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Helmbrecht V, Weingart M, Klein F, Braun D, Orsi WD. White and green rust chimneys accumulate RNA in a ferruginous chemical garden. GEOBIOLOGY 2023; 21:758-769. [PMID: 37615250 DOI: 10.1111/gbi.12572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/17/2023] [Accepted: 08/12/2023] [Indexed: 08/25/2023]
Abstract
Mechanisms of nucleic acid accumulation were likely critical to life's emergence in the ferruginous oceans of the early Earth. How exactly prebiotic geological settings accumulated nucleic acids from dilute aqueous solutions, is poorly understood. As a possible solution to this concentration problem, we simulated the conditions of prebiotic low-temperature alkaline hydrothermal vents in co-precipitation experiments to investigate the potential of ferruginous chemical gardens to accumulate nucleic acids via sorption. The injection of an alkaline solution into an artificial ferruginous solution under anoxic conditions (O2 < 0.01% of present atmospheric levels) and at ambient temperatures, caused the precipitation of amakinite ("white rust"), which quickly converted to chloride-containing fougerite ("green rust"). RNA was only extractable from the ferruginous solution in the presence of a phosphate buffer, suggesting RNA in solution was bound to Fe2+ ions. During chimney formation, this iron-bound RNA rapidly accumulated in the white and green rust chimney structure from the surrounding ferruginous solution at the fastest rates in the initial white rust phase and correspondingly slower rates in the following green rust phase. This represents a new mechanism for nucleic acid accumulation in the ferruginous oceans of the early Earth, in addition to wet-dry cycles and may have helped to concentrate RNA in a dilute prebiotic ocean.
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Affiliation(s)
- Vanessa Helmbrecht
- Department for Geo- and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Maximilian Weingart
- Systems Biophysics, Faculty of Physics, Ludwig-Maximilians-Universität, Munich, Germany
| | - Frieder Klein
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Dieter Braun
- Systems Biophysics, Faculty of Physics, Ludwig-Maximilians-Universität, Munich, Germany
| | - William D Orsi
- Department for Geo- and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität, Munich, Germany
- GeoBio-CenterLMU, Ludwig-Maximilians-Universität München, Munich, Germany
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Weingart M, Chen S, Donat C, Helmbrecht V, Orsi WD, Braun D, Alim K. Alkaline vents recreated in two dimensions to study pH gradients, precipitation morphology, and molecule accumulation. SCIENCE ADVANCES 2023; 9:eadi1884. [PMID: 37774032 PMCID: PMC10541008 DOI: 10.1126/sciadv.adi1884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/30/2023] [Indexed: 10/01/2023]
Abstract
Alkaline vents (AVs) are hypothesized to have been a setting for the emergence of life, by creating strong gradients across inorganic membranes within chimney structures. In the past, three-dimensional chimney structures were formed under laboratory conditions; however, no in situ visualization or testing of the gradients was possible. We develop a quasi-two-dimensional microfluidic model of AVs that allows spatiotemporal visualization of mineral precipitation in low-volume experiments. Upon injection of an alkaline fluid into an acidic, iron-rich solution, we observe a diverse set of precipitation morphologies, mainly controlled by flow rate and ion concentration. Using microscope imaging and pH-dependent dyes, we show that finger-like precipitates can facilitate formation and maintenance of microscale pH gradients and accumulation of dispersed particles in confined geometries. Our findings establish a model to investigate the potential of gradients across a semipermeable boundary for early compartmentalization, accumulation, and chemical reactions at the origins of life.
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Affiliation(s)
- Maximilian Weingart
- Systems Biophysics and Center for NanoScience (CeNS), Ludwig-Maximilians University Munich, Amalienstraße 54, 80799 München, Germany
| | - Siyu Chen
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany
| | - Clara Donat
- TUM School of Natural Sciences, Department of Bioscience; Center for Protein Assemblies (CPA), Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748 Garching b. München, Germany
| | - Vanessa Helmbrecht
- Department of Earth and Environmental Sciences, Ludwig-Maximilians University Munich, Richard-Wagner Straße 10, 80333 München, Germany
| | - William D. Orsi
- Department of Earth and Environmental Sciences, Ludwig-Maximilians University Munich, Richard-Wagner Straße 10, 80333 München, Germany
- GeoBio-CenterLMU, Ludwig-Maximilians University Munich, Richard-Wagner Straße 10, 80333 München, Germany
| | - Dieter Braun
- Systems Biophysics and Center for NanoScience (CeNS), Ludwig-Maximilians University Munich, Amalienstraße 54, 80799 München, Germany
| | - Karen Alim
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany
- TUM School of Natural Sciences, Department of Bioscience; Center for Protein Assemblies (CPA), Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748 Garching b. München, Germany
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3
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Russell MJ. A self-sustaining serpentinization mega-engine feeds the fougerite nanoengines implicated in the emergence of guided metabolism. Front Microbiol 2023; 14:1145915. [PMID: 37275164 PMCID: PMC10236563 DOI: 10.3389/fmicb.2023.1145915] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 03/22/2023] [Indexed: 06/07/2023] Open
Abstract
The demonstration by Ivan Barnes et al. that the serpentinization of fresh Alpine-type ultramafic rocks results in the exhalation of hot alkaline fluids is foundational to the submarine alkaline vent theory (AVT) for life's emergence to its 'improbable' thermodynamic state. In AVT, such alkaline fluids ≤ 150°C, bearing H2 > CH4 > HS--generated and driven convectively by a serpentinizing exothermic mega-engine operating in the ultramafic crust-exhale into the iron-rich, CO2> > > NO3--bearing Hadean ocean to result in hydrothermal precipitate mounds comprising macromolecular ferroferric-carbonate oxyhydroxide and minor sulfide. As the nanocrystalline minerals fougerite/green rust and mackinawite (FeS), they compose the spontaneously precipitated inorganic membranes that keep the highly contrasting solutions apart, thereby maintaining redox and pH disequilibria. They do so in the form of fine chimneys and chemical gardens. The same disequilibria drive the reduction of CO2 to HCOO- or CO, and the oxidation of CH4 to a methyl group-the two products reacting to form acetate in a sequence antedating the 'energy-producing' acetyl coenzyme-A pathway. Fougerite is a 2D-layered mineral in which the hydrous interlayers themselves harbor 2D solutions, in effect constricted to ~ 1D by preferentially directed electron hopping/tunneling, and proton Gröthuss 'bucket-brigading' when subject to charge. As a redox-driven nanoengine or peristaltic pump, fougerite forces the ordered reduction of nitrate to ammonium, the amination of pyruvate and oxalate to alanine and glycine, and their condensation to short peptides. In turn, these peptides have the flexibility to sequester the founding inorganic iron oxyhydroxide, sulfide, and pyrophosphate clusters, to produce metal- and phosphate-dosed organic films and cells. As the feed to the hydrothermal mound fails, the only equivalent sustenance on offer to the first autotrophs is the still mildly serpentinizing upper crust beneath. While the conditions here are very much less bountiful, they do offer the similar feed and disequilibria the survivors are accustomed to. Sometime during this transition, a replicating non-ribosomal guidance system is discovered to provide the rules to take on the incrementally changing surroundings. The details of how these replicating apparatuses emerged are the hard problem, but by doing so the progenote archaea and bacteria could begin to colonize what would become the deep biosphere. Indeed, that the anaerobic nitrate-respiring methanotrophic archaea and the deep-branching Acetothermia presently comprise a portion of that microbiome occupying serpentinizing rocks offers circumstantial support for this notion. However, the inescapable, if jarring conclusion is drawn that, absent fougerite/green rust, there would be no structured channelway to life.
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Affiliation(s)
- Michael J. Russell
- Dipartimento di Chimica, Università degli Studi di Torino, Torino, Italy
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4
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Angelis G, Katsanou ME, Giannopoulos-Dimitriou A, Vizirianakis IS, Pampalakis G. Generation of chemobrionic jellyfishes that mechanically divide, grow and exhibit biomimetic “symbiosis”. CHEMSYSTEMSCHEM 2022. [DOI: 10.1002/syst.202200001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Georgios Angelis
- Aristotle University of Thessaloniki: Aristoteleio Panepistemio Thessalonikes Pharmacy GREECE
| | - Maria-Eleni Katsanou
- Aristoteleio Panepistimio Thessalonikis: Aristoteleio Panepistemio Thessalonikes Pharmacy GREECE
| | | | - Ioannis S. Vizirianakis
- Aristoteleio Panepistimio Thessalonikis: Aristoteleio Panepistemio Thessalonikes Pharmacy GREECE
| | - Georgios Pampalakis
- Aristotle University of Thessaloniki School of Pharmacy Pharmacy Panepistimioupolis 54124 Thessaloniki GREECE
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Emmanuel M, Lantos E, Horváth D, Tóth Á. Formation and growth of lithium phosphate chemical gardens. SOFT MATTER 2022; 18:1731-1736. [PMID: 35156669 DOI: 10.1039/d1sm01808f] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We show that a chemical garden can be developed from an alkaline metal precipitate using a flow-driven setup. By injecting sodium phosphate solution into lithium chloride solution from below, a liquid jet appears, on which a precipitate grows forming a structure resembling a hydrothermal vent. The precipitate column continuously builds upward until a maximum height is reached. The vertical growth then significantly slows down while the tube diameter still increases. The analysis of the growth profiles has revealed a linear dependence of volume growth rate on the injection rate, hence yielding a universal growth profile. The expansion in diameter, localized at the tip of the structure, scales with a power law suggesting that the phenomenon is controlled by both diffusion and convection.
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Affiliation(s)
- Michael Emmanuel
- Department of Physical Chemistry and Materials Science, University of Szeged, Rerrich Béla tér 1., Szeged, H-6720, Hungary.
| | - Emese Lantos
- Department of Physical Chemistry and Materials Science, University of Szeged, Rerrich Béla tér 1., Szeged, H-6720, Hungary.
| | - Dezső Horváth
- Department of Applied and Environmental Chemistry, University of Szeged, Rerrich Béla tér 1., Szeged, H-6720, Hungary
| | - Ágota Tóth
- Department of Physical Chemistry and Materials Science, University of Szeged, Rerrich Béla tér 1., Szeged, H-6720, Hungary.
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6
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[NiFe]-(Oxy)Sulfides Derived from NiFe2O4 for the Alkaline Hydrogen Evolution Reaction. ENERGIES 2022. [DOI: 10.3390/en15020543] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The development of noble-metal-free electrocatalysts is regarded as a key factor for realizing industrial-scale hydrogen production powered by renewable energy sources. Inspired by nature, which uses Fe- and Ni-containing enzymes for efficient hydrogen generation, Fe/Ni-containing chalcogenides, such as oxides and sulfides, received increasing attention as promising electrocatalysts to produce hydrogen. We herein present a novel synthetic procedure for mixed Fe/Ni (oxy)sulfide materials by the controlled (partial) sulfidation of NiFe2O4 (NFO) nanoparticles in H2S-containing atmospheres. The variation in H2S concentration and the temperature allows for a precise control of stoichiometry and phase composition. The obtained sulfidized materials (NFS) catalyze the hydrogen evolution reaction (HER) with increased activity in comparison to NFO, up to −10 and −100 mA cm−2 at an overpotential of approx. 250 and 450 mV, respectively.
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Weber JM, Henderson BL, LaRowe DE, Goldman AD, Perl SM, Billings K, Barge LM. Testing Abiotic Reduction of NAD + Directly Mediated by Iron/Sulfur Minerals. ASTROBIOLOGY 2022; 22:25-34. [PMID: 34591607 DOI: 10.1089/ast.2021.0035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Life emerged in a geochemical context, possibly in the midst of mineral substrates. However, it is not known to what extent minerals and dissolved inorganic ions could have facilitated the evolution of biochemical reactions. Herein, we have experimentally shown that iron sulfide minerals can act as electron transfer agents for the reduction of the ubiquitous biological protein cofactor nicotinamide adenine dinucleotide (NAD+) under anaerobic prebiotic conditions, observing the NAD+/NADH redox transition by using ultraviolet-visible spectroscopy and 1H nuclear magnetic resonance. This reaction was mediated with iron sulfide minerals, which were likely abundant on early Earth in seafloor and hydrothermal settings; and the NAD+/NADH redox reaction occurred in the absence of UV light, peptide ligand(s), or dissolved mediators. To better understand this reaction, thermodynamic modeling was also performed. The ability of an iron sulfide mineral to transfer electrons to a biochemical cofactor that is found in every living cell demonstrates how geologic materials could have played a direct role in the evolution of certain cofactor-driven metabolic pathways.
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Affiliation(s)
- Jessica M Weber
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Bryana L Henderson
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Douglas E LaRowe
- Department of Earth Sciences, University of Southern California, Los Angeles, California, USA
| | - Aaron D Goldman
- Blue Marble Space Institute of Science, Seattle, Washington, United States of America
- Department of Biology, Oberlin College, Oberlin, Ohio, USA
| | - Scott M Perl
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Keith Billings
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Laura M Barge
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
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8
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Altair T, Borges LGF, Galante D, Varela H. Experimental Approaches for Testing the Hypothesis of the Emergence of Life at Submarine Alkaline Vents. Life (Basel) 2021; 11:777. [PMID: 34440521 PMCID: PMC8401828 DOI: 10.3390/life11080777] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/21/2021] [Accepted: 07/28/2021] [Indexed: 11/17/2022] Open
Abstract
Since the pioneering experimental work performed by Urey and Miller around 70 years ago, several experimental works have been developed for approaching the question of the origin of life based on very few well-constructed hypotheses. In recent years, attention has been drawn to the so-called alkaline hydrothermal vents model (AHV model) for the emergence of life. Since the first works, perspectives from complexity sciences, bioenergetics and thermodynamics have been incorporated into the model. Consequently, a high number of experimental works from the model using several tools have been developed. In this review, we present the key concepts that provide a background for the AHV model and then analyze the experimental approaches that were motivated by it. Experimental tools based on hydrothermal reactors, microfluidics and chemical gardens were used for simulating the environments of early AHVs on the Hadean Earth (~4.0 Ga). In addition, it is noteworthy that several works used techniques from electrochemistry to investigate phenomena in the vent-ocean interface for early AHVs. Their results provided important parameters and details that are used for the evaluation of the plausibility of the AHV model, and for the enhancement of it.
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Affiliation(s)
- Thiago Altair
- São Carlos Institute of Chemistry, University of São Paulo, São Carlos 13560-970, Brazil
| | - Luiz G. F. Borges
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-100, Brazil; (L.G.F.B.); (D.G.)
| | - Douglas Galante
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-100, Brazil; (L.G.F.B.); (D.G.)
| | - Hamilton Varela
- São Carlos Institute of Chemistry, University of São Paulo, São Carlos 13560-970, Brazil
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9
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Kotopoulou E, Lopez‐Haro M, Calvino Gamez JJ, García‐Ruiz JM. Nanoscale Anatomy of Iron-Silica Self-Organized Membranes: Implications for Prebiotic Chemistry. Angew Chem Int Ed Engl 2021; 60:1396-1402. [PMID: 33022871 PMCID: PMC7839773 DOI: 10.1002/anie.202012059] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Indexed: 12/26/2022]
Abstract
Iron-silica self-organized membranes, so-called chemical gardens, behave as fuel cells and catalyze the formation of amino/carboxylic acids and RNA nucleobases from organics that were available on early Earth. Despite their relevance for prebiotic chemistry, little is known about their structure and mineralogy at the nanoscale. Studied here are focused ion beam milled sections of iron-silica membranes, grown from synthetic and natural, alkaline, serpentinization-derived fluids thought to be widespread on early Earth. Electron microscopy shows they comprise amorphous silica and iron nanoparticles of large surface areas and inter/intraparticle porosities. Their construction resembles that of a heterogeneous catalyst, but they can also exhibit a bilayer structure. Surface-area measurements suggest that membranes grown from natural waters have even higher catalytic potential. Considering their geochemically plausible precipitation in the early hydrothermal systems where abiotic organics were produced, iron-silica membranes might have assisted the generation and organization of the first biologically relevant organics.
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Affiliation(s)
- Electra Kotopoulou
- Instituto Andaluz de Ciencias de la TierraConsejo Superior de Investigaciones Científicas- Universidad de GranadaAvda. de las Palmeras 418100GranadaSpain
| | - Miguel Lopez‐Haro
- Departamento de Ciencia de los Materiales e Ingeniería Metalúrgica y Química InorgánicaFacultad de CienciasUniversidad de CadizCampus Rio San PedroPuerto Real11510CádizSpain
| | - Jose Juan Calvino Gamez
- Departamento de Ciencia de los Materiales e Ingeniería Metalúrgica y Química InorgánicaFacultad de CienciasUniversidad de CadizCampus Rio San PedroPuerto Real11510CádizSpain
| | - Juan Manuel García‐Ruiz
- Instituto Andaluz de Ciencias de la TierraConsejo Superior de Investigaciones Científicas- Universidad de GranadaAvda. de las Palmeras 418100GranadaSpain
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10
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Kotopoulou E, Lopez‐Haro M, Calvino Gamez JJ, García‐Ruiz JM. Nanoscale Anatomy of Iron‐Silica Self‐Organized Membranes: Implications for Prebiotic Chemistry. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202012059] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Electra Kotopoulou
- Instituto Andaluz de Ciencias de la Tierra Consejo Superior de Investigaciones Científicas- Universidad de Granada Avda. de las Palmeras 4 18100 Granada Spain
| | - Miguel Lopez‐Haro
- Departamento de Ciencia de los Materiales e Ingeniería Metalúrgica y Química Inorgánica Facultad de Ciencias Universidad de Cadiz Campus Rio San Pedro Puerto Real 11510 Cádiz Spain
| | - Jose Juan Calvino Gamez
- Departamento de Ciencia de los Materiales e Ingeniería Metalúrgica y Química Inorgánica Facultad de Ciencias Universidad de Cadiz Campus Rio San Pedro Puerto Real 11510 Cádiz Spain
| | - Juan Manuel García‐Ruiz
- Instituto Andaluz de Ciencias de la Tierra Consejo Superior de Investigaciones Científicas- Universidad de Granada Avda. de las Palmeras 4 18100 Granada Spain
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11
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Hooks MR, Webster P, Weber JM, Perl S, Barge LM. Effects of Amino Acids on Iron-Silicate Chemical Garden Precipitation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:5793-5801. [PMID: 32421344 DOI: 10.1021/acs.langmuir.0c00502] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Understanding the structure and behavior of chemical gardens is of interest for materials science, for understanding organic-mineral interactions, and for simulating geological mineral structures in hydrothermal systems on Earth and other worlds. Herein, we explored the effects of amino acids on inorganic chemical garden precipitate systems of iron chloride and sodium silicate to determine if/how the addition of organics can affect self-assembling morphologies or crystal growth. Amino acids affect chemical garden growth and morphology at the macro-scale and at the nanoscale. In this reaction system, the concentration of amino acid had a greater impact than the amino acid side chain, and increasing concentrations of organics caused structures to have smoother exteriors as amino acids accumulated on the outside surface. These results provide an example of how organic compounds can become incorporated into and influence the growth of inorganic self-organizing precipitates in far-from-equilibrium systems. Additionally, sample handing methods were developed to successfully image these delicate structures.
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Affiliation(s)
- Michelle R Hooks
- NASA Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California 91109, United States
| | - Paul Webster
- Oak Crest Institute of Science, 132 W Chestnut Ave, Monrovia, California 91016, United States
| | - Jessica M Weber
- NASA Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California 91109, United States
| | - Scott Perl
- NASA Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California 91109, United States
| | - Laura M Barge
- NASA Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California 91109, United States
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12
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Szilagyi RK, Hanscam R, Shepard EM, McGlynn SE. Natural selection based on coordination chemistry: computational assessment of [4Fe-4S]-maquettes with non-coded amino acids. Interface Focus 2019; 9:20190071. [PMID: 31641437 DOI: 10.1098/rsfs.2019.0071] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 08/27/2019] [Indexed: 12/21/2022] Open
Abstract
Cysteine is the only coded amino acid in biology that contains a thiol functional group. Deprotonated thiolate is essential for anchoring iron-sulfur ([Fe-S]) clusters, as prosthetic groups to the protein matrix. [Fe-S] metalloproteins and metalloenzymes are involved in biological electron transfer, radical chemistry, small molecule activation and signalling. These are key metabolic and regulatory processes that would likely have been present in the earliest organisms. In the context of emergence of life theories, the selection and evolution of the cysteine-specific R-CH2-SH side chain is a fascinating question to confront. We undertook a computational [4Fe-4S]-maquette modelling approach to evaluate how side chain length can influence [Fe-S] cluster binding and stability in short 7-mer and long 16-mer peptides, which contained either thioglycine, cysteine or homocysteine. Force field-based molecular dynamics simulations for [4Fe-4S] cluster nest formation were supplemented with density functional theory calculations of a ligand-exchange reaction between a preassembled cluster and the peptide. Secondary structure analysis revealed that peptides with cysteine are found with greater frequency nested to bind preformed [4Fe-4S] clusters. Additionally, the presence of the single methylene group in cysteine ligands mitigates the steric bulk, maintains the H-bonding and dipole network, and provides covalent Fe-S(thiolate) bonds that together create the optimal electronic and geometric structural conditions for [4Fe-4S] cluster binding compared to thioglycine or homocysteine ligands. Our theoretical work forms an experimentally testable hypothesis of the natural selection of cysteine through coordination chemistry.
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Affiliation(s)
- Robert K Szilagyi
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Rebecca Hanscam
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Eric M Shepard
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Shawn E McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8550, Japan.,Blue Marble Space Institute of Science, Seattle, WA 98154, USA.,Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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13
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Bartlett SJ, Beckett P. Probing complexity: thermodynamics and computational mechanics approaches to origins studies. Interface Focus 2019; 9:20190058. [PMID: 31641432 DOI: 10.1098/rsfs.2019.0058] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/06/2019] [Indexed: 12/15/2022] Open
Abstract
This paper proposes new avenues for origins research that apply modern concepts from stochastic thermodynamics, information thermodynamics and complexity science. Most approaches to the emergence of life prioritize certain compounds, reaction pathways, environments or phenomena. What they all have in common is the objective of reaching a state that is recognizably alive, usually positing the need for an evolutionary process. As with life itself, this correlates with a growth in the complexity of the system over time. Complexity often takes the form of an intuition or a proxy for a phenomenon that defies complete understanding. However, recent progress in several theoretical fields allows the rigorous computation of complexity. We thus propose that measurement and control of the complexity and information content of origins-relevant systems can provide novel insights that are absent in other approaches. Since we have no guarantee that the earliest forms of life (or alien life) used the same materials and processes as extant life, an appeal to complexity and information processing provides a more objective and agnostic approach to the search for life's beginnings. This paper gives an accessible overview of the three relevant branches of modern thermodynamics. These frameworks are not commonly applied in origins studies, but are ideally suited to the analysis of such non-equilibrium systems. We present proposals for the application of these concepts in both theoretical and experimental origins settings.
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Affiliation(s)
- Stuart J Bartlett
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA.,Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | - Patrick Beckett
- Department of Chemical Engineering, University of California Davis, Davis, CA, USA.,Department of Civil and Environmental Engineering, University of California Davis, Davis, CA, USA
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14
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Ooka H, McGlynn SE, Nakamura R. Electrochemistry at Deep‐Sea Hydrothermal Vents: Utilization of the Thermodynamic Driving Force towards the Autotrophic Origin of Life. ChemElectroChem 2019. [DOI: 10.1002/celc.201801432] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Hideshi Ooka
- Biofunctional Catalyst Research TeamRIKEN Center for Sustainable Resource Science (CSRS) 2-1, Hirosawa, Wako Saitama 351-0198 Japan
| | - Shawn E. McGlynn
- Biofunctional Catalyst Research TeamRIKEN Center for Sustainable Resource Science (CSRS) 2-1, Hirosawa, Wako Saitama 351-0198 Japan
- Earth-Life Science Institute (ELSI)Tokyo Institute of Technology 2-12-1-1E-1 Ookayama, Meguro-ku Tokyo 152-8550 Japan
- Blue Marble Space Institute of Science Seattle, WA USA
| | - Ryuhei Nakamura
- Biofunctional Catalyst Research TeamRIKEN Center for Sustainable Resource Science (CSRS) 2-1, Hirosawa, Wako Saitama 351-0198 Japan
- Earth-Life Science Institute (ELSI)Tokyo Institute of Technology 2-12-1-1E-1 Ookayama, Meguro-ku Tokyo 152-8550 Japan
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15
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Miller CG, Holmgren A, Arnér ESJ, Schmidt EE. NADPH-dependent and -independent disulfide reductase systems. Free Radic Biol Med 2018; 127:248-261. [PMID: 29609022 PMCID: PMC6165701 DOI: 10.1016/j.freeradbiomed.2018.03.051] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 03/26/2018] [Accepted: 03/29/2018] [Indexed: 12/20/2022]
Abstract
Over the past seven decades, research on autotrophic and heterotrophic model organisms has defined how the flow of electrons ("reducing power") from high-energy inorganic sources, through biological systems, to low-energy inorganic products like water, powers all of Life's processes. Universally, an initial major biological recipient of these electrons is nicotinamide adenine dinucleotide-phosphate, which thereby transits from an oxidized state (NADP+) to a reduced state (NADPH). A portion of this reducing power is then distributed via the cellular NADPH-dependent disulfide reductase systems as sequential reductions of disulfide bonds. Along the disulfide reduction pathways, some enzymes have active sites that use the selenium-containing amino acid, selenocysteine, in place of the common but less reactive sulfur-containing cysteine. In particular, the mammalian/metazoan thioredoxin systems are usually selenium-dependent as, across metazoan phyla, most thioredoxin reductases are selenoproteins. Among the roles of the NADPH-dependent disulfide reductase systems, the most universal is that they provide the reducing power for the production of DNA precursors by ribonucleotide reductase (RNR). Some studies, however, have uncovered examples of NADPH-independent disulfide reductase systems that can also support RNR. These systems are summarized here and their implications are discussed.
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Affiliation(s)
- Colin G Miller
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA; Department of Microbiology & Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Arne Holmgren
- Division of Biochemistry, Department of Medical Biochemistry & Biophysics, Karolinska Institutet, SE 171 77 Stockholm, Sweden
| | - Elias S J Arnér
- Division of Biochemistry, Department of Medical Biochemistry & Biophysics, Karolinska Institutet, SE 171 77 Stockholm, Sweden
| | - Edward E Schmidt
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT 59717, USA.
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16
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Barge LM, Krause FC, Jones JP, Billings K, Sobron P. Geoelectrodes and Fuel Cells for Simulating Hydrothermal Vent Environments. ASTROBIOLOGY 2018; 18:1147-1158. [PMID: 30106308 DOI: 10.1089/ast.2017.1707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Gradients generated in hydrothermal systems provide a significant source of free energy for chemosynthetic life and may play a role in present-day habitability on ocean worlds. Electron/proton/ion gradients, particularly in the context of hydrothermal chimney structures, may also be relevant to the origins of life on Earth. Hydrothermal vents are similar in some ways to typical fuel cell devices: redox/pH gradients between seawater and hydrothermal fluid are analogous to the fuel cell oxidant and fuel reservoirs; the porous chimney wall is analogous to a separator or ion-exchange membrane and is also a conductive path for electrons; and the hydrothermal minerals are analogous to electrode catalysts. The modular and scalable characteristics of fuel cell systems make for a convenient planetary geology test bed in which geologically relevant components may be assembled and investigated in a controlled simulation environment. We have performed fuel cell experiments and electrochemical studies to better understand the catalytic potential of seafloor minerals and vent chimneys, using samples from a black smoker vent chimney as an initial demonstration. In a fuel cell with Na+-conducting Nafion® membranes and liquid fuel/oxidant reservoirs (simulating the vent environment), the black smoker mineral catalyst in the membrane electrode assembly was effective in reducing O2 and oxidizing sulfide. In a H2/O2 polymer electrolyte membrane (PEM) fuel cell with H+-conducting Nafion membranes, the black smoker catalyst was effective in reducing O2 but not in oxidizing H2. These fuel cell experiments accurately simulated the redox reactions that could occur in a geological setting with this particular catalyst, and also tested whether the minerals are sufficiently active to replace a commercial fuel cell catalyst. Similar experiments with other geocatalysts could be utilized to test which redox reactions could be driven in other hydrothermal systems, including hypothesized vent systems on other worlds.
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Affiliation(s)
- Laura M Barge
- 1 NASA Jet Propulsion Laboratory, California Institute of Technology , Pasadena, California
| | - Frederick C Krause
- 1 NASA Jet Propulsion Laboratory, California Institute of Technology , Pasadena, California
| | - John-Paul Jones
- 1 NASA Jet Propulsion Laboratory, California Institute of Technology , Pasadena, California
| | - Keith Billings
- 1 NASA Jet Propulsion Laboratory, California Institute of Technology , Pasadena, California
| | - Pablo Sobron
- 2 Carl Sagan Center, SETI Institute , Mountain View, California
- 3 Impossible Sensing , St. Louis, Missouri
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17
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Russell MJ. Green Rust: The Simple Organizing 'Seed' of All Life? Life (Basel) 2018; 8:E35. [PMID: 30150570 PMCID: PMC6161180 DOI: 10.3390/life8030035] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 06/28/2018] [Accepted: 08/14/2018] [Indexed: 01/18/2023] Open
Abstract
Korenaga and coworkers presented evidence to suggest that the Earth's mantle was dry and water filled the ocean to twice its present volume 4.3 billion years ago. Carbon dioxide was constantly exhaled during the mafic to ultramafic volcanic activity associated with magmatic plumes that produced the thick, dense, and relatively stable oceanic crust. In that setting, two distinct and major types of sub-marine hydrothermal vents were active: ~400 °C acidic springs, whose effluents bore vast quantities of iron into the ocean, and ~120 °C, highly alkaline, and reduced vents exhaling from the cooler, serpentinizing crust some distance from the heads of the plumes. When encountering the alkaline effluents, the iron from the plume head vents precipitated out, forming mounds likely surrounded by voluminous exhalative deposits similar to the banded iron formations known from the Archean. These mounds and the surrounding sediments, comprised micro or nano-crysts of the variable valence FeII/FeIII oxyhydroxide known as green rust. The precipitation of green rust, along with subsidiary iron sulfides and minor concentrations of nickel, cobalt, and molybdenum in the environment at the alkaline springs, may have established both the key bio-syntonic disequilibria and the means to properly make use of them-the elements needed to effect the essential inanimate-to-animate transitions that launched life. Specifically, in the submarine alkaline vent model for the emergence of life, it is first suggested that the redox-flexible green rust micro- and nano-crysts spontaneously precipitated to form barriers to the complete mixing of carbonic ocean and alkaline hydrothermal fluids. These barriers created and maintained steep ionic disequilibria. Second, the hydrous interlayers of green rust acted as engines that were powered by those ionic disequilibria and drove essential endergonic reactions. There, aided by sulfides and trace elements acting as catalytic promoters and electron transfer agents, nitrate could be reduced to ammonia and carbon dioxide to formate, while methane may have been oxidized to methyl and formyl groups. Acetate and higher carboxylic acids could then have been produced from these C1 molecules and aminated to amino acids, and thence oligomerized to offer peptide nests to phosphate and iron sulfides, and secreted to form primitive amyloid-bounded structures, leading conceivably to protocells.
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Affiliation(s)
- Michael J Russell
- Planetary Chemistry and Astrobiology, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109-8099, USA.
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18
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Branscomb E, Russell MJ. Frankenstein or a Submarine Alkaline Vent: Who is Responsible for Abiogenesis? Bioessays 2018; 40:e1700182. [DOI: 10.1002/bies.201700182] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 04/26/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Elbert Branscomb
- Department of Physics; Carl R. Woese Institute for Genomic Biology; University of Illinois; Urbana IL 61801 USA
| | - Michael J. Russell
- Planetary Chemistry and Astrobiology; Sec. 3225 MS:183-301; Jet Propulsion Laboratory; California Institute of Technology; Pasadena CA 91109-8099 USA
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19
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Möller F, Piontek S, Miller RG, Apfel UP. From Enzymes to Functional Materials-Towards Activation of Small Molecules. Chemistry 2017; 24:1471-1493. [PMID: 28816379 DOI: 10.1002/chem.201703451] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 08/15/2017] [Indexed: 12/12/2022]
Abstract
The design of non-noble metal-containing heterogeneous catalysts for the activation of small molecules is of utmost importance for our society. While nature possesses very sophisticated machineries to perform such conversions, rationally designed catalytic materials are rare. Herein, we aim to raise the awareness of the overall common design and working principles of catalysts incorporating aspects of biology, chemistry, and material sciences.
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Affiliation(s)
- Frauke Möller
- Inorganic Chemistry I/ Bioinorganic Chemistry, Ruhr-University Bochum, Universitätsstaße 150, 44801, Bochum, Germany
| | - Stefan Piontek
- Inorganic Chemistry I/ Bioinorganic Chemistry, Ruhr-University Bochum, Universitätsstaße 150, 44801, Bochum, Germany
| | - Reece G Miller
- Inorganic Chemistry I/ Bioinorganic Chemistry, Ruhr-University Bochum, Universitätsstaße 150, 44801, Bochum, Germany
| | - Ulf-Peter Apfel
- Inorganic Chemistry I/ Bioinorganic Chemistry, Ruhr-University Bochum, Universitätsstaße 150, 44801, Bochum, Germany
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20
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Cortese-Krott MM, Koning A, Kuhnle GG, Nagy P, Bianco CL, Pasch A, Wink DA, Fukuto JM, Jackson AA, van Goor H, Olson KR, Feelisch M. The Reactive Species Interactome: Evolutionary Emergence, Biological Significance, and Opportunities for Redox Metabolomics and Personalized Medicine. Antioxid Redox Signal 2017; 27:684-712. [PMID: 28398072 PMCID: PMC5576088 DOI: 10.1089/ars.2017.7083] [Citation(s) in RCA: 218] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 04/10/2017] [Indexed: 12/20/2022]
Abstract
SIGNIFICANCE Oxidative stress is thought to account for aberrant redox homeostasis and contribute to aging and disease. However, more often than not, administration of antioxidants is ineffective, suggesting that our current understanding of the underlying regulatory processes is incomplete. Recent Advances: Similar to reactive oxygen species and reactive nitrogen species, reactive sulfur species are now emerging as important signaling molecules, targeting regulatory cysteine redox switches in proteins, affecting gene regulation, ion transport, intermediary metabolism, and mitochondrial function. To rationalize the complexity of chemical interactions of reactive species with themselves and their targets and help define their role in systemic metabolic control, we here introduce a novel integrative concept defined as the reactive species interactome (RSI). The RSI is a primeval multilevel redox regulatory system whose architecture, together with the physicochemical characteristics of its constituents, allows efficient sensing and rapid adaptation to environmental changes and various other stressors to enhance fitness and resilience at the local and whole-organism level. CRITICAL ISSUES To better characterize the RSI-related processes that determine fluxes through specific pathways and enable integration, it is necessary to disentangle the chemical biology and activity of reactive species (including precursors and reaction products), their targets, communication systems, and effects on cellular, organ, and whole-organism bioenergetics using system-level/network analyses. FUTURE DIRECTIONS Understanding the mechanisms through which the RSI operates will enable a better appreciation of the possibilities to modulate the entire biological system; moreover, unveiling molecular signatures that characterize specific environmental challenges or other forms of stress will provide new prevention/intervention opportunities for personalized medicine. Antioxid. Redox Signal. 00, 000-000.
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Affiliation(s)
- Miriam M. Cortese-Krott
- Cardiovascular Research Laboratory, Department of Cardiology, Pneumology and Angiology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Anne Koning
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Gunter G.C. Kuhnle
- Department of Food and Nutritional Sciences, University of Reading, Reading, United Kingdom
| | - Peter Nagy
- Molecular Immunology and Toxicology, National Institute of Oncology, Budapest, Hungary
| | | | - Andreas Pasch
- Department of Clinical Chemistry, University of Bern and Calciscon AG, Bern, Switzerland
| | - David A. Wink
- Cancer and Inflammation Program, National Cancer Institute, National Institutes of Health, Frederick, Maryland
| | - Jon M. Fukuto
- Department of Chemistry, Sonoma State University, Rohnert Park, California
| | - Alan A. Jackson
- NIHR Southampton Biomedical Research Center, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Harry van Goor
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Kenneth R. Olson
- Indiana University School of Medicine-South Bend, South Bend, Indiana
| | - Martin Feelisch
- NIHR Southampton Biomedical Research Center, University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
- Clinical and Experimental Sciences, Faculty of Medicine, Southampton General Hospital and Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
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21
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Barge LM, White LM. Experimentally Testing Hydrothermal Vent Origin of Life on Enceladus and Other Icy/Ocean Worlds. ASTROBIOLOGY 2017; 17:820-833. [PMID: 28836818 DOI: 10.1089/ast.2016.1633] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We review various laboratory strategies and methods that can be utilized to simulate prebiotic processes and origin of life in hydrothermal vent systems on icy/ocean worlds. Crucial steps that could be simulated in the laboratory include simulations of water-rock chemistry (e.g., serpentinization) to produce hydrothermal fluids, the types of mineral catalysts and energy gradients produced in vent interfaces where hydrothermal fluids interface with the surrounding seawater, and simulations of biologically relevant chemistry in flow-through gradient systems (i.e., far-from-equilibrium experiments). We describe some examples of experimental designs in detail, which are adaptable and could be used to test particular hypotheses about ocean world energetics or mineral/organic chemistry. Enceladus among the ocean worlds provides an ideal test case, since the pressure at the ocean floor is more easily simulated in the lab. Results for Enceladus could be extrapolated with further experiments and modeling to understand other ocean worlds. Key Words: Enceladus-Ocean worlds-Icy worlds-Hydrothermal vent-Iron sulfide-Gradient. Astrobiology 17, 820-833.
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Affiliation(s)
- Laura M Barge
- NASA Jet Propulsion Laboratory, California Institute of Technology , Pasadena, California
| | - Lauren M White
- NASA Jet Propulsion Laboratory, California Institute of Technology , Pasadena, California
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22
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Barge LM, Branscomb E, Brucato JR, Cardoso SSS, Cartwright JHE, Danielache SO, Galante D, Kee TP, Miguel Y, Mojzsis S, Robinson KJ, Russell MJ, Simoncini E, Sobron P. Thermodynamics, Disequilibrium, Evolution: Far-From-Equilibrium Geological and Chemical Considerations for Origin-Of-Life Research. ORIGINS LIFE EVOL B 2017; 47:39-56. [PMID: 27271006 DOI: 10.1007/s11084-016-9508-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 04/19/2016] [Indexed: 10/21/2022]
Affiliation(s)
- L M Barge
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, 91125, USA.
- Icy Worlds Team, NASA Astrobiology Institute, Mountain View, CA, 94043, USA.
| | - E Branscomb
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Champaign, IL, USA
| | - J R Brucato
- Astrophysical Observatory of Arcetri, Florence, Italy
| | - S S S Cardoso
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Pembroke Street, Cambridge, CB2 3RA, UK
| | - J H E Cartwright
- Instituto Andaluz de Ciencias de la Tierra, CSIC-Universidad de Granada, E-18100 Armilla, Granada, Spain
- Instituto Carlos I de Física Teórica y Computacional, Universidad de Granada, E-18071, Granada, Spain
| | - S O Danielache
- Sophia University, Tokyo, Japan
- Earth and Life Science Institute, Tokyo Technical University, Tokyo, Japan
| | - D Galante
- Brazilian Synchrotron Light Laboratory, LNLS / CNPEM, Campinas, Brazil
| | - T P Kee
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Y Miguel
- Observatoire de Côte d'Azur, Nice, France
| | - S Mojzsis
- Department of Geological Sciences, University of Colorado, Boulder, CO, 80309-0399, USA
| | - K J Robinson
- School of Molecular Sciences and School of Earth & Space Exploration, Arizona State University, Tempe, AZ, 85287, USA
| | - M J Russell
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, 91125, USA
- Icy Worlds Team, NASA Astrobiology Institute, Mountain View, CA, 94043, USA
| | - E Simoncini
- Astrophysical Observatory of Arcetri, Florence, Italy
| | - P Sobron
- Carl Sagan Center, SETI Institute, Mountain View, CA, USA
- Impossible Sensing, St. Louis, MO, USA
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23
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Olson KR, Straub KD. The Role of Hydrogen Sulfide in Evolution and the Evolution of Hydrogen Sulfide in Metabolism and Signaling. Physiology (Bethesda) 2016; 31:60-72. [DOI: 10.1152/physiol.00024.2015] [Citation(s) in RCA: 136] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The chemical versatility of sulfur and its abundance in the prebiotic Earth as reduced sulfide (H2S) implicate this molecule in the origin of life 3.8 billion years ago and also as a major source of energy in the first seven-eighths of evolution. The tremendous increase in ambient oxygen ∼600 million years ago brought an end to H2S as an energy source, and H2S-dependent animals either became extinct, retreated to isolated sulfide niches, or adapted. The first 3 billion years of molecular tinkering were not lost, however, and much of this biochemical armamentarium easily adapted to an oxic environment where it contributes to metabolism and signaling even in humans. This review examines the role of H2S in evolution and the evolution of H2S metabolism and signaling.
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Affiliation(s)
- Kenneth R. Olson
- Indiana University School of Medicine, South Bend, South Bend, Indiana; and
| | - Karl D. Straub
- Central Arkansas Veteran's Healthcare System and University of Arkansas for Medical Sciences, Little Rock, Arkansas
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24
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Barge LM, Abedian Y, Doloboff IJ, Nuñez JE, Russell MJ, Kidd RD, Kanik I. Chemical Gardens as Flow-through Reactors Simulating Natural Hydrothermal Systems. J Vis Exp 2015:53015. [PMID: 26650915 PMCID: PMC4692733 DOI: 10.3791/53015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Here we report experimental simulations of hydrothermal chimney growth using injection chemical garden methods. The versatility of this type of experiment allows for testing of various proposed ocean / hydrothermal fluid chemistries that could have driven reactions toward the origin of life in environments on the early Earth, early Mars, or even other worlds such as the icy moons of the outer planets. We show experiments that include growth of chemical garden structures under anoxic conditions simulating the early Earth, inclusion of trace components of phosphates / organics in the injection solution to incorporate them into the structure, a switch of the injection solution to introduce a secondary precipitating anion, and the measurement of membrane potentials generated by chemical gardens. Using this method, self-assembling chemical garden structures were formed that mimic the natural chimneys precipitated at submarine hydrothermal springs, and these precipitates can be used successfully as flow-through reactors by feeding through multiple successive "hydrothermal" injections.
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Affiliation(s)
- Laura M Barge
- NASA Jet Propulsion Laboratory, California Institute of Technology; NASA Astrobiology Institute, Icy Worlds; Blue Marble Space Institute of Science;
| | - Yeghegis Abedian
- NASA Jet Propulsion Laboratory, California Institute of Technology; NASA Astrobiology Institute, Icy Worlds
| | - Ivria J Doloboff
- NASA Jet Propulsion Laboratory, California Institute of Technology; NASA Astrobiology Institute, Icy Worlds
| | - Jessica E Nuñez
- NASA Jet Propulsion Laboratory, California Institute of Technology; Blue Marble Space Institute of Science; Citrus College
| | - Michael J Russell
- NASA Jet Propulsion Laboratory, California Institute of Technology; NASA Astrobiology Institute, Icy Worlds
| | - Richard D Kidd
- NASA Jet Propulsion Laboratory, California Institute of Technology
| | - Isik Kanik
- NASA Jet Propulsion Laboratory, California Institute of Technology; NASA Astrobiology Institute, Icy Worlds
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25
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Burcar BT, Barge LM, Trail D, Watson EB, Russell MJ, McGown LB. RNA Oligomerization in Laboratory Analogues of Alkaline Hydrothermal Vent Systems. ASTROBIOLOGY 2015; 15:509-522. [PMID: 26154881 DOI: 10.1089/ast.2014.1280] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Discovering pathways leading to long-chain RNA formation under feasible prebiotic conditions is an essential step toward demonstrating the viability of the RNA World hypothesis. Intensive research efforts have provided evidence of RNA oligomerization by using circular ribonucleotides, imidazole-activated ribonucleotides with montmorillonite catalyst, and ribonucleotides in the presence of lipids. Additionally, mineral surfaces such as borates, apatite, and calcite have been shown to catalyze the formation of small organic compounds from inorganic precursors (Cleaves, 2008 ), pointing to possible geological sites for the origins of life. Indeed, the catalytic properties of these particular minerals provide compelling evidence for alkaline hydrothermal vents as a potential site for the origins of life since, at these vents, large metal-rich chimney structures can form that have been shown to be energetically favorable to diverse forms of life. Here, we test the ability of iron- and sulfur-rich chimneys to support RNA oligomerization reactions using imidazole-activated and non-activated ribonucleotides. The chimneys were synthesized in the laboratory in aqueous "ocean" solutions under conditions consistent with current understanding of early Earth. Effects of elemental composition, pH, inclusion of catalytic montmorillonite clay, doping of chimneys with small organic compounds, and in situ ribonucleotide activation on RNA polymerization were investigated. These experiments, under certain conditions, showed successful dimerization by using unmodified ribonucleotides, with the generation of RNA oligomers up to 4 units in length when imidazole-activated ribonucleotides were used instead. Elemental analysis of the chimney precipitates and the reaction solutions showed that most of the metal cations that were determined were preferentially partitioned into the chimneys.
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Affiliation(s)
- Bradley T Burcar
- 1 New York Center for Astrobiology, Rensselaer Polytechnic Institute , Troy, New York
- 2 Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute , Troy, New York
| | - Laura M Barge
- 3 NASA Jet Propulsion Laboratory, California Institute of Technology , Pasadena, California
- 4 NASA Astrobiology Institute , Icy Worlds
| | - Dustin Trail
- 1 New York Center for Astrobiology, Rensselaer Polytechnic Institute , Troy, New York
- 5 Department of Earth and Environmental Sciences, Rensselaer Polytechnic Institute School of Science , Troy, New York
| | - E Bruce Watson
- 1 New York Center for Astrobiology, Rensselaer Polytechnic Institute , Troy, New York
- 5 Department of Earth and Environmental Sciences, Rensselaer Polytechnic Institute School of Science , Troy, New York
| | - Michael J Russell
- 3 NASA Jet Propulsion Laboratory, California Institute of Technology , Pasadena, California
- 4 NASA Astrobiology Institute , Icy Worlds
| | - Linda B McGown
- 1 New York Center for Astrobiology, Rensselaer Polytechnic Institute , Troy, New York
- 2 Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute , Troy, New York
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26
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Makki R, Ji X, Mattoussi H, Steinbock O. Self-Organized Tubular Structures as Platforms for Quantum Dots. J Am Chem Soc 2014; 136:6463-9. [DOI: 10.1021/ja501941d] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rabih Makki
- Florida State University Department
of Chemistry and Biochemistry, Tallahassee, Florida 32306-4390, United States
| | - Xin Ji
- Florida State University Department
of Chemistry and Biochemistry, Tallahassee, Florida 32306-4390, United States
| | - Hedi Mattoussi
- Florida State University Department
of Chemistry and Biochemistry, Tallahassee, Florida 32306-4390, United States
| | - Oliver Steinbock
- Florida State University Department
of Chemistry and Biochemistry, Tallahassee, Florida 32306-4390, United States
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27
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Russell MJ, Barge LM, Bhartia R, Bocanegra D, Bracher PJ, Branscomb E, Kidd R, McGlynn S, Meier DH, Nitschke W, Shibuya T, Vance S, White L, Kanik I. The drive to life on wet and icy worlds. ASTROBIOLOGY 2014; 14:308-43. [PMID: 24697642 PMCID: PMC3995032 DOI: 10.1089/ast.2013.1110] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 02/02/2014] [Indexed: 05/22/2023]
Abstract
This paper presents a reformulation of the submarine alkaline hydrothermal theory for the emergence of life in response to recent experimental findings. The theory views life, like other self-organizing systems in the Universe, as an inevitable outcome of particular disequilibria. In this case, the disequilibria were two: (1) in redox potential, between hydrogen plus methane with the circuit-completing electron acceptors such as nitrite, nitrate, ferric iron, and carbon dioxide, and (2) in pH gradient between an acidulous external ocean and an alkaline hydrothermal fluid. Both CO2 and CH4 were equally the ultimate sources of organic carbon, and the metal sulfides and oxyhydroxides acted as protoenzymatic catalysts. The realization, now 50 years old, that membrane-spanning gradients, rather than organic intermediates, play a vital role in life's operations calls into question the idea of "prebiotic chemistry." It informs our own suggestion that experimentation should look to the kind of nanoengines that must have been the precursors to molecular motors-such as pyrophosphate synthetase and the like driven by these gradients-that make life work. It is these putative free energy or disequilibria converters, presumably constructed from minerals comprising the earliest inorganic membranes, that, as obstacles to vectorial ionic flows, present themselves as the candidates for future experiments. Key Words: Methanotrophy-Origin of life. Astrobiology 14, 308-343. The fixation of inorganic carbon into organic material (autotrophy) is a prerequisite for life and sets the starting point of biological evolution. (Fuchs, 2011 ) Further significant progress with the tightly membrane-bound H(+)-PPase family should lead to an increased insight into basic requirements for the biological transport of protons through membranes and its coupling to phosphorylation. (Baltscheffsky et al., 1999 ).
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28
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Barge LM, Kee TP, Doloboff IJ, Hampton JMP, Ismail M, Pourkashanian M, Zeytounian J, Baum MM, Moss JA, Lin CK, Kidd RD, Kanik I. The fuel cell model of abiogenesis: a new approach to origin-of-life simulations. ASTROBIOLOGY 2014; 14:254-270. [PMID: 24621309 DOI: 10.1089/ast.2014.1140] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In this paper, we discuss how prebiotic geo-electrochemical systems can be modeled as a fuel cell and how laboratory simulations of the origin of life in general can benefit from this systems-led approach. As a specific example, the components of what we have termed the "prebiotic fuel cell" (PFC) that operates at a putative Hadean hydrothermal vent are detailed, and we used electrochemical analysis techniques and proton exchange membrane (PEM) fuel cell components to test the properties of this PFC and other geo-electrochemical systems, the results of which are reported here. The modular nature of fuel cells makes them ideal for creating geo-electrochemical reactors with which to simulate hydrothermal systems on wet rocky planets and characterize the energetic properties of the seafloor/hydrothermal interface. That electrochemical techniques should be applied to simulating the origin of life follows from the recognition of the fuel cell-like properties of prebiotic chemical systems and the earliest metabolisms. Conducting this type of laboratory simulation of the emergence of bioenergetics will not only be informative in the context of the origin of life on Earth but may help in understanding whether life might emerge in similar environments on other worlds.
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Affiliation(s)
- Laura M Barge
- 1 Jet Propulsion Laboratory, California Institute of Technology , Pasadena, California, USA
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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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30
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Ball P. Material witness: Bringing crystals to life. NATURE MATERIALS 2012; 11:840. [PMID: 23001232 DOI: 10.1038/nmat3437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
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Cartwright JHE, Mackay AL. Beyond crystals: the dialectic of materials and information. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2012; 370:2807-2822. [PMID: 22615461 PMCID: PMC3367679 DOI: 10.1098/rsta.2012.0106] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We argue for a convergence of crystallography, materials science and biology, that will come about through asking materials questions about biology and biological questions about materials, illuminated by considerations of information. The complex structures now being studied in biology and produced in nanotechnology have outstripped the framework of classical crystallography, and a variety of organizing concepts are now taking shape into a more modern and dynamic science of structure, form and function. Absolute stability and equilibrium are replaced by metastable structures existing in a flux of energy-carrying information and moving within an energy landscape of complex topology. Structures give place to processes and processes to systems. The fundamental level is that of atoms. As smaller and smaller groups of atoms are used for their physical properties, quantum effects become important; already we see quantum computation taking shape. Concepts move towards those in life with the emergence of specifically informational structures. We now see the possibility of the artificial construction of a synthetic living system, different from biological life, but having many or all of the same properties. Interactions are essentially nonlinear and collective. Structures begin to have an evolutionary history with episodes of symbiosis. Underlying all the structures are constraints of time and space. Through hierarchization, a more general principle than the periodicity of crystals, structures may be found within structures on different scales. We must integrate unifying concepts from dynamical systems and information theory to form a coherent language and science of shape and structure beyond crystals. To this end, we discuss the idea of categorizing structures based on information according to the algorithmic complexity of their assembly.
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Affiliation(s)
- Julyan H. E. Cartwright
- Instituto Andaluz de Ciencias de la Tierra, CSIC–Universidad de Granada, Campus Fuentenueva, E-18071 Granada, Spain
| | - Alan L. Mackay
- Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK
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McGrath R, Sharma HR, Smerdon JA, Ledieu J. The memory of surfaces: epitaxial growth on quasi-crystals. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2012; 370:2930-2948. [PMID: 22615469 DOI: 10.1098/rsta.2011.0220] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
If crystal structures can be viewed as repositories of information, then crystal surfaces offer a pathway by which this information can be used to grow new structures through the process of epitaxy. The information transfer process is one of self-organization, and the kinetic and energetic factors influencing this are complex. They include the relative strengths of the adsorbate-adsorbate and adsorbate-substrate interactions, the flux of incoming species and the temperature of the system. In this brief review, we explore how the interplay of these factors influences the degree to which the epitaxial structures retain the 'memory' of the template, illustrating the discussion with examples from epitaxy on quasi-crystal surfaces.
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Affiliation(s)
- R McGrath
- Surface Science Research Centre and Department of Physics, The University of Liverpool, Liverpool L69 3BX, UK.
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