1
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Farr O, Gaudu N, Danger G, Russell MJ, Ferry D, Nitschke W, Duval S. Methanol on the rocks: green rust transformation promotes the oxidation of methane. J R Soc Interface 2023; 20:20230386. [PMID: 37727071 PMCID: PMC10509593 DOI: 10.1098/rsif.2023.0386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 08/30/2023] [Indexed: 09/21/2023] Open
Abstract
Shared coordination geometries between metal ions within reactive minerals and enzymatic metal cofactors hints at mechanistic and possibly evolutionary homology between particular abiotic chemical mineralogies and biological metabolism. The octahedral coordination of reactive Fe2+/3+ minerals such as green rusts, endemic to anoxic sediments and the early Earth's oceans, mirrors the di-iron reaction centre of soluble methane monooxygenase (sMMO), responsible for methane oxidation in methanotrophy. We show that methane oxidation occurs in tandem with the oxidation of green rust to lepidocrocite and magnetite, mimicking radical-mediated methane oxidation found in sMMO to yield not only methanol but also halogenated hydrocarbons in the presence of seawater. This naturally occurring geochemical pathway for CH4 oxidation elucidates a previously unidentified carbon cycling mechanism in modern and ancient environments and reveals clues into mineral-mediated reactions in the synthesis of organic compounds necessary for the emergence of life.
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Affiliation(s)
- Orion Farr
- CNRS, CINaM, Aix-Marseille Univ, 13009 Marseille, France
- CNRS, BIP (UMR 7281), Aix Marseille Univ, Marseille, France
| | - Nil Gaudu
- CNRS, BIP (UMR 7281), Aix Marseille Univ, Marseille, France
| | | | | | - Daniel Ferry
- CNRS, CINaM, Aix-Marseille Univ, 13009 Marseille, France
| | | | - Simon Duval
- CNRS, BIP (UMR 7281), Aix Marseille Univ, Marseille, France
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2
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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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3
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Spark of Life: Role of Electrotrophy in the Emergence of Life. Life (Basel) 2023; 13:life13020356. [PMID: 36836714 PMCID: PMC9961546 DOI: 10.3390/life13020356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/20/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
The emergence of life has been a subject of intensive research for decades. Different approaches and different environmental "cradles" have been studied, from space to the deep sea. Since the recent discovery of a natural electrical current through deep-sea hydrothermal vents, a new energy source is considered for the transition from inorganic to organic. This energy source (electron donor) is used by modern microorganisms via a new trophic type, called electrotrophy. In this review, we draw a parallel between this metabolism and a new theory for the emergence of life based on this electrical electron flow. Each step of the creation of life is revised in the new light of this prebiotic electrochemical context, going from the evaluation of similar electrical current during the Hadean, the CO2 electroreduction into a prebiotic primordial soup, the production of proto-membranes, the energetic system inspired of the nitrate reduction, the proton gradient, and the transition to a planktonic proto-cell. Finally, this theory is compared to the two other theories in hydrothermal context to assess its relevance and overcome the limitations of each. Many critical factors that were limiting each theory can be overcome given the effect of electrochemical reactions and the environmental changes produced.
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4
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Dujardin A, Himbert S, Pudritz R, Rheinstädter MC. The Formation of RNA Pre-Polymers in the Presence of Different Prebiotic Mineral Surfaces Studied by Molecular Dynamics Simulations. LIFE (BASEL, SWITZERLAND) 2022; 13:life13010112. [PMID: 36676060 PMCID: PMC9860743 DOI: 10.3390/life13010112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/21/2022] [Accepted: 12/24/2022] [Indexed: 01/04/2023]
Abstract
We used all-atom Molecular Dynamics (MD) computer simulations to study the formation of pre-polymers between the four nucleotides in RNA (AMP, UMP, CMP, GMP) in the presence of different substrates that could have been present in a prebiotic environment. Pre-polymers are C3'-C5' hydrogen-bonded nucleotides that have been suggested to be the precursors of phosphodiester-bonded RNA polymers. We simulated wet-dry cycles by successively removing water molecules from the simulations, from ~60 to 3 water molecules per nucleotide. The nine substrates in this study include three clay minerals, one mica, one phosphate mineral, one silica, and two metal oxides. The substrates differ in their surface charge and ability to form hydrogen bonds with the nucleotides. From the MD simulations, we quantify the interactions between different nucleotides, and between nucleotides and substrates. For comparison, we included graphite as an inert substrate, which is not charged and cannot form hydrogen bonds. We also simulated the dehydration of a nucleotide-only system, which mimics the drying of small droplets. The number of hydrogen bonds between nucleotides and nucleotides and substrates was found to increase significantly when water molecules were removed from the systems. The largest number of C3'-C5' hydrogen bonds between nucleotides occurred in the graphite and nucleotide-only systems. While the surface of the substrates led to an organization and periodic arrangement of the nucleotides, none of the substrates was found to be a catalyst for pre-polymer formation, neither at full hydration, nor when dehydrated. While confinement and dehydration seem to be the main drivers for hydrogen bond formation, substrate interactions reduced the interactions between nucleotides in all cases. Our findings suggest that small supersaturated water droplets that could have been produced by geysers or springs on the primitive Earth may play an important role in non-enzymatic RNA polymerization.
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Affiliation(s)
- Alix Dujardin
- Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4M1, Canada
- Origins Institute, McMaster University, Hamilton, ON L8S 4M1, Canada
| | - Sebastian Himbert
- Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4M1, Canada
- Origins Institute, McMaster University, Hamilton, ON L8S 4M1, Canada
| | - Ralph Pudritz
- Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4M1, Canada
- Origins Institute, McMaster University, Hamilton, ON L8S 4M1, Canada
| | - Maikel C. Rheinstädter
- Department of Physics and Astronomy, McMaster University, Hamilton, ON L8S 4M1, Canada
- Origins Institute, McMaster University, Hamilton, ON L8S 4M1, Canada
- Correspondence: ; Tel.: +1-(905)-525-9140-23134; Fax: +1-(905)-546-1252
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5
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Regulation of the electrocatalytic nitrogen cycle based on sequential proton–electron transfer. Nat Catal 2022. [DOI: 10.1038/s41929-022-00833-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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6
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McClain CR, Bryant SR, Hanks G, Bowles MW. Extremophiles in Earth's Deep Seas: A View Toward Life in Exo-Oceans. ASTROBIOLOGY 2022; 22:1009-1028. [PMID: 35549348 DOI: 10.1089/ast.2021.0120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Humanity's search for extraterrestrial life is a modern manifestation of the exploratory and curious nature that has led us through millennia of scientific discoveries. With the ongoing exploration of extraterrestrial bodies, the potential for discovery of extraterrestrial life has expanded. We may better inform this search through an understanding of how life persists and flourishes on Earth in a myriad of environmental extremes. A significant proportion of our knowledge of extremophiles on Earth comes from studies on deep ocean life. Here, we review and synthesize the range of environmental extremes observed in the deep sea, the life that persists in these extreme conditions, and the biological adaptations utilized by these remarkable life-forms. We also review confirmed and predicted extraterrestrial oceans in our solar system and propose deep-sea sites that may serve as planetary field analog environments. We show that the clever ingenuity of evolution under deep-sea conditions suggests that the plausibility of extraterrestrial life is much greater than previously thought.
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Affiliation(s)
- Craig R McClain
- Louisiana Universities Marine Consortium, Chauvin, Louisiana, USA
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, USA
| | - S River Bryant
- Louisiana Universities Marine Consortium, Chauvin, Louisiana, USA
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, USA
| | - Granger Hanks
- Louisiana Universities Marine Consortium, Chauvin, Louisiana, USA
- Department of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, USA
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7
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Bird LJ, Tender LM, Eddie B, Oh E, Phillips DA, Glaven SM. Microbial survival and growth on non-corrodible conductive materials. Environ Microbiol 2021; 23:7231-7244. [PMID: 34693634 DOI: 10.1111/1462-2920.15810] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 10/07/2021] [Indexed: 11/29/2022]
Abstract
Biofilms growing aerobically on conductive substrates are often correlated with a positive, sustained shift in their redox potential. This phenomenon has a beneficial impact on microbial fuel cells by increasing their overall power output but can be detrimental when occurring on stainless steel by enhancing corrosion. The biological mechanism behind this potential shift is unresolved and a metabolic benefit to cells has not been demonstrated. Here, biofilms containing the electroautotroph 'Candidatus Tenderia electrophaga' catalysed a shift in the open circuit potential of graphite and indium tin oxide electrodes by >100 mV. Biofilms on open circuit electrodes had increased biomass and a significantly higher proportion of 'Ca. Tenderia electrophaga' compared to those on plain glass. Addition of metabolic inhibitors showed that living cells were required to maintain the more positive potential. We propose a model to describe these observations, in which 'Ca. Tenderia electrophaga' drives the shift in open circuit potential through electron uptake for oxygen reduction and CO2 fixation. We further propose that the electrode is continuously recharged by oxidation of trace redox-active molecules in the medium at the more positive potential. A similar phenomenon is possible on natural conductive substrates in the environment.
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Affiliation(s)
- Lina J Bird
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC, 20375, USA
| | - Leonard M Tender
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC, 20375, USA
| | - Brian Eddie
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC, 20375, USA
| | - Eunkeu Oh
- Optical Sciences Division, Code 5600, U.S. Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC, 20375, USA
| | - Daniel A Phillips
- Oak Ridge Institute for Science and Education/US Army DEVCOM Chemical Biological Center, Biochemistry Branch, Aberdeen Proving Grounds, Edgewood, MD, USA
| | - Sarah M Glaven
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, 4555 Overlook Ave SW, Washington, DC, 20375, 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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Chu XY, Chen SM, Zhao KW, Tian T, Gao J, Zhang HY. Plausibility of Early Life in a Relatively Wide Temperature Range: Clues from Simulated Metabolic Network Expansion. Life (Basel) 2021; 11:life11080738. [PMID: 34440482 PMCID: PMC8398716 DOI: 10.3390/life11080738] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 01/29/2023] Open
Abstract
The debate on the temperature of the environment where life originated is still inconclusive. Metabolic reactions constitute the basis of life, and may be a window to the world where early life was born. Temperature is an important parameter of reaction thermodynamics, which determines whether metabolic reactions can proceed. In this study, the scale of the prebiotic metabolic network at different temperatures was examined by a thermodynamically constrained network expansion simulation. It was found that temperature has limited influence on the scale of the simulated metabolic networks, implying that early life may have occurred in a relatively wide temperature range.
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10
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Chin K, Pasalic J, Hermis N, Barge LM. Chemical Gardens as Electrochemical Systems: In Situ Characterization of Simulated Prebiotic Hydrothermal Vents by Impedance Spectroscopy. Chempluschem 2021; 85:2619-2628. [PMID: 33270995 DOI: 10.1002/cplu.202000600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/17/2020] [Indexed: 11/05/2022]
Abstract
In an early earth or planetary chimney systems, hydrothermal fluid chemistry and flow durations play a large role in the chimney's ability to drive electrochemical reactions for the origin of life. We performed continuous electrochemical impedance spectroscopy (EIS) characterization on inorganic membranes representing prebiotic hydrothermal chimney vents in natural seafloor systems, by incorporating an electrode array into a chimney growth experiment. Localized potential and capacitances profiles in the chimney reveal a dynamic system where redox processes are driven by transport phenomena, increasing rapidly due to disequilibrium until achieving equilibrium at about 100 mV and 1000 μF/cm2 . The impedance in the chimney interior is three orders of magnitude lower (100 Ohms/cm2 vs 100 KOhms/cm2 ) than at the ocean or the ocean/chimney interface. The calculated peak dissipation factor (DF) values are more than ten times higher (40.0 vs 3.0) and also confirm the elevated chemical reactivity in the chimney interior.
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Affiliation(s)
- Keith Chin
- NASA Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, CA, 91109, USA
| | - Jasmina Pasalic
- NASA Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, CA, 91109, USA
| | - Ninos Hermis
- NASA Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, CA, 91109, USA
| | - Laura M Barge
- NASA Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, CA, 91109, USA
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11
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Lee JE, Yamaguchi A, Ooka H, Kazami T, Miyauchi M, Kitadai N, Nakamura R. In situ FTIR study of CO 2 reduction on inorganic analogues of carbon monoxide dehydrogenase. Chem Commun (Camb) 2021; 57:3267-3270. [PMID: 33650585 DOI: 10.1039/d0cc07318k] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The CO2-to-CO reduction by carbon monoxide dehydrogenase (CODH) with a [NiFe4S4] cluster is considered to be the oldest pathway of biological carbon fixation and therefore may have been involved in the origin of life. Although previous studies have investigated CO2 reduction by Fe and Ni sulfides to identify the prebiotic origin of the [NiFe4S4] cluster, the reaction mechanism remains largely elusive. Herein, we applied in situ electrochemical ATR-FTIR spectroscopy to probe the reaction intermediates of greigite (Fe3S4) and violarite (FeNi2S4). Intermediate species assignable to surface-bound CO2 and formyl groups were found to be stabilized in the presence of Ni, lending insight into its role in enhancing the multistep CO2 reduction process.
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Affiliation(s)
- Ji-Eun Lee
- Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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12
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Altair T, Sartori LM, Rodrigues F, de Avellar MGB, Galante D. Natural Radioactive Environments as Sources of Local Disequilibrium for the Emergence of Life. ASTROBIOLOGY 2020; 20:1489-1497. [PMID: 32907342 DOI: 10.1089/ast.2019.2133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Certain subterranean environments of Earth have naturally accumulated long-lived radionuclides, such as 238U, 232Th, and 40K, near the presence of liquid water. In these natural radioactive environments, water radiolysis can produce chemical species of biological importance, such as H2. Although the proposal of radioactive decay as an alternative source of energy for living systems has existed for >30 years, this hypothesis gained strength after the recent discovery of a peculiar ecosystem in a gold mine in South Africa, whose existence is dependent on chemical species produced by water radiolysis. In this study, we calculate the chemical disequilibrium generated locally by water radiolysis due to gamma radiation. We then analyze the possible contribution of this disequilibrium for the emergence of life, considering conditions of early Earth and having as reference the alkaline hydrothermal vent theory. Results from our kinetic model point out the similarities between the conditions caused by water radiolysis and those found on alkaline hydrothermal systems. Our model produces a steady increase of pH with time, which favors the formation of a natural electrochemical gradient and the precipitation of minerals with catalytic activity for protometabolism in this aqueous environment. We conclude by describing a possible free-energy conversion mechanism based on protometabolism, which could be a requisite for the emergence of life in Hadean Earth.
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Affiliation(s)
- Thiago Altair
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
| | - Larissa M Sartori
- Instituto de Matemática e Estatística, Universidade de São Paulo, São Paulo, Brazil
| | - Fabio Rodrigues
- Departamento de Química Fundamental Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Marcio G B de Avellar
- Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo, Diadema, Brazil
| | - Douglas Galante
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
- Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, Brazil
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13
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Abstract
All life on Earth is built of organic molecules, so the primordial sources of reduced carbon remain a major open question in studies of the origin of life. A variant of the alkaline-hydrothermal-vent theory for life's emergence suggests that organics could have been produced by the reduction of CO2 via H2 oxidation, facilitated by geologically sustained pH gradients. The process would be an abiotic analog-and proposed evolutionary predecessor-of the Wood-Ljungdahl acetyl-CoA pathway of modern archaea and bacteria. The first energetic bottleneck of the pathway involves the endergonic reduction of CO2 with H2 to formate (HCOO-), which has proven elusive in mild abiotic settings. Here we show the reduction of CO2 with H2 at room temperature under moderate pressures (1.5 bar), driven by microfluidic pH gradients across inorganic Fe(Ni)S precipitates. Isotopic labeling with 13C confirmed formate production. Separately, deuterium (2H) labeling indicated that electron transfer to CO2 does not occur via direct hydrogenation with H2 but instead, freshly deposited Fe(Ni)S precipitates appear to facilitate electron transfer in an electrochemical-cell mechanism with two distinct half-reactions. Decreasing the pH gradient significantly, removing H2, or eliminating the precipitate yielded no detectable product. Our work demonstrates the feasibility of spatially separated yet electrically coupled geochemical reactions as drivers of otherwise endergonic processes. Beyond corroborating the ability of early-Earth alkaline hydrothermal systems to couple carbon reduction to hydrogen oxidation through biologically relevant mechanisms, these results may also be of significance for industrial and environmental applications, where other redox reactions could be facilitated using similarly mild approaches.
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14
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Preiner M, Asche S, Becker S, Betts HC, Boniface A, Camprubi E, Chandru K, Erastova V, Garg SG, Khawaja N, Kostyrka G, Machné R, Moggioli G, Muchowska KB, Neukirchen S, Peter B, Pichlhöfer E, Radványi Á, Rossetto D, Salditt A, Schmelling NM, Sousa FL, Tria FDK, Vörös D, Xavier JC. The Future of Origin of Life Research: Bridging Decades-Old Divisions. Life (Basel) 2020; 10:E20. [PMID: 32110893 PMCID: PMC7151616 DOI: 10.3390/life10030020] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/19/2020] [Accepted: 02/21/2020] [Indexed: 12/12/2022] Open
Abstract
Research on the origin of life is highly heterogeneous. After a peculiar historical development, it still includes strongly opposed views which potentially hinder progress. In the 1st Interdisciplinary Origin of Life Meeting, early-career researchers gathered to explore the commonalities between theories and approaches, critical divergence points, and expectations for the future. We find that even though classical approaches and theories-e.g. bottom-up and top-down, RNA world vs. metabolism-first-have been prevalent in origin of life research, they are ceasing to be mutually exclusive and they can and should feed integrating approaches. Here we focus on pressing questions and recent developments that bridge the classical disciplines and approaches, and highlight expectations for future endeavours in origin of life research.
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Affiliation(s)
- Martina Preiner
- Institute of Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany; (S.G.G.); (F.D.K.T.)
| | - Silke Asche
- School of Chemistry, University of Glasgow, Glasgow G128QQ, UK;
| | - Sidney Becker
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK;
| | - Holly C. Betts
- School of Earth Sciences, University of Bristol, Bristol BS8 1RL, UK;
| | - Adrien Boniface
- Environmental Microbial Genomics, Laboratoire Ampère, Ecole Centrale de Lyon, Université de Lyon, 69130 Ecully, France;
| | - Eloi Camprubi
- Origins Center, Department of Earth Sciences, Utrecht University, 3584 CB Utrecht, The Netherlands;
| | - Kuhan Chandru
- Space Science Center (ANGKASA), Institute of Climate Change, Level 3, Research Complex, National University of Malaysia, UKM Bangi 43600, Selangor, Malaysia;
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technicka 5, 16628 Prague 6–Dejvice, Czech Republic
| | - Valentina Erastova
- UK Centre for Astrobiology, School of Chemistry, University of Edinburgh, Edinburgh EH9 3FJ, UK;
| | - Sriram G. Garg
- Institute of Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany; (S.G.G.); (F.D.K.T.)
| | - Nozair Khawaja
- Institut für Geologische Wissenschaften, Freie Universität Berlin, 12249 Berlin, Germany;
| | | | - Rainer Machné
- Institute of Synthetic Microbiology, University of Düsseldorf, 40225 Düsseldorf, Germany; (R.M.); (N.M.S.)
- Quantitative and Theoretical Biology, University of Düsseldorf, 40225 Düsseldorf, Germany
| | - Giacomo Moggioli
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4DQ, UK;
| | - Kamila B. Muchowska
- Université de Strasbourg, CNRS, ISIS, 8 allée Gaspard Monge, 67000 Strasbourg, France;
| | - Sinje Neukirchen
- Archaea Biology and Ecogenomics Division, University of Vienna, 1090 Vienna, Austria; (S.N.); (E.P.); (F.L.S.)
| | - Benedikt Peter
- Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany;
| | - Edith Pichlhöfer
- Archaea Biology and Ecogenomics Division, University of Vienna, 1090 Vienna, Austria; (S.N.); (E.P.); (F.L.S.)
| | - Ádám Radványi
- Department of Plant Systematics, Ecology and Theoretical Biology, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary (D.V.)
- Institute of Evolution, MTA Centre for Ecological Research, Klebelsberg Kuno u. 3., H-8237 Tihany, Hungary
| | - Daniele Rossetto
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy;
| | - Annalena Salditt
- Systems Biophysics, Physics Department, Ludwig-Maximilians-Universität München, 80799 Munich, Germany;
| | - Nicolas M. Schmelling
- Institute of Synthetic Microbiology, University of Düsseldorf, 40225 Düsseldorf, Germany; (R.M.); (N.M.S.)
- Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674 Cologne, Germany
| | - Filipa L. Sousa
- Archaea Biology and Ecogenomics Division, University of Vienna, 1090 Vienna, Austria; (S.N.); (E.P.); (F.L.S.)
| | - Fernando D. K. Tria
- Institute of Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany; (S.G.G.); (F.D.K.T.)
| | - Dániel Vörös
- Department of Plant Systematics, Ecology and Theoretical Biology, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary (D.V.)
- Institute of Evolution, MTA Centre for Ecological Research, Klebelsberg Kuno u. 3., H-8237 Tihany, Hungary
| | - Joana C. Xavier
- Institute of Molecular Evolution, University of Düsseldorf, 40225 Düsseldorf, Germany; (S.G.G.); (F.D.K.T.)
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15
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Bains W. Getting Beyond the Toy Domain. Meditations on David Deamer's "Assembling Life". Life (Basel) 2020; 10:life10020018. [PMID: 32085425 PMCID: PMC7175206 DOI: 10.3390/life10020018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 02/09/2020] [Accepted: 02/15/2020] [Indexed: 11/16/2022] Open
Abstract
David Deamer has written another book, Assembling Life, on the origin of life. It is unapologetically polemic, presenting Deamer's view that life originated in fresh water hydrothermal fields on volcanic islands on early Earth, arguing that this provided a unique environment not just for organic chemistry but for the self-assembling structure that drive that chemistry and form the basis of structure in life. It is worth reading, it is an advance in the field, but is it convincing? I argue that the Origin of Life field as a whole is unconvincing, generating results in Toy Domains that cannot be scaled to any real world scenario. I suggest that, by analogy with the history of artificial intelligence and solar astronomy, we need much more scale, and fundamentally new ideas, to take the field forward.
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Affiliation(s)
- William Bains
- Five Alarm Bio Ltd., O2h Scitech Park, Mill Lane, Hauxton, Cambridge CB22 5HX, UK;
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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16
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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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17
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Sojo V, Ohno A, McGlynn SE, Yamada YMA, Nakamura R. Microfluidic Reactors for Carbon Fixation under Ambient-Pressure Alkaline-Hydrothermal-Vent Conditions. Life (Basel) 2019; 9:life9010016. [PMID: 30717250 PMCID: PMC6463036 DOI: 10.3390/life9010016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/22/2019] [Accepted: 01/25/2019] [Indexed: 12/13/2022] Open
Abstract
The alkaline-hydrothermal-vent theory for the origin of life predicts the spontaneous reduction of CO₂, dissolved in acidic ocean waters, with H₂ from the alkaline vent effluent. This reaction would be catalyzed by Fe(Ni)S clusters precipitated at the interface, which effectively separate the two fluids into an electrochemical cell. Using microfluidic reactors, we set out to test this concept. We produced thin, long Fe(Ni)S precipitates of less than 10 µm thickness. Mixing simplified analogs of the acidic-ocean and alkaline-vent fluids, we then tested for the reduction of CO₂. We were unable to detect reduced carbon products under a number of conditions. As all of our reactions were performed at atmospheric pressure, the lack of reduced carbon products may simply be attributable to the low concentration of hydrogen in our system, suggesting that high-pressure reactors may be a necessity.
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Affiliation(s)
- Victor Sojo
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
- Systems Biophysics, Ludwig-Maximilian University of Munich, Munich 80799, Germany.
- Institute for Advanced Study, Berlin. Wallotstr. 19, Berlin 14193, Germany.
| | - Aya Ohno
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
| | - Shawn E McGlynn
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.
- Blue Marble Space Institute of Science, Seattle, WA 98154, USA.
| | - Yoichi M A Yamada
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
| | - Ryuhei Nakamura
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.
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