1
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Khawaja N, Hortal Sánchez L, O'Sullivan TR, Bloema J, Napoleoni M, Klenner F, Beinlich A, Hillier J, John T, Postberg F. Laboratory characterization of hydrothermally processed oligopeptides in ice grains emitted by Enceladus and Europa. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2024; 382:20230201. [PMID: 38736335 DOI: 10.1098/rsta.2023.0201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 01/30/2024] [Indexed: 05/14/2024]
Abstract
The Cassini mission provided evidence for a global subsurface ocean and ongoing hydrothermal activity on Enceladus, based on results from Cassini's mass spectrometers. Laboratory simulations of hydrothermal conditions on icy moons are needed to further constrain the composition of ejected ice grains containing hydrothermally altered organic material. Here, we present results from our newly established facility to simulate the processing of ocean material within the temperature range 80-150°C and the pressure range 80-130 bar, representing conditions suggested for the water-rock interface on Enceladus. With this new facility, we investigate the hydrothermal processing of triglycine (GGG) peptide and, for the first time, analyse the extracted samples using laser-induced liquid beam ion desorption (LILBID) mass spectrometry, a laboratory analogue for impact ionization mass spectrometry of ice grains in space. We outline an approach to elucidate hydrothermally processed GGG in ice grains ejected from icy moons based on characteristic differences between GGG anion and cation mass spectra. These differences are linked to hydrothermal processing and thus provide a fingerprint of hydrothermal activity on extraterrestrial bodies. These results will serve as important guidelines for biosignatures potentially obtained by a future Enceladus mission and the SUrface Dust Analyzer (SUDA) instrument onboard Europa Clipper. This article is part of the theme issue 'Dust in the Solar System and beyond'.
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Affiliation(s)
- Nozair Khawaja
- Department of Planetary Sciences and Remote Sensing, Institut für Geologische Wissenschaften, Freie Universität Berlin , Malteserstraße, Berlin 12249, Germany
- Institute of Space Systems, University of Stuttgart , Stuttgart 70569, Germany
| | - Lucía Hortal Sánchez
- Department of Planetary Sciences and Remote Sensing, Institut für Geologische Wissenschaften, Freie Universität Berlin , Malteserstraße, Berlin 12249, Germany
| | - Thomas R O'Sullivan
- Department of Planetary Sciences and Remote Sensing, Institut für Geologische Wissenschaften, Freie Universität Berlin , Malteserstraße, Berlin 12249, Germany
| | - Judith Bloema
- Department of Planetary Sciences and Remote Sensing, Institut für Geologische Wissenschaften, Freie Universität Berlin , Malteserstraße, Berlin 12249, Germany
| | - Maryse Napoleoni
- Department of Planetary Sciences and Remote Sensing, Institut für Geologische Wissenschaften, Freie Universität Berlin , Malteserstraße, Berlin 12249, Germany
| | - Fabian Klenner
- Department of Earth and Space Sciences, University of Washington , Seattle, WA 98195, USA
| | - Andreas Beinlich
- Department of Mineralogy and Petrology, Institut für Geologische Wissenschaften, Freie Universität Berlin , Malteserstraße, Berlin 12249, Germany
| | - Jon Hillier
- Department of Planetary Sciences and Remote Sensing, Institut für Geologische Wissenschaften, Freie Universität Berlin , Malteserstraße, Berlin 12249, Germany
| | - Timm John
- Department of Mineralogy and Petrology, Institut für Geologische Wissenschaften, Freie Universität Berlin , Malteserstraße, Berlin 12249, Germany
| | - Frank Postberg
- Department of Planetary Sciences and Remote Sensing, Institut für Geologische Wissenschaften, Freie Universität Berlin , Malteserstraße, Berlin 12249, Germany
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2
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Sheng Q, Intoy BF, Halley JW. Effects of Activation Barriers on Quenching to Stabilize Prebiotic Chemical Systems. Life (Basel) 2024; 14:116. [PMID: 38255731 PMCID: PMC11232558 DOI: 10.3390/life14010116] [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: 12/04/2023] [Revised: 12/31/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
We have previously shown in model studies that rapid quenches of systems of monomers interacting to form polymer chains can fix nonequilibrium chemistries with some lifelike properties. We suggested that such quenching processes might have occurred at very high rates on early Earth, giving an efficient mechanism for natural sorting through enormous numbers of nonequilibrium chemistries from which the most lifelike ones could be naturally selected. However, the model used for these studies did not take account of activation barriers to polymer scission (peptide bond hydrolysis in the case of proteins). Such barriers are known to exist and are expected to enhance the quenching effect. Here, we introduce a modified model which takes activation barriers into account and we compare the results to data from experiments on quenched systems of amino acids. We find that the model results turn out to be sensitive to the width of the distribution of barrier heights but quite insensitive to its average value. The results of the new model are in significantly better agreement with the experiments than those found using our previous model. The new parametrization of the model only requires one new parameter and the parametrization is more physical than the previous one, providing a chemical interpretation of the parameter p in our previous models. Within the model, a characteristic temperature Tc emerges such that if the temperature of the hot stage is above Tc and the temperature of the cold stage is below it, then the 'freezing out', in a quench, of a disequilibrium ensemble of long polymers is expected. We discuss the possible relevance of this to models of the origin of life in emissions from deep ocean rifts.
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Affiliation(s)
| | | | - J. W. Halley
- School of Physics and Astronomy, University of Minnesota-Twin
Cities, Minneapolis, MN 55455, USA (B.F.I.)
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Some Factors from Theory, Simulation, Experiment and Proteomes in the Current Biosphere Supporting Deep Oceans as the Location of the Origin of Terrestrial Life. Life (Basel) 2022; 12:life12091330. [PMID: 36143367 PMCID: PMC9503746 DOI: 10.3390/life12091330] [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: 06/25/2022] [Revised: 08/01/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
Some standard arguments are reviewed supporting deep ocean trenches as a likely location for the origin of terrestrial life. An analysis of proteomes of contemporary prokaryotes carried out by this group is cited as supporting evidence, indicating that the original proteins were formed by quenching from temperatures close to the boiling point of water. Coarse-grained simulations of the network formation process which agree quite well with experiments of such quenches both in drying and rapid fluid emission from a hot to a cold fluid are also described and cited as support for such a scenario. We suggest further experiments, observations and theoretical and simulation work to explore this hypothesis.
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Cossu FL, Poddighe M, Stagi L, Anedda R, Innocenzi P. The Born of Fluorescence from Thermally Polymerized Glycine. MACROMOL CHEM PHYS 2022. [DOI: 10.1002/macp.202200052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Franca Lucia Cossu
- Laboratory of Materials Science and Nanotechnology CR‐INSTM Department of Biomedical Sciences University of Sassari Viale San Pietro 43/B Sassari 07100 Italy
| | - Matteo Poddighe
- Laboratory of Materials Science CR‐INSTM Department of Chemistry and Pharmacy University of Sassari Via Vienna 2 Sassari 07100 Italy
- Laboratory of Nanotechnology CR‐INSTM Department of Chemistry and Pharmacy University of Sassari Via Vienna 2 Sassari 07100 Italy
| | - Luigi Stagi
- Laboratory of Materials Science CR‐INSTM Department of Chemistry and Pharmacy University of Sassari Via Vienna 2 Sassari 07100 Italy
- Laboratory of Nanotechnology CR‐INSTM Department of Chemistry and Pharmacy University of Sassari Via Vienna 2 Sassari 07100 Italy
| | - Roberto Anedda
- Porto Conte Ricerche Strada Provinciale 55, Porto Conte Capo Caccia, km. 8,400 Alghero (SS) 07041 Italy
| | - Plinio Innocenzi
- Laboratory of Materials Science and Nanotechnology CR‐INSTM Department of Biomedical Sciences University of Sassari Viale San Pietro 43/B Sassari 07100 Italy
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5
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Sheng Q, Intoy B, Halley JW. Quenching to fix metastable states in models of prebiotic chemistry. Phys Rev E 2021; 102:062412. [PMID: 33465996 DOI: 10.1103/physreve.102.062412] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 11/13/2020] [Indexed: 11/07/2022]
Abstract
For prebiotic chemistry to succeed in producing a starting metastable, autocatalytic and reproducing system subject to evolutionary selection it must satisfy at least two apparently contradictory requirements: Because such systems are rare, a search among vast numbers of molecular combinations must take place naturally, requiring rapid rearrangement and breaking of covalent bonds. But once a relevant system is found, such rapid disruption and rearrangement would be very likely to destroy the system before much evolution could take place. In this paper we explore the possibility, using a model developed previously, that the search process could occur under different environmental conditions than the subsequent fixation and growth of a lifelike chemical system. We use the example of a rapid change in temperature to illustrate the effect and refer to the rapid change as a "quench"borrowing terminology from study of the physics and chemistry of glass formation. The model study shows that interrupting a high-temperature nonequilibrium state with a rapid quench to lower temperatures can substantially increase the probability of producing a chemical state with lifelike characteristics of nonequilibrium metastability, internal dynamics and exponential population growth in time. Previously published data on the length distributions of proteomes of prokaryotes may be consistent with such an idea and suggest a prebiotic high-temperature "search" phase near the boiling point of water. A rapid change in pH could have a similar effect. We discuss possible scenarios on early Earth which might have allowed frequent quenches of the sort considered here to have occurred. The models show a strong dependence of the effect on the number of chemical monomers available for bond formation.
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Affiliation(s)
- Qianyi Sheng
- School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Ben Intoy
- School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - J W Halley
- School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota 55455, USA
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Rimola A, Sodupe M, Ugliengo P. Role of Mineral Surfaces in Prebiotic Chemical Evolution. In Silico Quantum Mechanical Studies. Life (Basel) 2019; 9:E10. [PMID: 30658501 PMCID: PMC6463156 DOI: 10.3390/life9010010] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 01/10/2019] [Accepted: 01/12/2019] [Indexed: 01/07/2023] Open
Abstract
There is a consensus that the interaction of organic molecules with the surfaces of naturally-occurring minerals might have played a crucial role in chemical evolution and complexification in a prebiotic era. The hurdle of an overly diluted primordial soup occurring in the free ocean may have been overcome by the adsorption and concentration of relevant molecules on the surface of abundant minerals at the sea shore. Specific organic⁻mineral interactions could, at the same time, organize adsorbed molecules in well-defined orientations and activate them toward chemical reactions, bringing to an increase in chemical complexity. As experimental approaches cannot easily provide details at atomic resolution, the role of in silico computer simulations may fill that gap by providing structures and reactive energy profiles at the organic⁻mineral interface regions. Accordingly, numerous computational studies devoted to prebiotic chemical evolution induced by organic⁻mineral interactions have been proposed. The present article aims at reviewing recent in silico works, mainly focusing on prebiotic processes occurring on the mineral surfaces of clays, iron sulfides, titanium dioxide, and silica and silicates simulated through quantum mechanical methods based on the density functional theory (DFT). The DFT is the most accurate way in which chemists may address the behavior of the molecular world through large models mimicking chemical complexity. A perspective on possible future scenarios of research using in silico techniques is finally proposed.
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Affiliation(s)
- Albert Rimola
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
| | - Mariona Sodupe
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
| | - Piero Ugliengo
- Dipartimento di Chimica and Nanostructured Interfaces and Surfaces (NIS), Università degli Studi di Torino, Via P. Giuria 7, 10125 Torino, Italy.
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Dalai P, Pleyer HL, Strasdeit H, Fox S. The Influence of Mineral Matrices on the Thermal Behavior of Glycine. ORIGINS LIFE EVOL B 2017; 47:427-452. [PMID: 27757771 DOI: 10.1007/s11084-016-9523-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 08/27/2016] [Indexed: 10/20/2022]
Abstract
On the Hadean-Early Archean Earth, the first islands must have provided hot and dry environments for abiotically formed organic molecules. The heat sources, mainly volcanism and meteorite impacts, were also available on Mars during the Noachian period. In recent work simulating this scenario, we have shown that neat glycine forms a black, sparingly water-soluble polymer ("thermomelanoid") when dry-heated at 200 °C under pure nitrogen. The present study explores whether relevant minerals and mineral mixtures can change this thermal behavior. Most experiments were conducted at 200 or 250 °C for 2 or 7 days. The mineral matrices used were phyllosilicates (Ca-montmorillonites SAz-1 and STx-1, Na-montmorillonite SAz-1-Na, nontronite NAu-1, kaolinite KGa-1), salts (NaCl, NaCl-KCl, CaCl2, artificial sea salt, gypsum, magnesite), picritic basalt, and three Martian regolith simulants (P-MRS, S-MRS, JSC Mars-1A). The main analytical method employed was high-performance liquid chromatography (HPLC). Glycine intercalated in SAz-1 and SAz-1-Na was well protected against thermomelanoid formation and sublimation at 200 °C: after 2 days, 95 and 79 %, respectively, had either survived unaltered or been transformed into the cyclic dipeptide (DKP) and linear peptides up to Gly6. The glycine survival rate followed the order SAz-1 > SAz-1-Na > STx-1 ≈ NAu-1 > KGa-1. Very good protection was also provided by artificial sea salt (84 % unaltered glycine after 200 °C for 7 days). P-MRS promoted the condensation up to Gly6, consistent with its high phyllosilicate content. The remaining matrices were less effective in preserving glycine as such or as peptides.
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Affiliation(s)
- Punam Dalai
- Department of Bioinorganic Chemistry, Institute of Chemistry, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany
| | - Hannes Lukas Pleyer
- Department of Bioinorganic Chemistry, Institute of Chemistry, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany
| | - Henry Strasdeit
- Department of Bioinorganic Chemistry, Institute of Chemistry, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany.
| | - Stefan Fox
- Department of Bioinorganic Chemistry, Institute of Chemistry, University of Hohenheim, Garbenstr. 30, 70599, Stuttgart, Germany
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Mayer C, Schreiber U, Dávila MJ. Selection of Prebiotic Molecules in Amphiphilic Environments. Life (Basel) 2017; 7:life7010003. [PMID: 28067845 PMCID: PMC5370403 DOI: 10.3390/life7010003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/03/2017] [Accepted: 01/04/2017] [Indexed: 11/16/2022] Open
Abstract
A basic problem in all postulated pathways of prebiotic chemistry is the low concentration which generally is expected for interesting reactants in fluid environments. Even though compounds, like nucleobases, sugars or peptides, principally may form spontaneously under environmental conditions, they will always be rapidly diluted in an aqueous environment. In addition, any such reaction leads to side products which often exceed the desired compound and generally hamper the first steps of a subsequent molecular evolution. Therefore, a mechanism of selection and accumulation of relevant prebiotic compounds seems to be crucial for molecular evolution. A very efficient environment for selection and accumulation can be found in the fluid continuum circulating in tectonic fault zones. Vesicles which form spontaneously at a depth of approximately 1 km present a selective trap for amphiphilic molecules, especially for peptides composed of hydrophilic and hydrophobic amino acids in a suitable sequence. The accumulation effect is shown in a numeric simulation on a simplified model. Further, possible mechanisms of a molecular evolution in vesicle membranes are discussed. Altogether, the proposed scenario can be seen as an ideal environment for constant, undisturbed molecular evolution in and on cell-like compartments.
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Affiliation(s)
- Christian Mayer
- Institute of Physical Chemistry, CENIDE University of Duisburg-Essen, 45141 Essen, Germany.
| | - Ulrich Schreiber
- Department of Geology, University of Duisburg-Essen, 45141 Essen, Germany.
| | - María J Dávila
- Department of Geology, University of Duisburg-Essen, 45141 Essen, Germany.
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9
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Fox S, Dalai P, Lambert JF, Strasdeit H. Hypercondensation of an amino acid: synthesis and characterization of a black glycine polymer. Chemistry 2015; 21:8897-904. [PMID: 25933438 DOI: 10.1002/chem.201500820] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Indexed: 12/24/2022]
Abstract
A granular material was obtained by thermal polymerization of glycine at 200 °C. It has been named "thermomelanoid" because of its strikingly deep-black color. The polymerization process is mainly a dehydration condensation leading to conventional amide bonds, and also CC double bonds that are formed from CO and CH2 groups ("hypercondensation"). Spectroscopic data, in particular from (13) C and (15) N solid-state cross-polarization magic angle spinning (CP-MAS) NMR spectra, suggest that the black color is due to (cross-)conjugated CC, CO, and NH groups. Small glycine peptides, especially triglycine, appear to be key intermediates in the formation of the thermomelanoid. This has been concluded by comparing the thermal behavior of glyn homopeptides (n=2-6) and glycine. The glycine polymerization was accompanied by the formation of small amounts of byproducts. Notably, a few percent of alanine and aspartic acid could be detected in the polymer. By using (13) C-labeled glycine, it was shown that these two amino acids formed through a common pathway, namely CαCα bond formation between glycine molecules. The thermomelanoid is hydrolyzed by strong acids and bases at room temperature, forming brown solutions.
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Affiliation(s)
- Stefan Fox
- Institut für Chemie, Universität Hohenheim, Garbenstr. 30, 70599 Stuttgart (Germany)
| | - Punam Dalai
- Institut für Chemie, Universität Hohenheim, Garbenstr. 30, 70599 Stuttgart (Germany)
| | - Jean-François Lambert
- Laboratoire de Réactivité de Surface, UMR CNRS 7197, Université Pierre et Marie Curie, Paris 6, 4 place Jussieu, 75252 Paris Cedex 05 (France)
| | - Henry Strasdeit
- Institut für Chemie, Universität Hohenheim, Garbenstr. 30, 70599 Stuttgart (Germany).
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Periodic Vesicle Formation in Tectonic Fault Zones--an Ideal Scenario for Molecular Evolution. ORIGINS LIFE EVOL B 2015; 45:139-48. [PMID: 25716918 PMCID: PMC4457167 DOI: 10.1007/s11084-015-9411-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 11/12/2014] [Indexed: 11/19/2022]
Abstract
Tectonic fault systems in the continental crust offer huge networks of interconnected channels and cavities. Filled mainly with water and carbon dioxide (CO2), containing a wide variety of hydrothermal chemistry and numerous catalytic surfaces, they may offer ideal reaction conditions for prebiotic chemistry. In these systems, an accumulation zone for organic compounds will develop at a depth of approximately 1 km where CO2 turns sub-critical and dissolved components precipitate. At this point, periodic pressure changes caused for example by tidal influences or geyser activity may generate a cyclic process involving repeated phase transitions of carbon dioxide. In the presence of amphiphilic compounds, this will necessarily lead to the transient formation of coated water droplets in the gas phase and corresponding vesicular structures in the aqueous environment. During this process, the concentration of organic components inside the droplets and vesicles would be drastically increased, allowing for favorable reaction conditions and, in case of the vesicles generated, large trans-membrane concentration gradients. Altogether, the process of periodic formation and destruction of vesicles could offer a perfect environment for molecular evolution in small compartments and for the generation of protocells. The basic process of vesicle formation is reproduced experimentally with a lipid in a water/CO2 system.
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Olasagasti F, Maurel MC, Deamer D. Physico-chemical interactions between compartment-forming lipids and other prebiotically relevant biomolecules. BIO WEB OF CONFERENCES 2014. [DOI: 10.1051/bioconf/20140205001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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Ruiz-Mirazo K, Briones C, de la Escosura A. Prebiotic Systems Chemistry: New Perspectives for the Origins of Life. Chem Rev 2013; 114:285-366. [DOI: 10.1021/cr2004844] [Citation(s) in RCA: 563] [Impact Index Per Article: 51.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kepa Ruiz-Mirazo
- Biophysics
Unit (CSIC-UPV/EHU), Leioa, and Department of Logic and Philosophy
of Science, University of the Basque Country, Avenida de Tolosa 70, 20080 Donostia−San Sebastián, Spain
| | - Carlos Briones
- Department
of Molecular Evolution, Centro de Astrobiología (CSIC−INTA, associated to the NASA Astrobiology Institute), Carretera de Ajalvir, Km 4, 28850 Torrejón de Ardoz, Madrid, Spain
| | - Andrés de la Escosura
- Organic
Chemistry Department, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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Piedrafita G, Ruiz-Mirazo K, Monnard PA, Cornish-Bowden A, Montero F. Viability conditions for a compartmentalized protometabolic system: a semi-empirical approach. PLoS One 2012; 7:e39480. [PMID: 22761803 PMCID: PMC3384665 DOI: 10.1371/journal.pone.0039480] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 05/24/2012] [Indexed: 11/18/2022] Open
Abstract
In this work we attempt to find out the extent to which realistic prebiotic compartments, such as fatty acid vesicles, would constrain the chemical network dynamics that could have sustained a minimal form of metabolism. We combine experimental and simulation results to establish the conditions under which a reaction network with a catalytically closed organization (more specifically, an (M,R-system) would overcome the potential problem of self-suffocation that arises from the limited accessibility of nutrients to its internal reaction domain. The relationship between the permeability of the membrane, the lifetime of the key catalysts and their efficiency (reaction rate enhancement) turns out to be critical. In particular, we show how permeability values constrain the characteristic time scale of the bounded protometabolic processes. From this concrete and illustrative example we finally extend the discussion to a wider evolutionary context.
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Affiliation(s)
- Gabriel Piedrafita
- Departamento de Bioquímica y Biología Molecular I, Universidad Complutense de Madrid, Madrid, Spain
| | - Kepa Ruiz-Mirazo
- Departamento de Lógica y Filosofía de la Ciencia, Universidad del País Vasco, Donostia-San Sebastián, Spain
- Unidad de Biofísica, Consejo Superior de Investigaciones Científicas-Universidad del País Vasco, Leioa, Spain
| | - Pierre-Alain Monnard
- Center for Fundamental Living Technology, University of Southern Denmark, Odense, Denmark
| | - Athel Cornish-Bowden
- Unité de Bioénergétique et Ingénierie des Protéines, Centre National de la Recherche Scientifique, Marseille, France
| | - Francisco Montero
- Departamento de Bioquímica y Biología Molecular I, Universidad Complutense de Madrid, Madrid, Spain
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Saladino R, Botta G, Pino S, Costanzo G, Di Mauro E. Genetics first or metabolism first? The formamide clue. Chem Soc Rev 2012; 41:5526-65. [PMID: 22684046 DOI: 10.1039/c2cs35066a] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Life is made of the intimate interaction of metabolism and genetics, both built around the chemistry of the most common elements of the Universe (hydrogen, oxygen, nitrogen, and carbon). The transmissible interaction of metabolic and genetic cycles results in the hypercycles of organization and de-organization of chemical information, of living and non-living. The origin-of-life quest has long been split into several attitudes exemplified by the aphorisms "genetics-first" or "metabolism-first". Recently, the opposition between these approaches has been solved by more unitary theoretical and experimental frames taking into account energetic, evolutionary, proto-metabolic and environmental aspects. Nevertheless, a unitary and simple chemical frame is still needed that could afford both the precursors of the synthetic pathways eventually leading to RNA and to the key components of the central metabolic cycles, possibly connected with the synthesis of fatty acids. In order to approach the problem of the origin of life it is therefore reasonable to start from the assumption that both metabolism and genetics had a common origin, shared a common chemical frame, and were embedded under physical-chemical conditions favourable for the onset of both. The singleness of such a prebiotically productive chemical process would partake of Darwinian advantages over more complex fragmentary chemical systems. The prebiotic chemistry of formamide affords in a single and simple physical-chemical frame nucleic bases, acyclonucleosides, nucleotides, biogenic carboxylic acids, sugars, amino sugars, amino acids and condensing agents. Thus, we suggest the possibility that formamide could have jointly provided the main components for the onset of both (pre)genetic and (pre)metabolic processes. As a note of caution, we discuss the fact that these observations only indicate possible solutions at the level of organic substrates, not at the systemic chemical level.
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Affiliation(s)
- Raffaele Saladino
- Dipartimento di Agrobiologia ed Agrochimica, Università della Tuscia, Via San Camillo De Lellis, 01100 Viterbo, Italy.
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15
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Cohn CA, Lemieux CL, Long AS, Kystol J, Vogel U, White PA, Madsen AM. Physical-chemical and microbiological characterization, and mutagenic activity of airborne PM sampled in a biomass-fueled electrical production facility. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2011; 52:319-330. [PMID: 20872826 DOI: 10.1002/em.20628] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2010] [Accepted: 07/28/2010] [Indexed: 05/29/2023]
Abstract
Biomass combustion is used in heating and electric power generation in many areas of the world. Airborne particulate matter (PM) is released when biomass is brought to a facility, stored, and combusted. Occupational exposure to airborne PM within biomass-fueled facilities may lead to health problems. In March and August of 2006, airborne PM was collected from a biomass-fueled facility located in Denmark. In addition, source-specific PM was generated from straw and wood pellets using a rotating drum. The PM was analyzed for polycyclic aromatic hydrocarbons (PAHs), metals, microbial components, mutagenic activity, and ability to generate highly reactive oxygen species (hROS) in cell-free aqueous suspensions. PM collected from the boiler room and the biomass storage hall had higher levels of mutagenic activity, PAHs and metals, and a higher hROS generating potential than the source specific PM. The mutagenic activity was generally more potent without S9 activation, and on the metabolically enhanced strain YG1041, relative to TA98. Significant correlations were found between mutagenicity on YG1041 (without S9) and PAH concentration and mutagenicity on YG1041 (with S9) and hROS generating ability. PM collected in March was more toxic than PM collected in August. Overall, airborne PM collected from the facility, especially that from the boiler room, were more toxic than PM generated from straw and wood chips. The results suggest that exposure to combustion PM in a biomass-fueled facility, which likely includes PM from biomass combustion as well as internal combustion vehicles, may contribute to an elevated risk of adverse health effects.
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Affiliation(s)
- Corey A Cohn
- National Research Centre for the Working Environment, Copenhagen, Denmark
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Pizzarello S, Shock E. The organic composition of carbonaceous meteorites: the evolutionary story ahead of biochemistry. Cold Spring Harb Perspect Biol 2010; 2:a002105. [PMID: 20300213 PMCID: PMC2829962 DOI: 10.1101/cshperspect.a002105] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Carbon-containing meteorites provide a natural sample of the extraterrestrial organic chemistry that occurred in the solar system ahead of life's origin on the Earth. Analyses of 40 years have shown the organic content of these meteorites to be materials as diverse as kerogen-like macromolecules and simpler soluble compounds such as amino acids and polyols. Many meteoritic molecules have identical counterpart in the biosphere and, in a primitive group of meteorites, represent the majority of their carbon. Most of the compounds in meteorites have isotopic compositions that date their formation to presolar environments and reveal a long and active cosmochemical evolution of the biogenic elements. Whether this evolution resumed on the Earth to foster biogenesis after exogenous delivery of meteoritic and cometary materials is not known, yet, the selective abundance of biomolecule precursors evident in some cosmic environments and the unique L-asymmetry of some meteoritic amino acids are suggestive of their possible contribution to terrestrial molecular evolution.
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Affiliation(s)
- Sandra Pizzarello
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, USA.
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17
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Maheen G, Tian G, Wang Y, He C, Shi Z, Yuan H, Feng S. Resolving the enigma of prebiotic COP bond formation: Prebiotic hydrothermal synthesis of important biological phosphate esters. HETEROATOM CHEMISTRY 2010. [DOI: 10.1002/hc.20591] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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18
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Cleaves HJ, Aubrey AD, Bada JL. An evaluation of the critical parameters for abiotic peptide synthesis in submarine hydrothermal systems. ORIGINS LIFE EVOL B 2009; 39:109-26. [PMID: 19037745 DOI: 10.1007/s11084-008-9154-1] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2008] [Accepted: 10/18/2008] [Indexed: 10/21/2022]
Abstract
It has been proposed that oligopeptides may be formed in submarine hydrothermal systems (SHSs). Oligopeptides have been synthesized previously under simulated SHS conditions which are likely geochemically implausible. We have herein investigated the oligomerization of glycine under SHS-like conditions with respect to the limitations imposed by starting amino acid concentration, heating time, and temperature. When 10(-1) M glycine solutions were heated at 250 degrees C for < 20 min glycine oligomers up to tetramers and diketopiperazine (DKP) were detectable. At 200 degrees C, less oligomerization was noted. Peptides beyond glycylglycine (gly2) and DKP were not detected below 150 degrees C. At 10(-2) M initial glycine concentration and below, only gly2, DKP, and gly3 were detected, and then only above 200 degrees C at < 20 min reaction time. Gly3 was undetectable at longer reaction times. The major parameters limiting peptide synthesis in SHSs appear to be concentration, time, and temperature. Given the expected low concentrations of amino acids, the long residence times and range of temperatures in SHSs, it is unlikely that SHS environments were robust sources of even simple peptides. Possible unexplored solutions to the problems presented here are also discussed.
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Affiliation(s)
- H J Cleaves
- Geophysical Laboratory, The Carnegie Institution of Washington, Washington, DC 20015, USA
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19
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Benetoli LOB, de Souza CMD, da Silva KL, de Souza IG, de Santana H, Paesano A, da Costa ACS, Zaia CTBV, Zaia DAM. Amino acid interaction with and adsorption on clays: FT-IR and Mössbauer spectroscopy and X-ray diffractometry investigations. ORIGINS LIFE EVOL B 2007; 37:479-93. [PMID: 17578677 DOI: 10.1007/s11084-007-9072-7] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2006] [Accepted: 04/06/2007] [Indexed: 11/28/2022]
Abstract
In the present paper, the adsorption of amino acids (Ala, Met, Gln, Cys, Asp, Lys, His) on clays (bentonite, kaolinite) was studied at different pH (3.00, 6.00, 8.00). The amino acids were dissolved in seawater, which contains the major elements. There were two main findings in this study. First, amino acids with a charged R group (Asp, Lys, His) and Cys were adsorbed on clays more than Ala, Met and Gln (uncharged R groups). However, 74% of the amino acids in the proteins of modern organisms have uncharged R groups. These results raise some questions about the role of minerals in providing a prebiotic concentration mechanism for amino acids. Several mechanisms are also discussed that could produce peptide with a greater proportion of amino acids with uncharged R groups. Second, Cys could play an important role in prebiotic chemistry besides participating in the structure of peptides/proteins. The FT-IR spectra showed that the adsorption of amino acids on the clays occurs through the amine group. However, the Cys/clay interaction occurs through the sulfhydryl and amine groups. X-ray diffractometry showed that pH affects the bentonite interlayer, and at pH 3.00 the expansion of Cys/bentonite was greater than that of the samples of ethylene glycol/bentonite saturated with Mg. The Mössbauer spectrum for the sample with absorbed Cys showed a large increase ( approximately 20%) in ferrous ions. This means that Cys was able to partially reduce iron present in bentonite. This result is similar to that which occurs with aconitase where the ferric ions are reduced to Fe 2.5.
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Affiliation(s)
- Luís O B Benetoli
- Departamento de Química-CCE, Universidade Estadual de Londrina, 86051-990 Londrina-PR, Brazil
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20
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Abstract
Synthetic biology as a broad and novel field has also a chemical branch: whereas synthetic biology generally has to do with bioengineering of new forms of life (generally bacteria) which do not exist in nature, 'chemical synthetic biology' is concerned with the synthesis of chemical structures such as proteins, nucleic acids, vesicular forms, and other which do not exist in nature. Three examples of this 'chemical synthetic biology' approach are given in this article. The first example deals with the synthesis of proteins that do not exist in nature, and dubbed as 'the never born proteins' (NBPs). This research is related to the question why and how the protein structures existing in our world have been selected out, with the underlying question whether they have something very particular from the structural or thermodynamic point of view (for example, the folding). The NBPs are produced in the laboratory by the modern molecular biology technique, the phage display, so as to produce a very large library of proteins having no homology with known proteins. The second example of chemical synthetic biology has also to do with the laboratory synthesis of proteins, but, this time, adopting a prebiotic synthetic procedure, the fragment condensation of short peptides, where short means that they have a length that can be obtained by prebiotic methods; for example, from the condensation of N-carboxy anhydrides. The scheme is illustrated and discussed, being based on the fragment condensation catalyzed by peptides endowed with proteolitic activity. Selection during chain growth is determined by solubility under the contingent environmental conditions, i.e., the peptides which result insoluble are eliminated from further growth. The scheme is tested preliminarily with a synthetic chemical fragment-condensation method and brings to the synthesis of a 44-residues-long protein, which has no homology with known proteins, and which has a stable tertiary folding. Finally, the third example, dubbed as 'the minimal cell project'. Here, the aim is to synthesize a cell model having the minimal and sufficient number of components to be defined as living. For this purpose, liposomes are used as shell membranes, and attempts are made to introduce in the interior a minimal genome. Several groups all around the world are active in this field, and significant results have been obtained, which are reviewed in this article. For example, protein expression has been obtained inside liposomes, generally with the green fluorescent protein, GFP. Our last attempts are with a minimal genome consisting of 37 enzymes, a set which is able to express proteins using the ribosomal machinery. These minimal cells are not yet capable of self-reproduction, and this and other shortcomings within the project are critically reviewed.
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Affiliation(s)
- Pier Luigi Luisi
- Department Biology, University of Roma TRE, Viale G. Marconi 446, I-00146 Roma.
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Cockell CS. The origin and emergence of life under impact bombardment. Philos Trans R Soc Lond B Biol Sci 2006; 361:1845-55; discussion 1856. [PMID: 17008223 PMCID: PMC1664688 DOI: 10.1098/rstb.2006.1908] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Craters formed by asteroids and comets offer a number of possibilities as sites for prebiotic chemistry, and they invite a literal application of Darwin's 'warm little pond'. Some of these attributes, such as prolonged circulation of heated water, are found in deep-ocean hydrothermal vent systems, previously proposed as sites for prebiotic chemistry. However, impact craters host important characteristics in a single location, which include the formation of diverse metal sulphides, clays and zeolites as secondary hydrothermal minerals (which can act as templates or catalysts for prebiotic syntheses), fracturing of rock during impact (creating a large surface area for reactions), the delivery of iron in the case of the impact of iron-containing meteorites (which might itself act as a substrate for prebiotic reactions), diverse impact energies resulting in different rates of hydrothermal cooling and thus organic syntheses, and the indiscriminate nature of impacts into every available lithology-generating large numbers of 'experiments' in the origin of life. Following the evolution of life, craters provide cryptoendolithic and chasmoendolithic habitats, particularly in non-sedimentary lithologies, where limited pore space would otherwise restrict colonization. In impact melt sheets, shattered, mixed rocks ultimately provided diverse geochemical gradients, which in present-day craters support the growth of microbial communities.
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Affiliation(s)
- Charles S Cockell
- Centre for Earth, Planetary, Space and Astronomical Research, Open University, Milton Keynes MK7 6AA, UK.
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Chessari S, Thomas R, Polticelli F, Luisi PL. The Production ofde novo Folded Proteins by a Stepwise Chain Elongation: A Model for Prebiotic Chemical Evolution of Macromolecular Sequences. Chem Biodivers 2006; 3:1202-10. [PMID: 17193233 DOI: 10.1002/cbdv.200690121] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We describe an experimental procedure to mimic the formation of long (over 40 residues) co-oligopetide sequences in many identical copies which may have occurred in the prebiotic molecular evolution. The basic hypothesis is that chain formation is based on the stepwise fragment condensation of randomly generated short oligopeptides, whereby the elongation takes place under the contingent environmental constraints (solubility, pH, salinity), which eliminate most of the products, and thus determine the selection towards one particular small set of chains. The present work aims at verifying the validity of this scheme. In order to do so, we utilize a classic synthetic procedure based on the Merrifield solid-phase synthesis of peptides for the synthesis of randomly produced peptides as well as for their stepwise fragment condensation. Thus, starting from a library of peptides with n=10, the first condensation step produces a library of 16 peptides with 20 residues each (n=20), of which only four remain water-soluble and, therefore, capable to undergo the next fragment condensation step. This gives rise to 16 peptides with n=30, out of which twelve precipitate out under the chosen pH and buffer conditions and are eliminated. Finally, a 44-residue-long water-soluble de novo protein is obtained. This has no homologies or similarities with extant proteins, and, based on circular dichroism (CD), it assumes a stable three-dimensional folding. In agreement with CD data, molecular-modelling simulations suggest an helical fold for the protein with poor, if any, structural homology with known proteins. The implication of this procedure as a general mechanism for the etiology of de novo macromolecular sequences and globular proteins in the origin of life is briefly discussed.
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Affiliation(s)
- Salvatore Chessari
- Department of Materials, Swiss Federal Institute of Technology, ETHZ, CH-8093 Zürich
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Schmidt P. Evolution of homochirality by epimerization of random peptide chains. A stochastic model. ORIGINS LIFE EVOL B 2006; 36:391-411. [PMID: 16791733 DOI: 10.1007/s11084-005-9007-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2005] [Revised: 11/20/2005] [Accepted: 11/20/2005] [Indexed: 10/24/2022]
Abstract
A cyclic process is described which is constituted of polymerization, epimerization, and hydrolysis steps. During the first cycle peptides with random sequences are formed from racemic amino acids. A small portion of these peptides have substructures with a terminal residue linked to a homochiral sequence of optical antipodes. In such a substructure the terminal residue is assumed to invert into its mirror image so that a thermodynamically favourable epimeric stucture with continuous homochirality is formed. In the hydrolysis step the peptides are split back to monomeric units with retention of configuration. Due to stochastic differences between L- and D-substructures a net excess of one of the enantiomers results. This excess enhances the probability of the formation of substructures having the dominant configuration in the next cycle. It is shown by probabilistic considerations and computer simulations that this mechanism generates an autocatalytic growth of one of the enantiomers which finally results in homochiral populations of amino acids. The number of cycles necessary to attain homochirality depends on the number of residues of the substructure, on the chain length distribution of the polymers and on the total number of amino acid units.
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Affiliation(s)
- Peter Schmidt
- Suedtiroler Ring 28, D 67273, Weisenheim/Berg, Germany.
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Togashi T, Umetsu M, Tsuchizaki H, Ohara S, Naka T, Adschiri T. Simultaneous Synthesis and Self-assembly of Cyclic Diphenylalanine at Hydrothermal Condition. CHEM LETT 2006. [DOI: 10.1246/cl.2006.636] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Furuuchi R, Imai EI, Honda H, Hatori K, Matsuno K. Evolving lipid vesicles in prebiotic hydrothermal environments. ORIGINS LIFE EVOL B 2005; 35:333-43. [PMID: 16228647 DOI: 10.1007/s11084-005-2039-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2003] [Accepted: 04/05/2004] [Indexed: 10/25/2022]
Abstract
We compared three different kinds of lipid vesicles made of saturated fatty acids, unsaturated fatty acids, and phospholipids for their evolutionary capabilities in a simulated hydrothermal environment. Encapsulation of the glycine monomers enhanced the oligomerization of peptides in all cases. Fatty acid vesicles remained stable at higher temperatures and efficiently utilized heat energy for this synthetic reaction. Phospholipid vesicles were destabilized by higher temperatures, and thus were found to be better suited to enhance synthetic reactions at lower temperatures.
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Affiliation(s)
- Ryo Furuuchi
- Department of BioEngineering, Nagaoka University of Technology, Nagaoka, 940-2188, Japan
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Abstract
Popular hypotheses that attempt to explain the origin of prebiotic molecules and cellular life capable of growth and division are not always agreed upon. In this manuscript, information on early bacterial life on Earth is examined using information from several disciplines. For example, knowledge can be integrated from physics, thermodynamics, planetary sciences, geology, biogeochemistry, lipid chemistry, primordial cell structures, cell and molecular biology, microbiology, metabolism and genetics. The origin of life also required a combination of elements, compounds and environmental physical-chemical conditions that allowed cells to assemble in less than a billion years. This may have been widespread in the subsurface of the early Earth located at microscopic physical domains.
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Affiliation(s)
- J T Trevors
- Laboratory of Microbial Technology, Department of Environmental Biology, University of Guelph, Guelph, Ont., Canada N1G 2W1.
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