, 682-0193, Japan
| | - Rehana Afrin
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Christian Potiszil
- The Pheasant Memorial Laboratory for Geochemistry and Cosmochemistry, Institute for Planetary Materials, Okayama University, Misasa, Tottori, 682-0193, Japan
| | - Tak Kunihiro
- The Pheasant Memorial Laboratory for Geochemistry and Cosmochemistry, Institute for Planetary Materials, Okayama University, Misasa, Tottori, 682-0193, Japan
| | - Katsura Kobayashi
- The Pheasant Memorial Laboratory for Geochemistry and Cosmochemistry, Institute for Planetary Materials, Okayama University, Misasa, Tottori, 682-0193, Japan
| | - Eizo Nakamura
- The Pheasant Memorial Laboratory for Geochemistry and Cosmochemistry, Institute for Planetary Materials, Okayama University, Misasa, Tottori, 682-0193, Japan
| | - Yuichiro Ueno
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan
- Department of Earth and Planetary Sciences, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8551, Japan
| | - André Antunes
- State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology (MUST), Taipa, Macau, SAR, China
- Blue Marble Space Institute of Science, Seattle, WA, 98104, USA
| | - Anna Wang
- School of Chemistry, UNSW Sydney, Sydney, NSW, 2052, Australia
- Australian Centre for Astrobiology, UNSW Sydney, Sydney, NSW, 2052, Australia
- RNA Institute, UNSW Sydney, Sydney, NSW, 2052, Australia
- ARC Centre of Excellence for Synthetic Biology, UNSW Sydney, Sydney, NSW, 2052, Australia
| | - Kuhan Chandru
- Space Science Center (ANGKASA), Institute of Climate Change, National University of Malaysia, Selangor, 43650, Malaysia
| | - Jihua Hao
- Blue Marble Space Institute of Science, Seattle, WA, 98104, USA
- Deep Space Exploration Laboratory/CAS Laboratory of Crust-Mantle Materials and Environments, University of Science and Technology of China, Hefei, 230026, China
| | - Tony Z Jia
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
- Blue Marble Space Institute of Science, Seattle, WA, 98104, USA
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15
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Brown SM, Mayer-Bacon C, Freeland S. Xeno Amino Acids: A Look into Biochemistry as We Do Not Know It. Life (Basel) 2023; 13:2281. [PMID: 38137883 PMCID: PMC10744825 DOI: 10.3390/life13122281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/18/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
Would another origin of life resemble Earth's biochemical use of amino acids? Here, we review current knowledge at three levels: (1) Could other classes of chemical structure serve as building blocks for biopolymer structure and catalysis? Amino acids now seem both readily available to, and a plausible chemical attractor for, life as we do not know it. Amino acids thus remain important and tractable targets for astrobiological research. (2) If amino acids are used, would we expect the same L-alpha-structural subclass used by life? Despite numerous ideas, it is not clear why life favors L-enantiomers. It seems clearer, however, why life on Earth uses the shortest possible (alpha-) amino acid backbone, and why each carries only one side chain. However, assertions that other backbones are physicochemically impossible have relaxed into arguments that they are disadvantageous. (3) Would we expect a similar set of side chains to those within the genetic code? Many plausible alternatives exist. Furthermore, evidence exists for both evolutionary advantage and physicochemical constraint as explanatory factors for those encoded by life. Overall, as focus shifts from amino acids as a chemical class to specific side chains used by post-LUCA biology, the probable role of physicochemical constraint diminishes relative to that of biological evolution. Exciting opportunities now present themselves for laboratory work and computing to explore how changing the amino acid alphabet alters the universe of protein folds. Near-term milestones include: (a) expanding evidence about amino acids as attractors within chemical evolution; (b) extending characterization of other backbones relative to biological proteins; and (c) merging computing and laboratory explorations of structures and functions unlocked by xeno peptides.
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16
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Mrnjavac N, Wimmer JLE, Brabender M, Schwander L, Martin WF. The Moon-Forming Impact and the Autotrophic Origin of Life. Chempluschem 2023; 88:e202300270. [PMID: 37812146 PMCID: PMC7615287 DOI: 10.1002/cplu.202300270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/29/2023] [Accepted: 10/03/2023] [Indexed: 10/10/2023]
Abstract
The Moon-forming impact vaporized part of Earth's mantle, and turned the rest into a magma ocean, from which carbon dioxide degassed into the atmosphere, where it stayed until water rained out to form the oceans. The rain dissolved CO2 and made it available to react with transition metal catalysts in the Earth's crust so as to ultimately generate the organic compounds that form the backbone of microbial metabolism. The Moon-forming impact was key in building a planet with the capacity to generate life in that it converted carbon on Earth into a homogeneous and accessible substrate for organic synthesis. Today all ecosystems, without exception, depend upon primary producers, organisms that fix CO2 . According to theories of autotrophic origin, it has always been that way, because autotrophic theories posit that the first forms of life generated all the molecules needed to build a cell from CO2 , forging a direct line of continuity between Earth's initial CO2 -rich atmosphere and the first microorganisms. By modern accounts these were chemolithoautotrophic archaea and bacteria that initially colonized the crust and still inhabit that environment today.
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Affiliation(s)
- Natalia Mrnjavac
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
| | - Jessica L. E. Wimmer
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
| | - Max Brabender
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
| | - Loraine Schwander
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
| | - William F. Martin
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
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17
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Sweeney KJ, Le T, Jorge MZ, Schellinger JG, Leman LJ, Müller UF. Peptide conjugates with polyaromatic hydrocarbons can benefit the activity of catalytic RNAs. Chem Sci 2023; 14:10318-10328. [PMID: 37772096 PMCID: PMC10529712 DOI: 10.1039/d3sc03540a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/08/2023] [Indexed: 09/30/2023] Open
Abstract
Early stages of life likely employed catalytic RNAs (ribozymes) in many functions that are today filled by proteins. However, the earliest life forms must have emerged from heterogenous chemical mixtures, which included amino acids, short peptides, and many other compounds. Here we explored whether the presence of short peptides can help the emergence of catalytic RNAs. To do this, we conducted an in vitro selection for catalytic RNAs from randomized sequence in the presence of ten different peptides with a prebiotically plausible length of eight amino acids. This in vitro selection generated dozens of ribozymes, one of them with ∼900-fold higher activity in the presence of one specific peptide. Unexpectedly, the beneficial peptide had retained its N-terminal Fmoc protection group, and this group was required to benefit ribozyme activity. The same, or higher benefit resulted from peptide conjugates with prebiotically plausible polyaromatic hydrocarbons (PAHs) such as fluorene and naphthalene. This shows that PAH-peptide conjugates can act as potent cofactors to enhance ribozyme activity. The results are discussed in the context of the origin of life.
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Affiliation(s)
- Kevin J Sweeney
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093 USA
| | - Tommy Le
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093 USA
| | - Micaella Z Jorge
- Department of Chemistry & Biochemistry, University of San Diego San Diego CA 92110 USA
| | - Joan G Schellinger
- Department of Chemistry & Biochemistry, University of San Diego San Diego CA 92110 USA
| | - Luke J Leman
- Department of Chemistry, The Scripps Research Institute La Jolla CA 92037 USA
| | - Ulrich F Müller
- Department of Chemistry and Biochemistry, University of California San Diego La Jolla CA 92093 USA
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18
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Meyer MO, Yamagami R, Choi S, Keating CD, Bevilacqua PC. RNA folding studies inside peptide-rich droplets reveal roles of modified nucleosides at the origin of life. SCIENCE ADVANCES 2023; 9:eadh5152. [PMID: 37729412 PMCID: PMC10511188 DOI: 10.1126/sciadv.adh5152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 08/16/2023] [Indexed: 09/22/2023]
Abstract
Compartmentalization of RNA in biopolymer-rich membraneless organelles is now understood to be pervasive and critical for the function of extant biology and has been proposed as a prebiotically plausible way to accumulate RNA. However, compartment-RNA interactions that drive encapsulation have the potential to influence RNA structure and function in compartment- and RNA sequence-dependent ways. Here, we detail next-generation sequencing (NGS) experiments performed in membraneless compartments called complex coacervates to characterize the fold of many different transfer RNAs (tRNAs) simultaneously under the potentially denaturing conditions of these compartments. Notably, we find that natural modifications favor the native fold of tRNAs in these compartments. This suggests that covalent RNA modifications could have played a critical role in metabolic processes at the origin of life.
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Affiliation(s)
- McCauley O. Meyer
- Department of Biochemistry, Microbiology, and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Ryota Yamagami
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Saehyun Choi
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Christine D. Keating
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Philip C. Bevilacqua
- Department of Biochemistry, Microbiology, and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
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19
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Goldman AD, Weber JM, LaRowe DE, Barge LM. Electron transport chains as a window into the earliest stages of evolution. Proc Natl Acad Sci U S A 2023; 120:e2210924120. [PMID: 37579147 PMCID: PMC10451490 DOI: 10.1073/pnas.2210924120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023] Open
Abstract
The origin and early evolution of life is generally studied under two different paradigms: bottom up and top down. Prebiotic chemistry and early Earth geochemistry allow researchers to explore possible origin of life scenarios. But for these "bottom-up" approaches, even successful experiments only amount to a proof of principle. On the other hand, "top-down" research on early evolutionary history is able to provide a historical account about ancient organisms, but is unable to investigate stages that occurred during and just after the origin of life. Here, we consider ancient electron transport chains (ETCs) as a potential bridge between early evolutionary history and a protocellular stage that preceded it. Current phylogenetic evidence suggests that ancestors of several extant ETC components were present at least as late as the last universal common ancestor of life. In addition, recent experiments have shown that some aspects of modern ETCs can be replicated by minerals, protocells, or organic cofactors in the absence of biological proteins. Here, we discuss the diversity of ETCs and other forms of chemiosmotic energy conservation, describe current work on the early evolution of membrane bioenergetics, and advocate for several lines of research to enhance this understanding by pairing top-down and bottom-up approaches.
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Affiliation(s)
- Aaron D. Goldman
- Department of Biology, Oberlin College, Oberlin, OH44074
- Blue Marble Space Institute of Science, Seattle, WA98154
| | - Jessica M. Weber
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA91109
| | - Douglas E. LaRowe
- Department of Earth Sciences, University of Southern California, Los Angeles, CA90089
| | - Laura M. Barge
- Blue Marble Space Institute of Science, Seattle, WA98154
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA91109
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20
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Rangachari V. Biomolecular condensates - extant relics or evolving microcompartments? Commun Biol 2023; 6:656. [PMID: 37344557 PMCID: PMC10284869 DOI: 10.1038/s42003-023-04963-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/22/2023] [Indexed: 06/23/2023] Open
Abstract
Unprecedented discoveries during the past decade have unearthed the ubiquitous presence of biomolecular condensates (BCs) in diverse organisms and their involvement in a plethora of biological functions. A predominant number of BCs involve coacervation of RNA and proteins that demix from homogenous solutions by a process of phase separation well described by liquid-liquid phase separation (LLPS), which results in a phase with higher concentration and density from the bulk solution. BCs provide a simple and effective means to achieve reversible spatiotemporal control of cellular processes and adaptation to environmental stimuli in an energy-independent manner. The journey into the past of this phenomenon provides clues to the evolutionary origins of life itself. Here I assemble some current and historic discoveries on LLPS to contemplate whether BCs are extant biological hubs or evolving microcompartments. I conclude that BCs in biology could be extant as a phenomenon but are co-evolving as functionally and compositionally complex microcompartments in cells alongside the membrane-bound organelles.
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Affiliation(s)
- Vijayaraghavan Rangachari
- Department of Chemistry and Biochemistry, School of Mathematics and Natural Sciences and Center for Molecular and Cellular Biosciences, University of Southern Mississippi, Hattiesburg, MS, 39402, USA.
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21
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Le Vay KK, Salibi E, Ghosh B, Tang TYD, Mutschler H. Ribozyme activity modulates the physical properties of RNA-peptide coacervates. eLife 2023; 12:e83543. [PMID: 37326308 DOI: 10.7554/elife.83543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 06/01/2023] [Indexed: 06/17/2023] Open
Abstract
Condensed coacervate phases are now understood to be important features of modern cell biology, as well as valuable protocellular models in origin-of-life studies and synthetic biology. In each of these fields, the development of model systems with varied and tuneable material properties is of great importance for replicating properties of life. Here, we develop a ligase ribozyme system capable of concatenating short RNA fragments into long chains. Our results show that the formation of coacervate microdroplets with the ligase ribozyme and poly(L-lysine) enhances ribozyme rate and yield, which in turn increases the length of the anionic polymer component of the system and imparts specific physical properties to the droplets. Droplets containing active ribozyme sequences resist growth, do not wet or spread on unpassivated surfaces, and exhibit reduced transfer of RNA between droplets when compared to controls containing inactive sequences. These altered behaviours, which stem from RNA sequence and catalytic activity, constitute a specific phenotype and potential fitness advantage, opening the door to selection and evolution experiments based on a genotype-phenotype linkage.
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Affiliation(s)
- Kristian Kyle Le Vay
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Elia Salibi
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
| | - Basusree Ghosh
- Max-Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - T Y Dora Tang
- Max-Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Hannes Mutschler
- Department of Chemistry and Chemical Biology, TU Dortmund University, Dortmund, Germany
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22
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Mandal R, Ghosh A, Rout NK, Prasad M, Hazra B, Sar S, Das S, Datta A, Tarafdar PK. Self-assembled prebiotic amphiphile-mixture exhibits tunable catalytic properties. Org Biomol Chem 2023; 21:4473-4481. [PMID: 37194351 DOI: 10.1039/d3ob00606a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Protocellular surface formation via the self-assembly of amphiphiles, and catalysis by simple peptides/proto-RNA are two important pillars in the evolution of protocells. To hunt for prebiotic self-assembly-supported catalytic reactions, we thought that amino-acid-based amphiphiles might play an important role. In this paper, we investigate the formation of histidine-based and serine-based amphiphiles under mild prebiotic conditions from amino acid : fatty alcohol and amino acid : fatty acid mixtures. The histidine-based amphiphiles were able to catalyze hydrolytic reactions at the self-assembled surface (with a rate increase of ∼1000-fold), and the catalytic ability can be tuned by linkage of the fatty carbon part to histidine (N-acylated vs. O-acylated). Moreover, the presence of cationic serine-based amphiphiles on the surface enhances the catalytic efficiency by another ∼2-fold, whereas the presence of anionic aspartic acid-based amphiphiles reduces the catalytic activity. Ester partitioning into the surface, reactivity, and the accumulation of liberated fatty acid explain the substrate selectivity of the catalytic surface, where the hexyl esters were found to be more hydrolytic than other fatty acyl esters. Di-methylation of the -NH2 of OLH increases the catalytic efficacy by a further ∼2-fold, whereas trimethylation reduces the catalytic ability. The self-assembly, charge-charge repulsion, and the H-bonding to the ester carbonyl are likely to be responsible for the superior (∼2500-fold higher rate than the pre-micellar OLH) catalytic efficiency of O-lauryl dimethyl histidine (OLDMH). Thus, prebiotic amino-acid-based surfaces served as an efficient catalyst that exhibits regulation of catalytic function, substrate selectivity, and further adaptability to perform bio-catalysis.
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Affiliation(s)
- Raki Mandal
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India.
| | - Anupam Ghosh
- Indian Association for the Cultivation of Science, Raja S. C. Mullick Road, Kolkata 700032, India
| | - Nilesh K Rout
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India.
| | - Mahesh Prasad
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India.
| | - Bibhas Hazra
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India.
| | - Sanu Sar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India.
| | - Subrata Das
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India.
| | - Ayan Datta
- Indian Association for the Cultivation of Science, Raja S. C. Mullick Road, Kolkata 700032, India
| | - Pradip K Tarafdar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India.
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23
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Brown SM, Voráček V, Freeland S. What Would an Alien Amino Acid Alphabet Look Like and Why? ASTROBIOLOGY 2023; 23:536-549. [PMID: 37022727 DOI: 10.1089/ast.2022.0107] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Life on Earth builds genetically encoded proteins by using a standard alphabet of just 20 L-α-amino acids, although many others were available to life's origins and early evolution. To better understand the causes of this foundational evolutionary outcome, we extend previous analyses which have identified a highly unusual distribution of biophysical properties within the set used by life. Specifically, we use a heuristic search algorithm to identify other sets of amino acids, from a library of plausible alternatives, that emulate life's signature. We find that a subset of amino acids seems predisposed to forming such sets. We present other examples of such alphabets under various assumptions, along with analysis and reasoning about why each might be simplistic. We do so to introduce the central, open question that remains: while fundamental biophysics related to protein folding can potentially reduce a library of 1054 possible amino acid alphabets by 7 orders of magnitude, the framework of assumptions that does so leaves a further 1045 possibilities. It is therefore tempting to ask what additional assumptions can further reduce these 45 orders of magnitude? We thus conclude with a focus on library and alphabet construction as a useful target for subsequent research that may help future science speak with more confidence about what an alien amino acid alphabet would look like and why.
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Affiliation(s)
- Sean M Brown
- Department of Biological Sciences, University of Maryland, Baltimore County, Maryland, USA
| | - Václav Voráček
- Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Stephen Freeland
- Department of Biological Sciences, University of Maryland, Baltimore County, Maryland, USA
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24
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Kobayashi K, Ise JI, Aoki R, Kinoshita M, Naito K, Udo T, Kunwar B, Takahashi JI, Shibata H, Mita H, Fukuda H, Oguri Y, Kawamura K, Kebukawa Y, Airapetian VS. Formation of Amino Acids and Carboxylic Acids in Weakly Reducing Planetary Atmospheres by Solar Energetic Particles from the Young Sun. Life (Basel) 2023; 13:life13051103. [PMID: 37240748 DOI: 10.3390/life13051103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 05/28/2023] Open
Abstract
Life most likely started during the Hadean Eon; however, the environmental conditions which contributed to the complexity of its chemistry are poorly known. A better understanding of various environmental conditions, including global (heliospheric) and local (atmospheric, surface, and oceanic), along with the internal dynamic conditions of the early Earth, are required to understand the onset of abiogenesis. Herein, we examine the contributions of galactic cosmic rays (GCRs) and solar energetic particles (SEPs) associated with superflares from the young Sun to the formation of amino acids and carboxylic acids in weakly reduced gas mixtures representing the early Earth's atmosphere. We also compare the products with those introduced by lightning events and solar ultraviolet light (UV). In a series of laboratory experiments, we detected and characterized the formation of amino acids and carboxylic acids via proton irradiation of a mixture of carbon dioxide, methane, nitrogen, and water in various mixing ratios. These experiments show the detection of amino acids after acid hydrolysis when 0.5% (v/v) of initial methane was introduced to the gas mixture. In the set of experiments with spark discharges (simulation of lightning flashes) performed for the same gas mixture, we found that at least 15% methane was required to detect the formation of amino acids, and no amino acids were detected in experiments via UV irradiation, even when 50% methane was used. Carboxylic acids were formed in non-reducing gas mixtures (0% methane) by proton irradiation and spark discharges. Hence, we suggest that GCRs and SEP events from the young Sun represent the most effective energy sources for the prebiotic formation of biologically important organic compounds from weakly reducing atmospheres. Since the energy flux of space weather, which generated frequent SEPs from the young Sun in the first 600 million years after the birth of the solar system, was expected to be much greater than that of GCRs, we conclude that SEP-driven energetic protons are the most promising energy sources for the prebiotic production of bioorganic compounds in the atmosphere of the Hadean Earth.
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Affiliation(s)
- Kensei Kobayashi
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Jun-Ichi Ise
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Ryohei Aoki
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Miei Kinoshita
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Koki Naito
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Takumi Udo
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Bhagawati Kunwar
- Chubu Institute of Advanced Studies, Chubu University, 1200 Matsumoto-cho, Kasugai 487-8501, Japan
| | - Jun-Ichi Takahashi
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Hiromi Shibata
- SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Ibaraki 567-0047, Japan
| | - Hajime Mita
- Department of Life, Environment and Applied Chemistry, Faculty of Engineering, Fukuoka Institute of Technology, Fukuoka 811-0295, Japan
| | - Hitoshi Fukuda
- Open Facility Center, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Yoshiyuki Oguri
- Institute of Innovative Research, Tokyo Institute of Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Kimitaka Kawamura
- Chubu Institute of Advanced Studies, Chubu University, 1200 Matsumoto-cho, Kasugai 487-8501, Japan
| | - Yoko Kebukawa
- Department of Chemistry and Life Science, Graduate School of Engineering Science, Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku, Yokohama 240-8501, Japan
| | - Vladimir S Airapetian
- NASA Goddard Space Flight Center/Sellers Exoplanetary Environments Collaboration, Greenbelt, MD 20771, USA
- Department of Physics, American University, Washington, DC 20016, USA
- Graduate School of Advanced Integrated Studies in Human Survivability, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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25
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Kassem S, McPhee SA, Berisha N, Ulijn RV. Emergence of Cooperative Glucose-Binding Networks in Adaptive Peptide Systems. J Am Chem Soc 2023; 145:9800-9807. [PMID: 37075194 DOI: 10.1021/jacs.3c01620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
Minimalistic peptide-based systems that bind sugars in water are challenging to design due to the weakness of interactions and required cooperative contributions from specific amino-acid side chains. Here, we used a bottom-up approach to create peptide-based adaptive glucose-binding networks by mixing glucose with selected sets of input dipeptides (up to 4) in the presence of an amidase to enable in situ reversible peptide elongation, forming mixtures of up to 16 dynamically interacting tetrapeptides. The choice of input dipeptides was based on amino-acid abundance in glucose-binding sites found in the protein data bank, with side chains that can support hydrogen bonding and CH-π interactions. Tetrapeptide sequence amplification patterns, determined through LC-MS analysis, served as a readout for collective interactions and led to the identification of optimized binding networks. Systematic variation of dipeptide input revealed the emergence of two networks of non-covalent hydrogen bonding and CH-π interactions that can co-exist, are cooperative and context-dependent. A cooperative binding mode was determined by studying the binding of the most amplified tetrapeptide (AWAD) with glucose in isolation. Overall, these results demonstrate that the bottom-up design of complex systems can recreate emergent behaviors driven by covalent and non-covalent self-organization that are not observed in reductionist designs and lead to the identification of system-level cooperative binding motifs.
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Affiliation(s)
- Salma Kassem
- Nanoscience Initiative at Advanced Science Research Center of the Graduate Center of the City University of New York, New York, New York 10031, United States
| | - Scott A McPhee
- Nanoscience Initiative at Advanced Science Research Center of the Graduate Center of the City University of New York, New York, New York 10031, United States
| | - Naxhije Berisha
- Nanoscience Initiative at Advanced Science Research Center of the Graduate Center of the City University of New York, New York, New York 10031, United States
- Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
- Department of Pharmacology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Department of Chemistry Hunter College, City University of New York, New York, New York 10065, United States
| | - Rein V Ulijn
- Nanoscience Initiative at Advanced Science Research Center of the Graduate Center of the City University of New York, New York, New York 10031, United States
- Ph.D. Programs in Biochemistry and Chemistry, The Graduate Center of the City University of New York, New York, New York 10016, United States
- Department of Chemistry Hunter College, City University of New York, New York, New York 10065, United States
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26
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Deal AM, Vaida V. Oxygen Effect on the Ultraviolet-C Photochemistry of Lactic Acid. J Phys Chem A 2023; 127:2936-2945. [PMID: 36962071 DOI: 10.1021/acs.jpca.3c00992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
Lactic acid, a small α-hydroxyacid, is ubiquitous in both indoor and outdoor environments. Recently, the photochemistry of lactic acid has garnered interest among the abiotic organic chemistry community as it would have been present in abiotic settings and photoactive with the high-energy solar radiation that would have been available in the low oxygen early Earth environment. Additionally, we propose that the photochemistry of lactic acid is relevant to modern Earth during indoor ultraviolet-C (UVC) sterilization procedures as lactic acid is emitted by humans and is thus prevalent in indoor environments where UVC sterilization is increasingly being used. Here, we study the oxygen effect on the gas phase photolysis of lactic acid using Fourier-transform infrared (FTIR) spectroscopy and isotopically labeled oxygen (18O2). We find that the major products of gas phase lactic acid photolysis are CO2, CO, acetaldehyde, and acetic acid. Furthermore, these products are the same with or without added oxygen, but the partial pressures of produced CO2, CO, and acetaldehyde increase with the amount of added oxygen. Notably, the added oxygen is primarily incorporated into produced CO2 and CO, while little or none is incorporated into acetaldehyde. We combine the results presented here with those in the literature to propose a mechanism for the gas phase photolysis of lactic acid and the role of oxygen in this mechanism. Finally, we compare the output of a krypton-chloride excimer lamp (λ = 222 nm), one of the lamps proposed for UVC sterilization procedures, to the absorption of lactic acid. We show that lactic acid would be photoactive during UVC sterilization procedures, and we use the gas phase results presented here and aqueous lactic acid photolysis results previously published to assess potential byproducts from lactic acid reactions during UVC sterilization procedures.
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Affiliation(s)
- Alexandra M Deal
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Veronica Vaida
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, Colorado 80309, United States
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27
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Dance A. How did life begin? One key ingredient is coming into view. Nature 2023; 615:22-25. [PMID: 36854922 DOI: 10.1038/d41586-023-00574-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
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28
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Meyer MO, Yamagami R, Choi S, Keating CD, Bevilacqua PC. RNA folding studies inside peptide-rich droplets reveal roles of modified nucleosides at the origin of life. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.27.530264. [PMID: 36909509 PMCID: PMC10002651 DOI: 10.1101/2023.02.27.530264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Compartmentalization of RNA in biopolymer-rich membraneless organelles is now understood to be pervasive and critical for the function of extant biology and has been proposed as a prebiotically-plausible way to accumulate RNA. However, compartment-RNA interactions that drive encapsulation have the potential to influence RNA structure and function in compartment- and RNA sequence-dependent ways. Herein, we detail Next-Generation Sequencing (NGS) experiments performed for the first time in membraneless compartments called complex coacervates to characterize the fold of many different transfer RNAs (tRNAs) simultaneously under the potentially denaturing conditions of these compartments. Strikingly, we find that natural modifications favor the native fold of tRNAs in these compartments. This suggests that covalent RNA modifications could have played a critical role in metabolic processes at the origin of life. One Sentence Summary We demonstrate that RNA folds into native secondary and tertiary structures in protocell models and that this is favored by covalent modifications, which is critical for the origins of life.
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29
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"Sea Water" Supplemented with Calcium Phosphate and Magnesium Sulfate in a Long-Term Miller-Type Experiment Yields Sugars, Nucleic Acids Bases, Nucleosides, Lipids, Amino Acids, and Oligopeptides. Life (Basel) 2023; 13:life13020265. [PMID: 36836628 PMCID: PMC9959757 DOI: 10.3390/life13020265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/13/2023] [Accepted: 01/15/2023] [Indexed: 01/20/2023] Open
Abstract
The standard approach to exploring prebiotic chemistry is to use a small number of highly purified reactants and to attempt to optimize the conditions required to produce a particular end product. However, purified reactants do not exist in nature. We have previously proposed that what drives prebiotic evolution are complex chemical ecologies. Therefore, we have begun to explore what happens if one substitutes "sea water", with its complex mix of minerals and salts, for distilled water in the classic Miller experiment. We have also adapted the apparatus to permit it to be regassed at regular intervals so as to maintain a relatively constant supply of methane, hydrogen, and ammonia. The "sea water" used in the experiments was created from Mediterranean Sea salt with the addition of calcium phosphate and magnesium sulfate. Tests included several types of mass spectrometry, an ATP-monitoring device capable of measuring femtomoles of ATP, and a high-sensitivity cAMP enzyme-linked immunoadsorption assay. As expected, amino acids appeared within a few days of the start of the experiment and accumulated thereafter. Sugars, including glucose and ribose, followed as did long-chain fatty acids (up to C20). At three-to-five weeks after starting the experiment, ATP was repeatedly detected. Thus, we have shown that it is possible to produce a "one-pot synthesis" of most of the key chemical prerequisites for living systems within weeks by mimicking more closely the complexity of real-world chemical ecologies.
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30
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Westall F, Brack A, Fairén AG, Schulte MD. Setting the geological scene for the origin of life and continuing open questions about its emergence. FRONTIERS IN ASTRONOMY AND SPACE SCIENCES 2023; 9:1095701. [PMID: 38274407 PMCID: PMC7615569 DOI: 10.3389/fspas.2022.1095701] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
The origin of life is one of the most fundamental questions of humanity. It has been and is still being addressed by a wide range of researchers from different fields, with different approaches and ideas as to how it came about. What is still incomplete is constrained information about the environment and the conditions reigning on the Hadean Earth, particularly on the inorganic ingredients available, and the stability and longevity of the various environments suggested as locations for the emergence of life, as well as on the kinetics and rates of the prebiotic steps leading to life. This contribution reviews our current understanding of the geological scene in which life originated on Earth, zooming in specifically on details regarding the environments and timescales available for prebiotic reactions, with the aim of providing experimenters with more specific constraints. Having set the scene, we evoke the still open questions about the origin of life: did life start organically or in mineralogical form? If organically, what was the origin of the organic constituents of life? What came first, metabolism or replication? What was the time-scale for the emergence of life? We conclude that the way forward for prebiotic chemistry is an approach merging geology and chemistry, i.e., far-from-equilibrium, wet-dry cycling (either subaerial exposure or dehydration through chelation to mineral surfaces) of organic reactions occurring repeatedly and iteratively at mineral surfaces under hydrothermal-like conditions.
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Affiliation(s)
| | - André Brack
- Centre de Biophysique Moléculaire, CNRS, Orléans, France
| | - Alberto G. Fairén
- Centro de Astrobiología (CAB, CSIC-INTA), Madrid, Spain
- Cornell University, Ithaca, NY, United States
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31
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El Samrout O, Fabbiani M, Berlier G, Lambert JF, Martra G. Emergence of Order in Origin-of-Life Scenarios on Mineral Surfaces: Polyglycine Chains on Silica. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:15516-15525. [PMID: 36469018 PMCID: PMC9776562 DOI: 10.1021/acs.langmuir.2c02106] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/21/2022] [Indexed: 06/17/2023]
Abstract
The polymerization of amino acids (AAs) to peptides on oxide surfaces has attracted interest owing to its high importance in biotechnology, prebiotic chemistry, and origin of life theories. However, its mechanism is still poorly understood. We tried to elucidate the reactivity of glycine (Gly) from the vapor phase on the surface of amorphous silica under controlled atmosphere at 160 °C. Infrared (IR) spectroscopy reveals that Gly functionalizes the silica surface through the formation of ester species, which represent, together with the weakly interacting silanols, crucial elements for monomers activation and polymerization. Once activated, β-turns start to form as initiators for the growth of long linear polypeptides (poly-Gly) chains, which elongate into ordered structures containing both β-sheet and helical conformations. The work also points to the role of water vapor in the formation of further self-assembled β-sheet structures that are highly resistant to hydrolysis.
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Affiliation(s)
- Ola El Samrout
- Department
of Chemistry, University of Torino, Via P. Giuria 7, 10125 Torino, Italy
- Laboratoire
de Réactivité de Surface, LRS, Sorbonne Université, Place Jussieu, 75005 Paris, France
| | - Marco Fabbiani
- Department
of Chemistry, University of Torino, Via P. Giuria 7, 10125 Torino, Italy
| | - Gloria Berlier
- Department
of Chemistry, University of Torino, Via P. Giuria 7, 10125 Torino, Italy
| | - Jean-François Lambert
- Laboratoire
de Réactivité de Surface, LRS, Sorbonne Université, Place Jussieu, 75005 Paris, France
| | - Gianmario Martra
- Department
of Chemistry, University of Torino, Via P. Giuria 7, 10125 Torino, Italy
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32
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Hazra B, Mondal A, Prasad M, Gayen S, Mandal R, Sardar A, Tarafdar PK. Lipidated Lysine and Fatty Acids Assemble into Protocellular Membranes to Assist Regioselective Peptide Formation: Correlation to the Natural Selection of Lysine over Nonproteinogenic Lower Analogues. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:15422-15432. [PMID: 36450098 DOI: 10.1021/acs.langmuir.2c02849] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The self-assembly of prebiotically plausible amphiphiles (fatty acids) to form a bilayer membrane for compartmentalization is an important factor during protocellular evolution. Such fatty acid-based membranes assemble at relatively high concentrations, and they lack robust stability. We have demonstrated that a mixture of lipidated lysine (cationic) and prebiotic fatty acids (decanoic acid, anionic) can form protocellular membranes (amino acid-based membranes) at low concentrations via electrostatic, hydrogen bonding, and hydrophobic interactions. The formation of vesicular membranes was characterized by dynamic light scattering (DLS), pyrene and Nile Red partitioning, cryo-transmission electron microscopy (TEM) images, and glucose encapsulation studies. The lipidated nonproteinogenic analogues of lysine (Lys), such as ornithine (Orn) and 2,4-diaminobutyric acid (Dab), also form membranes with decanoate (DA). Time-dependent turbidimetric and 1H NMR studies suggested that the Lys-based membrane is more stable than the membranes prepared from nonproteinogenic lower analogues. The Lys-based membrane embeds a model acylating agent (aminoacyl-tRNA mimic) and facilitates the colocalization of substrates to support regioselective peptide formation via the α-amine of Lys. These membranes thereby assist peptide formation and control the positioning of the reactants (model acylating agent and -NH2 of amino acids) to initiate biologically relevant reactions during early evolution.
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Affiliation(s)
- Bibhas Hazra
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia 741246, West Bengal, India
| | - Anoy Mondal
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia 741246, West Bengal, India
| | - Mahesh Prasad
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia 741246, West Bengal, India
| | - Soumajit Gayen
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia 741246, West Bengal, India
| | - Raki Mandal
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia 741246, West Bengal, India
| | - Avijit Sardar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia 741246, West Bengal, India
| | - Pradip K Tarafdar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia 741246, West Bengal, India
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33
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A Short Tale of the Origin of Proteins and Ribosome Evolution. Microorganisms 2022; 10:microorganisms10112115. [DOI: 10.3390/microorganisms10112115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 09/30/2022] [Accepted: 10/19/2022] [Indexed: 11/16/2022] Open
Abstract
Proteins are the workhorses of the cell and have been key players throughout the evolution of all organisms, from the origin of life to the present era. How might life have originated from the prebiotic chemistry of early Earth? This is one of the most intriguing unsolved questions in biology. Currently, however, it is generally accepted that amino acids, the building blocks of proteins, were abiotically available on primitive Earth, which would have made the formation of early peptides in a similar fashion possible. Peptides are likely to have coevolved with ancestral forms of RNA. The ribosome is the most evident product of this coevolution process, a sophisticated nanomachine that performs the synthesis of proteins codified in genomes. In this general review, we explore the evolution of proteins from their peptide origins to their folding and regulation based on the example of superoxide dismutase (SOD1), a key enzyme in oxygen metabolism on modern Earth.
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34
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Root-Bernstein R, Brown AW. Novel Apparatuses for Incorporating Natural Selection Processes into Origins-of-Life Experiments to Produce Adaptively Evolving Chemical Ecosystems. Life (Basel) 2022; 12:life12101508. [PMID: 36294944 PMCID: PMC9605314 DOI: 10.3390/life12101508] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 11/21/2022] Open
Abstract
Origins-of-life chemical experiments usually aim to produce specific chemical end-products such as amino acids, nucleic acids or sugars. The resulting chemical systems do not evolve or adapt because they lack natural selection processes. We have modified Miller origins-of-life apparatuses to incorporate several natural, prebiotic physicochemical selection factors that can be tested individually or in tandem: freezing-thawing cycles; drying-wetting cycles; ultraviolet light-dark cycles; and catalytic surfaces such as clays or minerals. Each process is already known to drive important origins-of-life chemical reactions such as the production of peptides and synthesis of nucleic acid bases and each can also destroy various reactants and products, resulting selection within the chemical system. No previous apparatus has permitted all of these selection processes to work together. Continuous synthesis and selection of products can be carried out over many months because the apparatuses can be re-gassed. Thus, long-term chemical evolution of chemical ecosystems under various combinations of natural selection may be explored for the first time. We argue that it is time to begin experimenting with the long-term effects of such prebiotic natural selection processes because they may have aided biotic life to emerge by taming the combinatorial chemical explosion that results from unbounded chemical syntheses.
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Affiliation(s)
- Robert Root-Bernstein
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA
- Correspondence:
| | - Adam W. Brown
- Department of Art, Art History and Design, Michigan State University, East Lansing, MI 48824, USA
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35
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Krishnamurthy R, Goldman AD, Liberles DA, Rogers KL, Tor Y. Nucleobases in Meteorites to Nucleobases in RNA and DNA? J Mol Evol 2022; 90:328-331. [PMID: 35960316 DOI: 10.1007/s00239-022-10069-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/29/2022] [Indexed: 10/16/2022]
Abstract
Nucleic acids likely played a foundational role in the origin of life. However, the prebiotic chemistry of nucleoside and nucleotide synthesis has proved challenging on a number of fronts. The recent discovery of both pyrimidine and purine nucleobases in carbonaceous chondrite meteorites has garnered much attention from both the popular press and the scientific community. Here, we discuss these findings in the context of nucleoside/nucleotide prebiotic chemistry. We consider that the main challenge of prebiotic nucleoside synthesis, that of nucleosidic bond formation, is not addressed by the identification nucleobases in meteorites. We further discuss issues of selection that arise from the observation that such meteorites contain both canonical and non-canonical nucleobases. In sum, we argue that, despite the major analytical achievement of identifying and characterizing nucleobases in meteorites, this observation does little to advance our understanding of the prebiotic chemistry that could have led to the first genetic molecules that gave rise to us.
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Affiliation(s)
- Ramanarayanan Krishnamurthy
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA. .,NSF-NASA Center for Chemical Evolution, Atlanta, GA, USA.
| | - Aaron D Goldman
- Department of Biology, Oberlin College and Conservatory, Oberlin, OH, USA.,Blue Marble Space Institute of Science, Seattle, WA, USA
| | - David A Liberles
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, USA
| | - Karyn L Rogers
- Department of Earth and Environmental Sciences and Rensselaer Astrobiology Research and Education Center, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA, USA
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36
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Gan D, Ying J, Zhao Y. Prebiotic Chemistry: The Role of Trimetaphosphate in Prebiotic Chemical Evolution. Front Chem 2022; 10:941228. [PMID: 35910738 PMCID: PMC9326000 DOI: 10.3389/fchem.2022.941228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/23/2022] [Indexed: 11/22/2022] Open
Abstract
Life’s origins have always been a scientific puzzle. Understanding the production of biomolecules is crucial for understanding the evolution of life on Earth. Numerous studies on trimetaphosphate have been conducted in the field of prebiotic chemistry. However, its role in prebiotic chemistry has been documented infrequently in the review literature. The goal of this thesis is to review the role of trimetaphosphate in the early Earth’s biomolecule synthesis and phosphorylation. Additionally, various trimetaphosphate-mediated reaction pathways are discussed, as well as the role of trimetaphosphate in prebiotic chemistry. Finally, in our opinion, interactions between biomolecules should be considered in prebiotic synthesis scenarios since this may result in some advances in subsequent research on this subject. The research establishes an essential and opportune foundation for an in-depth examination of the “mystery of life".
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Affiliation(s)
- Dingwei Gan
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China
| | - Jianxi Ying
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China
- *Correspondence: Jianxi Ying,
| | - Yufen Zhao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo, China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo, China
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
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37
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Müller UF, Elsila J, Trail D, DasGupta S, Giese CC, Walton CR, Cohen ZR, Stolar T, Krishnamurthy R, Lyons TW, Rogers KL, Williams LD. Frontiers in Prebiotic Chemistry and Early Earth Environments. ORIGINS LIFE EVOL B 2022; 52:165-181. [PMID: 35796897 PMCID: PMC9261198 DOI: 10.1007/s11084-022-09622-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 04/29/2022] [Indexed: 11/28/2022]
Abstract
The Prebiotic Chemistry and Early Earth Environments (PCE3) Consortium is a community of researchers seeking to understand the origins of life on Earth and in the universe. PCE3 is one of five Research Coordination Networks (RCNs) within NASA’s Astrobiology Program. Here we report on the inaugural PCE3 workshop, intended to cross-pollinate, transfer information, promote cooperation, break down disciplinary barriers, identify new directions, and foster collaborations. This workshop, entitled, “Building a New Foundation”, was designed to propagate current knowledge, identify possibilities for multidisciplinary collaboration, and ultimately define paths for future collaborations. Presentations addressed the likely conditions on early Earth in ways that could be incorporated into prebiotic chemistry experiments and conceptual models to improve their plausibility and accuracy. Additionally, the discussions that followed among workshop participants helped to identify within each subdiscipline particularly impactful new research directions. At its core, the foundational knowledge base presented in this workshop should underpin future workshops and enable collaborations that bridge the many disciplines that are part of PCE3.
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Affiliation(s)
| | - Jamie Elsila
- NASA/Goddard Space Flight Center, Greenbelt, United States
| | - Dustin Trail
- University of Rochester, Rochester, United States
| | | | - Claudia-Corina Giese
- Leiden University, Leiden, The Netherlands.,Utrecht University, Utrecht, The Netherlands
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38
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Cronin L, Kitson PJ. Selection of assembly complexity in a space of tetrapeptides. Chem 2022. [DOI: 10.1016/j.chempr.2022.06.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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39
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Deamer D, Cary F, Damer B. Urability: A Property of Planetary Bodies That Can Support an Origin of Life. ASTROBIOLOGY 2022; 22:889-900. [PMID: 35675644 DOI: 10.1089/ast.2021.0173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The concept of habitability is now widely used to describe zones in a solar system in which planets with liquid water can sustain life. Because habitability does not explicitly incorporate the origin of life, this article proposes a new word-urability-which refers to the conditions that allow life to begin. The utility of the word is tested by applying it to combinations of multiple geophysical and geochemical factors that support plausible localized zones that are conducive to the chemical reactions and molecular assembly processes required for the origin of life. The concept of urable worlds, planetary bodies that can sustain an arising of life, is considered for bodies in our own solar system and exoplanets beyond.
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Affiliation(s)
- David Deamer
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, USA
| | - Francesca Cary
- Hawai'i Institute of Geophysics and Planetology, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
| | - Bruce Damer
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, USA
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40
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C M, Frenkel-Pinter M, Smith KH, Rivera-Santana VF, Sargon AB, Jacobson KC, Guzman-Martinez A, Williams LD, Leman LJ, Liotta CL, Grover MA, Hud NV. Water-Based Dynamic Depsipeptide Chemistry: Building Block Recycling and Oligomer Distribution Control Using Hydration-Dehydration Cycles. JACS AU 2022; 2:1395-1404. [PMID: 35783166 PMCID: PMC9241005 DOI: 10.1021/jacsau.2c00087] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/31/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
The high kinetic barrier to amide bond formation has historically placed narrow constraints on its utility in reversible chemistry applications. Slow kinetics has limited the use of amides for the generation of diverse combinatorial libraries and selection of target molecules. Current strategies for peptide-based dynamic chemistries require the use of nonpolar co-solvents or catalysts or the incorporation of functional groups that facilitate dynamic chemistry between peptides. In light of these limitations, we explored the use of depsipeptides: biorelevant copolymers of amino and hydroxy acids that would circumvent the challenges associated with dynamic peptide chemistry. Here, we describe a model system of N-(α-hydroxyacyl)-amino acid building blocks that reversibly polymerize to form depsipeptides when subjected to two-step evaporation-rehydration cycling under moderate conditions. The hydroxyl groups of these units allow for dynamic ester chemistry between short peptide segments through unmodified carboxyl termini. Selective recycling of building blocks is achieved by exploiting the differential hydrolytic lifetimes of depsipeptide amide and ester bonds, which we show are controllable by adjusting the solution pH, temperature, and time as well as the building blocks' side chains. We demonstrate that the polymerization and breakdown of the depsipeptides are facilitated by cyclic morpholinedione intermediates, and further show how structural properties dictate half-lives and product oligomer distributions using multifunctional building blocks. These results establish a cyclic mode of ester-based reversible depsipeptide formation that temporally separates the polymerization and depolymerization steps for the building blocks and may have implications for prebiotic polymer chemical evolution.
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Affiliation(s)
- Martin C
- NSF/NASA
Center for Chemical Evolution, Atlanta, Georgia 30332, United States
- School
of Chemistry & Biochemistry, Georgia
Institute of Technology, Atlanta, Georgia 30332, United States
| | - Moran Frenkel-Pinter
- NSF/NASA
Center for Chemical Evolution, Atlanta, Georgia 30332, United States
- School
of Chemistry & Biochemistry, Georgia
Institute of Technology, Atlanta, Georgia 30332, United States
| | - Kelvin H. Smith
- NSF/NASA
Center for Chemical Evolution, Atlanta, Georgia 30332, United States
- School
of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | | | - Alyssa B. Sargon
- NSF/NASA
Center for Chemical Evolution, Atlanta, Georgia 30332, United States
- School
of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Kaitlin C. Jacobson
- NSF/NASA
Center for Chemical Evolution, Atlanta, Georgia 30332, United States
- School
of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | | | - Loren Dean Williams
- NSF/NASA
Center for Chemical Evolution, Atlanta, Georgia 30332, United States
- School
of Chemistry & Biochemistry, Georgia
Institute of Technology, Atlanta, Georgia 30332, United States
| | - Luke J. Leman
- NSF/NASA
Center for Chemical Evolution, Atlanta, Georgia 30332, United States
- Department
of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Charles L. Liotta
- NSF/NASA
Center for Chemical Evolution, Atlanta, Georgia 30332, United States
- School
of Chemistry & Biochemistry, Georgia
Institute of Technology, Atlanta, Georgia 30332, United States
| | - Martha A. Grover
- NSF/NASA
Center for Chemical Evolution, Atlanta, Georgia 30332, United States
- School
of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Nicholas V. Hud
- NSF/NASA
Center for Chemical Evolution, Atlanta, Georgia 30332, United States
- School
of Chemistry & Biochemistry, Georgia
Institute of Technology, Atlanta, Georgia 30332, United States
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41
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Hydrophobic-cationic peptides modulate RNA polymerase ribozyme activity by accretion. Nat Commun 2022; 13:3050. [PMID: 35665749 PMCID: PMC9166800 DOI: 10.1038/s41467-022-30590-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 05/04/2022] [Indexed: 11/09/2022] Open
Abstract
Accretion and the resulting increase in local concentration is a widespread mechanism in biology to enhance biomolecular functions (for example, in liquid-liquid demixing phases). Such macromolecular aggregation phases (e.g., coacervates, amyloids) may also have played a role in the origin of life. Here, we report that a hydrophobic-cationic RNA binding peptide selected by phage display (P43: AKKVWIIMGGS) forms insoluble amyloid-containing aggregates, which reversibly accrete RNA on their surfaces in an RNA-length and Mg2+-concentration dependent manner. The aggregates formed by P43 or its sequence-simplified version (K2V6: KKVVVVVV) inhibited RNA polymerase ribozyme (RPR) activity at 25 mM MgCl2, while enhancing it significantly at 400 mM MgCl2. Our work shows that such hydrophobic-cationic peptide aggregates can reversibly concentrate RNA and enhance the RPR activity, and suggests that they could have aided the emergence and evolution of longer and functional RNAs in the fluctuating environments of the prebiotic earth.
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42
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Sahai N, Adebayo S, Schoonen MA. Freshwater and Evaporite Brine Compositions on Hadean Earth: Priming the Origins of Life. ASTROBIOLOGY 2022; 22:641-671. [PMID: 35447041 DOI: 10.1089/ast.2020.2396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The chemical composition of aqueous solutions during the Hadean era determined the availability of essential elements for prebiotic synthesis of the molecular building blocks of life. Here we conducted quantitative reaction path modeling of atmosphere-water-rock interactions over a range of environmental conditions to estimate freshwater and evaporite brine compositions. We then evaluated the solution chemistries for their potential to influence ribonucleotide synthesis and polymerization as well as protocell membrane stability. Specifically, solutions formed by komatiite and tonalite (primitive crustal rocks) weathering and evaporation-rehydration (drying-wetting) cycles were studied assuming neutral atmospheric composition over a wide range of values of atmospheric partial pressure of CO2 (PCO2) and temperatures (T). Solution pH decreased and total dissolved concentrations of inorganic P, Mg, Ca, Fe, and C (PT, MgT, CaT, FeT, and CT) increased with increasing PCO2. The PCO2 and T dictated how the solution evolved with regard to minerals precipitated and ions left in solution. At T = 75°C and PCO2 < 0.05 atm, the concentration ratio of magnesium to calcium ion concentrations (Mg2+/Ca2+) was < 1 and predominantly metal aluminosilicates (including clays), dolomite, gibbsite, and pyrite (FeS2) precipitated, whereas at PCO2 > 0.05 atm, Mg2+/Ca2+ was > 1 and mainly magnesite, dolomite, pyrite, chalcedony (SiO2), and kaolinite (Al2Si2O5) precipitated. At T = 75°C and PCO2 > 0.05 atm, hydroxyapatite (HAP) precipitated during weathering but not during evaporation, and so, PT increased with each evaporation-rehydration cycle, while MgT, CaT, and FeT decreased as other minerals precipitated. At T = 75°C and PCO2 ∼5 atm, reactions with komatiite provided end-of-weathering solutions with high enough Mg2+ concentrations to promote RNA-template directed and montmorillonite-promoted nonenzymatic RNA polymerization, but incompatible with protocell membranes; however, montmorillonite-promoted RNA polymerization could proceed with little or no Mg2+ present. Cyclically evaporating/rehydrating brines from komatiite weathering at T = 75°C and PCO2 ∼5 atm yielded the following: (1) high PT values that could promote ribonucleotide synthesis, and (2) low divalent cation concentrations compatible with amino acid-promoted, montmorillonite-catalyzed RNA polymerization and with protocell membranes, but too low for template-directed nonenzymatic RNA polymerization. For all PCO2 values, Mg2+ and PT concentrations decreased, whereas the HCO3- concentration increased within increasing temperature, due to the retrograde solubility of the minerals controlling these ions' concentrations; Fe2+ concentration increased because of prograde pyrite solubility. Tonalite weathering and cyclical wetting-drying reactions did not produce solution compositions favorable for promoting prebiotic RNA formation. Conversely, the ion concentrations compatible with protocell emergence, placed constraints on PCO2 of early Earth's atmosphere. In summary: (1) prebiotic RNA synthesis and membrane self-assembly could have been achieved even under neutral atmosphere conditions by atmosphere-water-komatiite rock interactions; and (2) constraints on element availability for the origins of life and early PCO2 were addressed by a single, globally operating mechanism of atmosphere-water-rock interactions without invoking special microenvironments. The present results support a facile origins-of-life hypothesis even under a neutral atmosphere as long as other favorable geophysical and planetary conditions are also met.
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Affiliation(s)
- Nita Sahai
- School of Polymer Science and Polymer Engineering and University of Akron, Akron, Ohio, USA
- Department of Geoscience, University of Akron, Akron, Ohio, USA
- Integrated Bioscience Program, University of Akron, Akron, Ohio, USA
| | - Segun Adebayo
- School of Polymer Science and Polymer Engineering and University of Akron, Akron, Ohio, USA
| | - Martin A Schoonen
- Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, New York, USA
- Department of Geosciences, Stony Brook University, Stony Brook, New York, USA
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43
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Rossetto D, Valer L, Yeh Martín N, Guella G, Hongo Y, Mansy SS. Prebiotic Environments with Mg 2+ and Thiophilic Metal Ions Increase the Thermal Stability of Cysteine and Non-cysteine Peptides. ACS EARTH & SPACE CHEMISTRY 2022; 6:1221-1226. [PMID: 35620317 PMCID: PMC9126146 DOI: 10.1021/acsearthspacechem.2c00042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 06/15/2023]
Abstract
Wet-dry cycles driven by heating to high temperatures are frequently invoked for the prebiotic synthesis of peptides. Similarly, iron-sulfur clusters are often cited as an example of an ancient catalyst that helped prune early chemical systems into metabolic-like pathways. Because extant iron-sulfur clusters are metallocofactors of protein enzymes and nearly ubiquitous across biology, a reasonable hypothesis is that prebiotic iron-sulfur peptides formed on the early Earth. However, iron-sulfur clusters are coordinated by multiple cysteine residues, and the stability of cysteines to the heat steps of wet-dry cycles has not been determined. It, therefore, has remained unclear if the peptides needed to stabilize the formation of iron-sulfur clusters could have formed. If not, then iron-sulfur-dependent activity may have emerged later, when milder, more biological-like peptide synthesis machinery took hold. Here, we report the thermal stability of cysteine-containing peptides. We show that temperatures of 150 °C lead to the rapid degradation of cysteinyl peptides. However, the presence of Mg2+ at environmentally reasonable concentrations leads to significant protection. Thiophilic metal ions also protect against degradation at 150 °C but require concentrations not frequently observed in the environment. Nevertheless, cysteine-containing peptides are stable at lower, prebiotically plausible temperatures in seawater, carbonate lake, and ferrous lake conditions. The data are consistent with the persistence of cysteine-containing peptides on the early Earth in environments rich in metal ions. High concentrations of Mg2+ are common intra- and extra-cellularly, suggesting that the protection afforded by Mg2+ may reflect conditions that were present on the prebiotic Earth.
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Affiliation(s)
- Daniele Rossetto
- D-CIBIO, University of Trento, Via Sommarive 9, 38123 Povo, Italy
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta T6G 2G2, Canada
| | - Luca Valer
- D-CIBIO, University of Trento, Via Sommarive 9, 38123 Povo, Italy
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta T6G 2G2, Canada
| | - Noël Yeh Martín
- D-CIBIO, University of Trento, Via Sommarive 9, 38123 Povo, Italy
| | - Graziano Guella
- Department
of Physics, University of Trento, Via Sommarive 14, 38123 Povo, Italy
| | - Yayoi Hongo
- Earth-Life
Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
- Okinawa
Institute of Science and Technology Graduate University, Onna-son, Kunigami, Okinawa 904-0495, Japan
| | - Sheref S. Mansy
- D-CIBIO, University of Trento, Via Sommarive 9, 38123 Povo, Italy
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, Alberta T6G 2G2, Canada
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44
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Abstract
The RNA world concept1 is one of the most fundamental pillars of the origin of life theory2–4. It predicts that life evolved from increasingly complex self-replicating RNA molecules1,2,4. The question of how this RNA world then advanced to the next stage, in which proteins became the catalysts of life and RNA reduced its function predominantly to information storage, is one of the most mysterious chicken-and-egg conundrums in evolution3–5. Here we show that non-canonical RNA bases, which are found today in transfer and ribosomal RNAs6,7, and which are considered to be relics of the RNA world8–12, are able to establish peptide synthesis directly on RNA. The discovered chemistry creates complex peptide-decorated RNA chimeric molecules, which suggests the early existence of an RNA–peptide world13 from which ribosomal peptide synthesis14 may have emerged15,16. The ability to grow peptides on RNA with the help of non-canonical vestige nucleosides offers the possibility of an early co-evolution of covalently connected RNAs and peptides13,17,18, which then could have dissociated at a higher level of sophistication to create the dualistic nucleic acid–protein world that is the hallmark of all life on Earth. Peptide synthesis can take place directly on RNA, which suggests how a nucleic acid–protein world might have originated on early Earth.
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45
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Frenkel-Pinter M, Bouza M, Fernández FM, Leman LJ, Williams LD, Hud NV, Guzman-Martinez A. Thioesters provide a plausible prebiotic path to proto-peptides. Nat Commun 2022; 13:2569. [PMID: 35562173 PMCID: PMC9095695 DOI: 10.1038/s41467-022-30191-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/19/2022] [Indexed: 11/15/2022] Open
Abstract
It is widely assumed that the condensation of building blocks into oligomers and polymers was important in the origins of life. High activation energies, unfavorable thermodynamics and side reactions are bottlenecks for abiotic peptide formation. All abiotic reactions reported thus far for peptide bond formation via thioester intermediates have relied on high energy molecules, which usually suffer from short half-life in aqueous conditions and therefore require constant replenishment. Here we report plausible prebiotic reactions of mercaptoacids with amino acids that result in the formation of thiodepsipeptides, which contain both peptide and thioester bonds. Thiodepsipeptide formation was achieved under a wide range of pH and temperature by simply drying and heating mercaptoacids with amino acids. Our results offer a robust one-pot prebiotically-plausible pathway for proto-peptide formation. These results support the hypothesis that thiodepsipeptides and thiol-terminated peptides formed readily on prebiotic Earth and were possible contributors to early chemical evolution. One of the early processes enabling the origins of life is thought to be the condensation of building blocks into oligomers and polymers. In this article, the authors report the synthesis of thiodepsipeptides and HS-peptides under mild temperatures and various pH, suggesting they could have formed on early prebiotic Earth.
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Affiliation(s)
- Moran Frenkel-Pinter
- NSF-NASA Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, GA, 30332, USA.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA.,Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Marcos Bouza
- NSF-NASA Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, GA, 30332, USA.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Facundo M Fernández
- NSF-NASA Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, GA, 30332, USA.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Luke J Leman
- NSF-NASA Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, GA, 30332, USA.,Department of Chemistry, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Loren Dean Williams
- NSF-NASA Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, GA, 30332, USA.,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Nicholas V Hud
- NSF-NASA Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, GA, 30332, USA. .,School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
| | - Aikomari Guzman-Martinez
- NSF-NASA Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, GA, 30332, USA. .,Department of Chemistry, University of Puerto Rico, Mayagüez, Mayagüez, PR, 00681, USA.
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46
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Barge LM, Rodriguez LE, Weber JM, Theiling BP. Determining the "Biosignature Threshold" for Life Detection on Biotic, Abiotic, or Prebiotic Worlds. ASTROBIOLOGY 2022; 22:481-493. [PMID: 34898272 DOI: 10.1089/ast.2021.0079] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The field of prebiotic chemistry has demonstrated that complex organic chemical systems that exhibit various life-like properties can be produced abiotically in the laboratory. Understanding these chemical systems is important for astrobiology and life detection since we do not know the extent to which prebiotic chemistry might exist or have existed on other worlds. Nor do we know what signatures are diagnostic of an extant or "failed" prebiotic system. On Earth, biology has suppressed most abiotic organic chemistry and overprints geologic records of prebiotic chemistry; therefore, it is difficult to validate whether chemical signatures from future planetary missions are remnant or extant prebiotic systems. The "biosignature threshold" between whether a chemical signature is more likely to be produced by abiotic versus biotic chemistry on a given world could vary significantly, depending on the particular environment, and could change over time, especially if life were to emerge and diversify on that world. To interpret organic signatures detected during a planetary mission, we advocate for (1) gaining a more complete understanding of prebiotic/abiotic chemical possibilities in diverse planetary environments and (2) involving experimental prebiotic samples as analogues when generating comparison libraries for "life-detection" mission instruments.
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Affiliation(s)
- Laura M Barge
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Laura E Rodriguez
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Jessica M Weber
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
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47
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Differential Oligomerization of Alpha versus Beta Amino Acids and Hydroxy Acids in Abiotic Proto-Peptide Synthesis Reactions. Life (Basel) 2022; 12:life12020265. [PMID: 35207553 PMCID: PMC8876357 DOI: 10.3390/life12020265] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/24/2022] [Accepted: 01/28/2022] [Indexed: 12/13/2022] Open
Abstract
The origin of biopolymers is a central question in origins of life research. In extant life, proteins are coded linear polymers made of a fixed set of twenty alpha-L-amino acids. It is likely that the prebiotic forerunners of proteins, or protopeptides, were more heterogenous polymers with a greater diversity of building blocks and linkage stereochemistry. To investigate a possible chemical selection for alpha versus beta amino acids in abiotic polymerization reactions, we subjected mixtures of alpha and beta hydroxy and amino acids to single-step dry-down or wet-dry cycling conditions. The resulting model protopeptide mixtures were analyzed by a variety of analytical techniques, including mass spectrometry and NMR spectroscopy. We observed that amino acids typically exhibited a higher extent of polymerization in reactions that also contained alpha hydroxy acids over beta hydroxy acids, whereas the extent of polymerization by beta amino acids was higher compared to their alpha amino acid analogs. Our results suggest that a variety of heterogenous protopeptide backbones existed during the prebiotic epoch, and that selection towards alpha backbones occurred later as a result of polymer evolution.
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48
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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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49
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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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50
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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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