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Huang XL. Unveiling the role of inorganic nanoparticles in Earth's biochemical evolution through electron transfer dynamics. iScience 2024; 27:109555. [PMID: 38638571 PMCID: PMC11024932 DOI: 10.1016/j.isci.2024.109555] [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] [Indexed: 04/20/2024] Open
Abstract
This article explores the intricate interplay between inorganic nanoparticles and Earth's biochemical history, with a focus on their electron transfer properties. It reveals how iron oxide and sulfide nanoparticles, as examples of inorganic nanoparticles, exhibit oxidoreductase activity similar to proteins. Termed "life fossil oxidoreductases," these inorganic enzymes influence redox reactions, detoxification processes, and nutrient cycling in early Earth environments. By emphasizing the structural configuration of nanoparticles and their electron conformation, including oxygen defects and metal vacancies, especially electron hopping, the article provides a foundation for understanding inorganic enzyme mechanisms. This approach, rooted in physics, underscores that life's origin and evolution are governed by electron transfer principles within the framework of chemical equilibrium. Today, these nanoparticles serve as vital biocatalysts in natural ecosystems, participating in critical reactions for ecosystem health. The research highlights their enduring impact on Earth's history, shaping ecosystems and interacting with protein metal centers through shared electron transfer dynamics, offering insights into early life processes and adaptations.
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Affiliation(s)
- Xiao-Lan Huang
- Center for Clean Water Technology, School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794-6044, USA
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2
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Shisler KA, Kincannon WM, Mattice JR, Larson J, Valaydon-Pillay A, Mus F, Flusche T, Kumar Nath A, Stoian SA, Raugei S, Bothner B, DuBois JL, Peters JW. Homologous acetone carboxylases select Fe(II) or Mn(II) as the catalytic cofactor. mBio 2024; 15:e0298723. [PMID: 38126751 PMCID: PMC10865871 DOI: 10.1128/mbio.02987-23] [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: 11/13/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023] Open
Abstract
Acetone carboxylases (ACs) catalyze the metal- and ATP-dependent conversion of acetone and bicarbonate to form acetoacetate. Interestingly, two homologous ACs that have been biochemically characterized have been reported to have different metal complements, implicating different metal dependencies in catalysis. ACs from proteobacteria Xanthobacter autotrophicus and Aromatoleum aromaticum share 68% sequence identity but have been proposed to have different catalytic metals. In this work, the two ACs were expressed under the same conditions in Escherichia coli and were subjected to parallel chelation and reconstitution experiments with Mn(II) or Fe(II). Electron paramagnetic and Mössbauer spectroscopies identified signatures, respectively, of Mn(II) or Fe(II) bound at the active site. These experiments showed that the respective ACs, without the assistance of chaperones, second metal sites, or post-translational modifications facilitate correct metal incorporation, and despite the expected thermodynamic preference for Fe(II), each preferred a distinct metal. Catalysis was likewise associated uniquely with the cognate metal, though either could potentially serve the proposed Lewis acidic role. Subtle differences in the protein structure are implicated in serving as a selectivity filter for Mn(II) or Fe(II).IMPORTANCEThe Irving-Williams series refers to the predicted stabilities of transition metal complexes where the observed general stability for divalent first-row transition metal complexes increase across the row. Acetone carboxylases (ACs) use a coordinated divalent metal at their active site in the catalytic conversion of bicarbonate and acetone to form acetoacetate. Highly homologous ACs discriminate among different divalent metals at their active sites such that variations of the enzyme prefer Mn(II) over Fe(II), defying Irving-Williams-predicted behavior. Defining the determinants that promote metal discrimination within the first-row transition metals is of broad fundamental importance in understanding metal-mediated catalysis and metal catalyst design.
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Affiliation(s)
- Krista A. Shisler
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
| | - William M. Kincannon
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Jenna R. Mattice
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - James Larson
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | | | - Florence Mus
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Tamara Flusche
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Arnab Kumar Nath
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | | | - Simone Raugei
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Jennifer L. DuBois
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - John W. Peters
- Institute of Biological Chemistry, Washington State University, Pullman, Washington, USA
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA
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3
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de Graaf R, De Decker Y, Sojo V, Hudson R. Quantifying Catalysis at the Origin of Life. Chemistry 2023; 29:e202301447. [PMID: 37578090 DOI: 10.1002/chem.202301447] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Indexed: 08/15/2023]
Abstract
The construction of hypothetical environments to produce organic molecules such as metabolic intermediates or amino acids is the subject of ongoing research into the emergence of life. Experiments specifically focused on an anabolic approach typically rely on a mineral catalyst to facilitate the supply of organics that may have produced prebiotic building blocks for life. Alternatively to a true catalytic system, a mineral could be sacrificially oxidized in the production of organics, necessitating the emergent 'life' to turn to virgin materials for each iteration of metabolic processes. The aim of this perspective is to view the current 'metabolism-first' literature through the lens of materials chemistry to evaluate the need for higher catalytic activity and materials analyses. While many elegant studies have detailed the production of chemical building blocks under geologically plausible and biologically relevant conditions, few appear to do so with sub-stoichiometric amounts of metals or minerals. Moving toward sub-stoichiometric metals with rigorous materials analyses is necessary to demonstrate the viability of an elusive cornerstone of the 'metabolism-first' hypotheses: catalysis. We emphasize that future work should aim to demonstrate decreased catalyst loading, increased productivity, and/or rigorous materials analyses for evidence of true catalysis.
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Affiliation(s)
- Ruvan de Graaf
- Department of Chemistry, College of the Atlantic, 105 Eden Street, Bar Harbor, Maine, 04609, USA
| | - Yannick De Decker
- Center for Nonlinear Phenomena and Complex Systems, Université libre de Bruxelles, CP 231, 1050, Ixelles, Belgium
| | - Victor Sojo
- Institute for Comparative Genomics & Richard Gilder Graduate School, Université libre de Bruxelles, American Museum of Natural History, 79th Street at Central Park West. New York, NY, 10024-5192, USA
| | - Reuben Hudson
- Department of Chemistry, College of the Atlantic, 105 Eden Street, Bar Harbor, Maine, 04609, USA
- Department of Chemistry, Colby College, 4000 Mayflower Hill Drive, Waterville, Maine, 04901, USA
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4
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Goldman AD, Weber JM, LaRowe DE, Barge LM. Electron transport chains as a window into the earliest stages of evolution. Proc Natl Acad Sci U S A 2023; 120:e2210924120. [PMID: 37579147 PMCID: PMC10451490 DOI: 10.1073/pnas.2210924120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023] Open
Abstract
The origin and early evolution of life is generally studied under two different paradigms: bottom up and top down. Prebiotic chemistry and early Earth geochemistry allow researchers to explore possible origin of life scenarios. But for these "bottom-up" approaches, even successful experiments only amount to a proof of principle. On the other hand, "top-down" research on early evolutionary history is able to provide a historical account about ancient organisms, but is unable to investigate stages that occurred during and just after the origin of life. Here, we consider ancient electron transport chains (ETCs) as a potential bridge between early evolutionary history and a protocellular stage that preceded it. Current phylogenetic evidence suggests that ancestors of several extant ETC components were present at least as late as the last universal common ancestor of life. In addition, recent experiments have shown that some aspects of modern ETCs can be replicated by minerals, protocells, or organic cofactors in the absence of biological proteins. Here, we discuss the diversity of ETCs and other forms of chemiosmotic energy conservation, describe current work on the early evolution of membrane bioenergetics, and advocate for several lines of research to enhance this understanding by pairing top-down and bottom-up approaches.
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Affiliation(s)
- Aaron D. Goldman
- Department of Biology, Oberlin College, Oberlin, OH44074
- Blue Marble Space Institute of Science, Seattle, WA98154
| | - Jessica M. Weber
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA91109
| | - Douglas E. LaRowe
- Department of Earth Sciences, University of Southern California, Los Angeles, CA90089
| | - Laura M. Barge
- Blue Marble Space Institute of Science, Seattle, WA98154
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA91109
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Abstract
α-Amino acids are essential molecular constituents of life, twenty of which are privileged because they are encoded by the ribosomal machinery. The question remains open as to why this number and why this 20 in particular, an almost philosophical question that cannot be conclusively resolved. They are closely related to the evolution of the genetic code and whether nucleic acids, amino acids, and peptides appeared simultaneously and were available under prebiotic conditions when the first self-sufficient complex molecular system emerged on Earth. This report focuses on prebiotic and metabolic aspects of amino acids and proteins starting with meteorites, followed by their formation, including peptides, under plausible prebiotic conditions, and the major biosynthetic pathways in the various kingdoms of life. Coenzymes play a key role in the present analysis in that amino acid metabolism is linked to glycolysis and different variants of the tricarboxylic acid cycle (TCA, rTCA, and the incomplete horseshoe version) as well as the biosynthesis of the most important coenzymes. Thus, the report opens additional perspectives and facets on the molecular evolution of primary metabolism.
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Affiliation(s)
- Andreas Kirschning
- Institute of Organic ChemistryLeibniz University HannoverSchneiderberg 1B30167HannoverGermany
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Abstract
Covering: up to 2022The report provides a broad approach to deciphering the evolution of coenzyme biosynthetic pathways. Here, these various pathways are analyzed with respect to the coenzymes required for this purpose. Coenzymes whose biosynthesis relies on a large number of coenzyme-mediated reactions probably appeared on the scene at a later stage of biological evolution, whereas the biosyntheses of pyridoxal phosphate (PLP) and nicotinamide (NAD+) require little additional coenzymatic support and are therefore most likely very ancient biosynthetic pathways.
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Affiliation(s)
- Andreas Kirschning
- Institute of Organic Chemistry, Leibniz University Hannover, Schneiderberg 1B, D-30167 Hannover, Germany.
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7
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Carbon dioxide photoreduction in prebiotic environments. Photochem Photobiol Sci 2022; 21:863-878. [PMID: 35107790 DOI: 10.1007/s43630-021-00168-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/27/2021] [Indexed: 10/19/2022]
Abstract
The reduction of carbon dioxide is one of the hottest topics due to the concern of global warming. Carbon dioxide reduction is also an essential step for life's origins as photoautotrophs arose soon after Earth formation. Both the topics are of high general interest, and possibly, there could be a fruitful cross-fertilization of the two fields. Herein, we selected and collected papers related to photoreduction of carbon dioxide using compounds easily available on the Earth and considered of prebiotic relevance. This work might be useful also to scientists interested in carbon dioxide photoreduction and/or to have an overview of the techniques available.
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8
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Dong Y, Zhang S, Zhao L. Unraveling the Structural Development of
Peptide‐Coordinated Iron‐Sulfur
Clusters: Prebiotic Evolution and Biosynthetic Strategies. CHINESE J CHEM 2022. [DOI: 10.1002/cjoc.202100892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Yijun Dong
- School of Life Sciences, Tsinghua University Beijing 100084 China
| | - Siqi Zhang
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry Tsinghua University Beijing 100084 China
| | - Liang Zhao
- Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry Tsinghua University Beijing 100084 China
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9
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Huang XL. What are the inorganic nanozymes? Artificial or inorganic enzymes! NEW J CHEM 2022. [DOI: 10.1039/d2nj02088b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The research on inorganic nanozymes remains very active since the first paper on the “intrinsic peroxidase-like properties of ferromagnetic nanoparticles” was published in Nature Nanotechnology in 2007. However, there is...
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10
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Kouznetsov VV, Hernández JG. Nanostructured silicate catalysts for environmentally benign Strecker-type reactions: status quo and quo vadis. RSC Adv 2022; 12:20807-20828. [PMID: 35919186 PMCID: PMC9299969 DOI: 10.1039/d2ra03102g] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/30/2022] [Indexed: 01/26/2023] Open
Abstract
Chemical processes are usually catalytic transformations. The use of catalytic reagents can reduce the reaction temperature, decrease reagent-based waste, and enhance the selectivity of a reaction potentially avoiding unwanted side reactions leading to green technology. Chemical processes are also frequently based on multicomponent reactions (MCRs) that possess evident improvements over multistep processes. Both MCRs and catalysis tools are the most valuable principles of green chemistry. Among diverse MCRs, the three-component Strecker reaction (S-3-CR) is a particular transformation conducive to the formation of valuable bifunctional building blocks (α-amino nitriles) in organic synthesis, medicinal chemistry, drug research, and organic materials science. To be a practical synthetic tool, the S-3-CR must be achieved using alternative energy input systems, safe reaction media, and effective catalysts. These latter reagents are now deeply associated with nanoscience and nanocatalysis. Continuously developed, nanostructured silicate catalysts symbolize green pathways in our quest to attain sustainability. Studying and developing nanocatalyzed S-3-CR condensations as an important model will be suitable for achieving the current green mission. This critical review aims to highlight the advances in the development of nanostructured catalysts for technologically important Strecker-type reactions and to analyze this progress from the viewpoint of green and sustainable chemistry. The innovations in the development of nanostructured silicate catalysts for Strecker reactions are analyzed discussing the advantages and drawbacks of existing protocols based on the use of nanocatalytic systems for α-amino nitrile formation.![]()
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Affiliation(s)
- Vladimir V. Kouznetsov
- Laboratorio de Química Orgánica y Biomolecular, CMN, Universidad Industrial de Santander, Parque Tecnológico Guatiguará, Km 2 Vía Refugio, Piedecuesta 681011, Colombia
| | - José G. Hernández
- Grupo Ciencia de los Materiales, Instituto de Química, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Calle 70 No. 52-21, Medellín, Colombia
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11
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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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12
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Park Y, Faivre D. Diversity of Microbial Metal Sulfide Biomineralization. Chempluschem 2021; 87:e202100457. [PMID: 34898036 DOI: 10.1002/cplu.202100457] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/25/2021] [Indexed: 01/30/2023]
Abstract
Since the emergence of life on Earth, microorganisms have contributed to biogeochemical cycles. Sulfate-reducing bacteria are an example of widespread microorganisms that participate in the metal and sulfur cycles by biomineralization of biogenic metal sulfides. In this work, we review the microbial biomineralization of metal sulfide particles and summarize distinctive features from exemplary cases. We highlight that metal sulfide biomineralization is highly metal- and organism-specific. The properties of metal sulfide biominerals depend on the degree of cellular control and on environmental factors, such as pH, temperature, and concentration of metals. Moreover, biogenic macromolecules, including peptides and proteins, help cells control their extracellular and intracellular environments that regulate biomineralization. Accordingly, metal sulfide biominerals exhibit unique features when compared to abiotic minerals or biominerals produced by dead cell debris.
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Affiliation(s)
- Yeseul Park
- Aix-Marseille Université, CEA, CNRS, BIAM, 13108, Saint-Paul-lez-Durance, France
| | - Damien Faivre
- Aix-Marseille Université, CEA, CNRS, BIAM, 13108, Saint-Paul-lez-Durance, France
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13
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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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14
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'Whole Organism', Systems Biology, and Top-Down Criteria for Evaluating Scenarios for the Origin of Life. Life (Basel) 2021; 11:life11070690. [PMID: 34357062 PMCID: PMC8306273 DOI: 10.3390/life11070690] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 12/22/2022] Open
Abstract
While most advances in the study of the origin of life on Earth (OoLoE) are piecemeal, tested against the laws of chemistry and physics, ultimately the goal is to develop an overall scenario for life's origin(s). However, the dimensionality of non-equilibrium chemical systems, from the range of possible boundary conditions and chemical interactions, renders the application of chemical and physical laws difficult. Here we outline a set of simple criteria for evaluating OoLoE scenarios. These include the need for containment, steady energy and material flows, and structured spatial heterogeneity from the outset. The Principle of Continuity, the fact that all life today was derived from first life, suggests favoring scenarios with fewer non-analog (not seen in life today) to analog (seen in life today) transitions in the inferred first biochemical pathways. Top-down data also indicate that a complex metabolism predated ribozymes and enzymes, and that full cellular autonomy and motility occurred post-LUCA. Using these criteria, we find the alkaline hydrothermal vent microchamber complex scenario with a late evolving exploitation of the natural occurring pH (or Na+ gradient) by ATP synthase the most compelling. However, there are as yet so many unknowns, we also advocate for the continued development of as many plausible scenarios as possible.
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15
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Rasmussen B, Muhling J, Fischer W. Greenalite Nanoparticles in Alkaline Vent Plumes as Templates for the Origin of Life. ASTROBIOLOGY 2021; 21:246-259. [PMID: 33085498 PMCID: PMC7876356 DOI: 10.1089/ast.2020.2270] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 09/07/2020] [Indexed: 05/07/2023]
Abstract
Mineral templates are thought to have played keys roles in the emergence of life. Drawing on recent findings from 3.45-2.45 billion-year-old iron-rich hydrothermal sedimentary rocks, we hypothesize that greenalite (Fe3Si2O5(OH)4) was a readily available mineral in hydrothermal environments, where it may have acted as a template and catalyst in polymerization, vesicle formation and encapsulation, and protocell replication. We argue that venting of dissolved Fe2+ and SiO2(aq) into the anoxic Hadean ocean favored the precipitation of nanometer-sized particles of greenalite in hydrothermal plumes, producing a continuous flow of free-floating clay templates that traversed the ocean. The mixing of acidic, metal-bearing hydrothermal plumes from volcanic ridge systems with more alkaline, organic-bearing plumes generated by serpentinization of ultramafic rocks brought together essential building blocks for life in solutions conducive to greenalite precipitation. We suggest that the extreme disorder in the greenalite crystal lattice, producing structural modulations resembling parallel corrugations (∼22 Å wide) on particle edges, promoted the assembly and alignment of linear RNA-type molecules (∼20 Å diameter). In alkaline solutions, greenalite nanoparticles could have accelerated the growth of membrane vesicles, while their encapsulation allowed RNA-type molecules to continue to form on the mineral templates, potentially enhancing the growth and division of primitive cell membranes. Once self-replicating RNA evolved, the mineral template became redundant, and protocells were free to replicate and roam the ocean realm.
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Affiliation(s)
- B. Rasmussen
- School of Earth Sciences, The University of Western Australia, Perth, Australia
| | - J.R. Muhling
- School of Earth Sciences, The University of Western Australia, Perth, Australia
| | - W.W. Fischer
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, California, USA
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16
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Zhao D, Bartlett S, Yung YL. Quantifying Mineral-Ligand Structural Similarities: Bridging the Geological World of Minerals with the Biological World of Enzymes. Life (Basel) 2020; 10:life10120338. [PMID: 33321803 PMCID: PMC7764262 DOI: 10.3390/life10120338] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/15/2020] [Accepted: 12/07/2020] [Indexed: 01/10/2023] Open
Abstract
Metal compounds abundant on Early Earth are thought to play an important role in the origins of life. Certain iron-sulfur minerals for example, are proposed to have served as primitive metalloenzyme cofactors due to their ability to catalyze organic synthesis processes and facilitate electron transfer reactions. An inherent difficulty with studying the catalytic potential of many metal compounds is the wide range of data and parameters to consider when searching for individual minerals and ligands of interest. Detecting mineral-ligand pairs that are structurally analogous enables more relevant selections of data to study, since structural affinity is a key indicator of comparable catalytic function. However, current structure-oriented approaches tend to be subjective and localized, and do not quantify observations or compare them with other potential targets. Here, we present a mathematical approach that compares structural similarities between various minerals and ligands using molecular similarity metrics. We use an iterative substructure search in the crystal lattice, paired with benchmark structural similarity methods. This structural comparison may be considered as a first stage in a more advanced analysis tool that will include a range of chemical and physical factors when computing mineral-ligand similarity. This approach will seek relationships between the mineral and enzyme worlds, with applications to the origins of life, ecology, catalysis, and astrobiology.
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Affiliation(s)
- Daniel Zhao
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA; (D.Z.); (Y.L.Y.)
- Department of Mathematics, Harvard University, Massachusetts Hall, Cambridge, MA 02138, USA
| | - Stuart Bartlett
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA; (D.Z.); (Y.L.Y.)
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan
- Correspondence:
| | - Yuk L. Yung
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA; (D.Z.); (Y.L.Y.)
- NASA Jet Propulsion Laboratory, Oak Grove Dr, La Cañada Flintridge, CA 91011, USA
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17
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Jones JP, Firdosy SA, Barge LM, Bescup JC, Perl SM, Zhang X, Pate AM, Price RE. 3D Printed Minerals as Astrobiology Analogs of Hydrothermal Vent Chimneys. ASTROBIOLOGY 2020; 20:1405-1412. [PMID: 32924535 DOI: 10.1089/ast.2020.2260] [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: 06/11/2023]
Abstract
Hydrothermal vents, which are highly plausible habitable environments for life and of interest for some origin-of-life scenarios, may exist on icy moons such as Europa or Enceladus in addition to Earth. Some hydrothermal vent chimney structures are extremely porous and friable, making their reconstruction in the lab challenging (e.g., brucite or saponite in alkaline hydrothermal settings). Here, we present the results from our efforts to reconstruct a simplified chimney structure directly out of mineral powder using binder jet additive manufacturing. Olivine sand was chosen for this initial method development effort since it represents a naturally occurring seafloor material and is inexpensively available in large quantities in powder form. The crystal structure of olivine used for the print was not modified during the process, as confirmed by powder X-ray diffraction (XRD). To characterize the microstructure of our 3D printed precipitates, we used computed tomography (CT) X-ray scan techniques. We also evaluated a chimney precipitate from a sample collected from the Prony Hydrothermal Field (PHF), southern New Caledonia, an alkaline system driven by serpentinization with mineralogy composed of brucite and carbonates. While not directly comparable from a mineralogical point of view, the microstructure and porosity of both precipitates was similar, suggesting that our 3D printing technique may be a valuable tool for future astrobiology research on hydrothermal vent precipitates.
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Affiliation(s)
- John-Paul Jones
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Samad A Firdosy
- 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
| | - John C Bescup
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Scott M Perl
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Xu Zhang
- College of Engineering Center for Design and Manufacturing Excellence, Ohio State University, Columbus, Ohio, USA
| | - Andre M Pate
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Roy E Price
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, USA
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Russell MJ, Ponce A. Six 'Must-Have' Minerals for Life's Emergence: Olivine, Pyrrhotite, Bridgmanite, Serpentine, Fougerite and Mackinawite. Life (Basel) 2020; 10:E291. [PMID: 33228029 PMCID: PMC7699418 DOI: 10.3390/life10110291] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/13/2020] [Accepted: 11/14/2020] [Indexed: 12/25/2022] Open
Abstract
Life cannot emerge on a planet or moon without the appropriate electrochemical disequilibria and the minerals that mediate energy-dissipative processes. Here, it is argued that four minerals, olivine ([Mg>Fe]2SiO4), bridgmanite ([Mg,Fe]SiO3), serpentine ([Mg,Fe,]2-3Si2O5[OH)]4), and pyrrhotite (Fe(1-x)S), are an essential requirement in planetary bodies to produce such disequilibria and, thereby, life. Yet only two minerals, fougerite ([Fe2+6xFe3+6(x-1)O12H2(7-3x)]2+·[(CO2-)·3H2O]2-) and mackinawite (Fe[Ni]S), are vital-comprising precipitate membranes-as initial "free energy" conductors and converters of such disequilibria, i.e., as the initiators of a CO2-reducing metabolism. The fact that wet and rocky bodies in the solar system much smaller than Earth or Venus do not reach the internal pressure (≥23 GPa) requirements in their mantles sufficient for producing bridgmanite and, therefore, are too reduced to stabilize and emit CO2-the staple of life-may explain the apparent absence or negligible concentrations of that gas on these bodies, and thereby serves as a constraint in the search for extraterrestrial life. The astrobiological challenge then is to search for worlds that (i) are large enough to generate internal pressures such as to produce bridgmanite or (ii) boast electron acceptors, including imported CO2, from extraterrestrial sources in their hydrospheres.
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Affiliation(s)
- Michael J. Russell
- Dipartimento di Chimica, Università degli Studi di Torino, via P. Giuria 7, 10125 Turin, Italy
| | - Adrian Ponce
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, USA;
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19
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Wansleben M, Vinson J, Wählisch A, Bzheumikhova K, Hönicke P, Beckhoff B, Kayser Y. Speciation of iron sulfide compounds by means of X-ray Emission Spectroscopy using a compact full-cylinder von Hamos spectrometer. JOURNAL OF ANALYTICAL ATOMIC SPECTROMETRY 2020; 35:10.1039/d0ja00244e. [PMID: 34092880 PMCID: PMC8176736 DOI: 10.1039/d0ja00244e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We present experimental and theoretical X-ray emission spectroscopy (XES) data of the Fe Kβ line for Iron(II)sulfide (FeS) and Iron(II)disulfide (FeS2). In comparison to X-ray absorption spectroscopy (XAS), XES offers different discrimination capabilities for chemical speciation, depending on the valence states of the compounds probed and, more importantly in view of a a broader, laboratory-based use, a larger flexibility with respect to the excitation source used. The experimental Fe Kβ XES data was measured using polychromatic X-ray radiation and a compact full-cylinder von Hamos spectrometer while the calculations were realized using the OCEAN code. The von Hamos spectrometer used is characterized by an energy window of up to 700 eV and a spectral resolving power of E/ΔE = 800. The large energy window at a single position of the spectrometer components is made profit of to circumvent the instrumental sensitivity of wavelength-dispersive spectrometers to sample positioning. This results in a robust energy scale which is used to compare experimental data with ab initio valence-to-core calculations, which are carried out using the ocean package. To validate the reliability of the ocean package for the two sample systems, near edge X-ray absorption fine structure measurements of the Fe K absorption edge are compared to theory using the same input parameters as in the case of the X-ray emission calculations. Based on the example of iron sulfide compounds, the combination of XES experiments and ocean calculations allows unravelling the electronic structure of different transition metal sulfides and qualifying XES investigations for the speciation of different compounds.
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Affiliation(s)
- Malte Wansleben
- Physikalisch-Technische Bundesanstalt, Abbestraße 2-12, 10587 Berlin, Germany
- Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Hahn-Meitner-Platz 1, 14109 Berlin, Germany
| | - John Vinson
- National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - André Wählisch
- Physikalisch-Technische Bundesanstalt, Abbestraße 2-12, 10587 Berlin, Germany
| | - Karina Bzheumikhova
- Physikalisch-Technische Bundesanstalt, Abbestraße 2-12, 10587 Berlin, Germany
| | - Philipp Hönicke
- Physikalisch-Technische Bundesanstalt, Abbestraße 2-12, 10587 Berlin, Germany
| | - Burkhard Beckhoff
- Physikalisch-Technische Bundesanstalt, Abbestraße 2-12, 10587 Berlin, Germany
| | - Yves Kayser
- Physikalisch-Technische Bundesanstalt, Abbestraße 2-12, 10587 Berlin, Germany
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20
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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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21
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Kitadai N, Nakamura R, Yamamoto M, Takai K, Yoshida N, Oono Y. Metals likely promoted protometabolism in early ocean alkaline hydrothermal systems. SCIENCE ADVANCES 2019; 5:eaav7848. [PMID: 31223650 PMCID: PMC6584212 DOI: 10.1126/sciadv.aav7848] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 05/15/2019] [Indexed: 06/01/2023]
Abstract
One of the most plausible scenarios of the origin of life assumes the preceding prebiotic autotrophic metabolism in sulfide-rich hydrothermal vent environments. However, geochemical mechanisms to harness the reductive power provided by hydrothermal systems remain to be elucidated. Here, we show that, under a geoelectrochemical condition realizable in the early ocean hydrothermal systems, several metal sulfides (FeS, Ag2S, CuS, and PbS) undergo hour- to day-scale conversion to the corresponding metals at ≤-0.7 V (versus the standard hydrogen electrode). The electrochemically produced FeS-Fe0 assemblage promoted various reactions including certain steps in the reductive tricarboxylic acid cycle with efficiencies far superior to those due to pure FeS. The threshold potential is readily generated in the H2-rich alkaline hydrothermal systems that were probably ubiquitous on the Hadean seafloor. Thus, widespread metal production and metal-sustained primordial metabolism were likely to occur as a natural consequence of the active hydrothermal processes on the Hadean Earth.
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Affiliation(s)
- Norio Kitadai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Ryuhei Nakamura
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Masahiro Yamamoto
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Ken Takai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Naohiro Yoshida
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Department of Environmental Chemistry and Engineering, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, Kanazawa 226-8503, Japan
| | - Yoshi Oono
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 W. Green Street, Urbana, IL 61801-3080, USA
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22
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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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