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Zimmermann J, Werner E, Sodei S, Moran J. Pinpointing Conditions for a Metabolic Origin of Life: Underlying Mechanisms and the Role of Coenzymes. Acc Chem Res 2024; 57:3032-3043. [PMID: 39367831 DOI: 10.1021/acs.accounts.4c00423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2024]
Abstract
ConspectusFamously found written on the blackboard of physicist Richard Feynman after his death was the phrase, "What I cannot create, I do not understand." From this perspective, recreating the origin of life in the lab is a necessary condition for achieving a deep theoretical understanding of biology. The "metabolism-first" hypothesis is one of the leading frameworks for the origin of life. A complex self-organized reaction network is thought to have been driven into existence as a chemical path of least resistance to release free energy in the environment that could otherwise not be dissipated, rerouting energy from planetary processes to organic chemistry. To increase in complexity, the reaction network, initially under catalysis provided by its geochemical environment, must have produced organic catalysts that pruned the existing flux through the network or expanded it in new directions. This boot-strapping process would gradually lessen the dependence on the initial catalytic environment and allow the reaction network to persist using catalysts of its own making. Eventually, this process leads to the seemingly inseparable interdependence at the heart of biology between catalysts (coenzymes, enzymes, genes) and the metabolic pathways that synthesize them. Experimentally, the primary challenge is to recreate the conditions where such a network emerged. However, the near infinite number of microenvironments and sources of energy available on the early Earth or elsewhere poses an enormous combinatorial challenge. To constrain the search, our lab has been surveying conditions where the reactions making up the core of some of the most ancient chemolithoautotrophic metabolisms, which consist of only a small number of repeating chemical mechanisms, occur nonenzymatically. To give a fresh viewpoint in the first part of this account, we have organized the results of our search (along with important results from other laboratories) by reaction mechanism, rather than by pathway. We expect that identifying a common set of conditions for each type of reaction mechanism will help pinpoint the conditions for the emergence of a self-organized reaction network resembling core metabolism. Many of the reaction mechanisms were found to occur in a wide variety of nonenzymatic conditions. Others, such as carboxylate phosphorylation and C-C bond formation from CO2, were found to be the most constraining, and thus help narrow the scope of environments where a reaction network could emerge. In the second part of this account, we highlight examples where small molecules produced by metabolism, known as coenzymes, mediate nonenzymatic chemistry of the type needed for the coenzyme's own synthesis or that turn on new reactivity of interest for expanding a hypothetical protometabolic network. These examples often feature cooperativity between small organic coenzymes and metal ions, recapitulating the transition from inorganic to organic catalysis during the origin of life. Overall, the most interesting conditions are those containing a reducing potential equivalent to H2 gas (electrochemical or H2 itself), Fe in both reduced and more oxidized forms (possibly with other metals like Ni) and localized strong electric fields. Environments that satisfy these criteria simultaneously will be of prime interest for reconstructing a metabolic origin of life.
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Affiliation(s)
- Joris Zimmermann
- University of Strasbourg, CNRS, ISIS UMR 7006, 67000 Strasbourg, France
| | - Emilie Werner
- University of Strasbourg, CNRS, ISIS UMR 7006, 67000 Strasbourg, France
| | - Shunjiro Sodei
- University of Strasbourg, CNRS, ISIS UMR 7006, 67000 Strasbourg, France
| | - Joseph Moran
- University of Strasbourg, CNRS, ISIS UMR 7006, 67000 Strasbourg, France
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
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2
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Lee HE, Okumura T, Ooka H, Adachi K, Hikima T, Hirata K, Kawano Y, Matsuura H, Yamamoto M, Yamamoto M, Yamaguchi A, Lee JE, Takahashi H, Nam KT, Ohara Y, Hashizume D, McGlynn SE, Nakamura R. Osmotic energy conversion in serpentinite-hosted deep-sea hydrothermal vents. Nat Commun 2024; 15:8193. [PMID: 39322632 PMCID: PMC11424637 DOI: 10.1038/s41467-024-52332-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 08/28/2024] [Indexed: 09/27/2024] Open
Abstract
Cells harvest energy from ionic gradients by selective ion transport across membranes, and the same principle is recently being used for osmotic power generation from salinity gradients at ocean-river interfaces. Common to these ionic gradient conversions is that they require intricate nanoscale structures. Here, we show that natural submarine serpentinite-hosted hydrothermal vent (HV) precipitates are capable of converting ionic gradients into electrochemical energy by selective transport of Na+, K+, H+, and Cl-. Layered hydroxide nanocrystals are aligned radially outwards from the HV fluid channels, constituting confined nanopores that span millimeters in the HV wall. The nanopores change the surface charge depending on adsorbed ions, allowing the mineral to function as a cation- and anion-selective ion transport membrane. Our findings indicate that chemical disequilibria originating from flow and concentration gradients in geologic environments generate confined nanospaces which enable the spontaneous establishment of osmotic energy conversion.
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Affiliation(s)
- Hye-Eun Lee
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan.
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.
| | | | - Hideshi Ooka
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Kiyohiro Adachi
- RIKEN Center for Emergent Matter Science, Wako, Saitama, Japan
| | | | | | | | | | | | - Masahiro Yamamoto
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa, Japan
| | - Akira Yamaguchi
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
- Department of Materials Science and Engineering, Tokyo Institute of Technology, Tokyo, Japan
| | - Ji-Eun Lee
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Hiroya Takahashi
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | - Ki Tae Nam
- Department of Materials Science and Engineering, Seoul National University, Seoul, South Korea
| | - Yasuhiko Ohara
- Research Institute for Marine Geodynamics, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Kanagawa, Japan
- Hydrographic and Oceanographic Department of Japan, Tokyo, Japan
- Graduate School of Environmental Studies, Nagoya University, Nagoya, Japan
| | | | - Shawn Erin McGlynn
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan
| | - Ryuhei Nakamura
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan.
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.
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3
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Mrnjavac N, Martin WF. GTP before ATP: The energy currency at the origin of genes. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1866:149514. [PMID: 39326542 DOI: 10.1016/j.bbabio.2024.149514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/08/2024] [Accepted: 09/23/2024] [Indexed: 09/28/2024]
Abstract
Life is an exergonic chemical reaction. Many individual reactions in metabolism entail slightly endergonic steps that are coupled to free energy release, typically as ATP hydrolysis, in order to go forward. ATP is almost always supplied by the rotor-stator ATP synthase, which harnesses chemiosmotic ion gradients. Because the ATP synthase is a protein, it arose after the ribosome did. What was the energy currency of metabolism before the origin of the ATP synthase and how (and why) did ATP come to be the universal energy currency? About 27 % of a cell's energy budget is consumed as GTP during translation. The universality of GTP-dependence in ribosome function indicates that GTP was the ancestral energy currency of protein synthesis. The use of GTP in translation and ATP in small molecule synthesis are conserved across all lineages, representing energetic compartments that arose in the last universal common ancestor, LUCA. And what came before GTP? Recent findings indicate that the energy supporting the origin of LUCA's metabolism stemmed from H2-dependent CO2 reduction along routes that strongly resemble the reactions and transition metal catalysts of the acetyl-CoA pathway.
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Affiliation(s)
- Natalia Mrnjavac
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - William F Martin
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany.
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4
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Zhu P, Wang C, Lang J, He D, Jin F. Prebiotic Synthesis of Microdroplets from Formate over a Bimetallic Cobalt-Nickel Nanomotif. J Am Chem Soc 2024; 146:25005-25015. [PMID: 39219062 DOI: 10.1021/jacs.4c06989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
The hypothesis underlying the abiogenic origin of life suggests that the nonenzymatic synthesis of long-chain fatty acids led to the construction of vesicles for compartmentalization in an early stage during the transition from geochemistry to biochemistry. However, evidence for this theory remains elusive as C5+ carboxylic acids cannot be synthesized using current laboratory simulations. Here, we report the synthesis of long-chain carboxylic acids (C3-C7) with a 42 mmol/gCo+Ni yield and 87.7% selectivity from formate (an intermediate of the acetyl-CoA pathway) over a cobalt-nickel alloy under alkaline hydrothermal conditions and the subsequent formation of microdroplets from organics. Density functional theory (DFT) calculations confirmed that the synergistic effect of the bimetal catalyst is key for catalyzing C-C coupling. Investigations by infrared spectroscopy, electron paramagnetic resonance, and isotope-labeled experiments revealed that HCO* serves as a reaction intermediate and is involved in the subsequent elementary steps for synthesizing long-chain carboxylic acids from formate. Taken together, these findings may help explain how the first protocells emerged geochemically and provide support for the hypothesis of the abiogenic origin of life. The hydrothermal system developed may also be applicable for the sustainable synthesis of long-chain carboxylates from one-carbon substrates using nonnoble metal catalysts.
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Affiliation(s)
- Peidong Zhu
- School of Environmental Science and Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chunling Wang
- School of Environmental Science and Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Junyu Lang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Daoping He
- China-UK Low Carbon College, Shanghai Jiao Tong University, Shanghai 201306, China
| | - Fangming Jin
- School of Environmental Science and Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Key Laboratory of Hydrogen Science & Center of Hydrogen Science, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
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Stewart SV, Erastova V. Understanding the Role of Layered Minerals in the Emergence and Preservation of Proto-Proteins and Detection of Traces of Early Life. Acc Chem Res 2024; 57:2453-2463. [PMID: 39141709 PMCID: PMC11375777 DOI: 10.1021/acs.accounts.4c00173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Abstract
ConspectusThe origin of life remains one of the most profound mysteries in science. Over millennia, theories have evolved, yet the question persists: How did life emerge from inanimate matter? At its core, the study of life's origin offers insights into our place in the universe and the nature of life itself. By delving into the chemical and geological processes that led to life's emergence, scientists gain a deeper understanding of the fundamental principles that govern living systems. This knowledge not only expands our scientific understanding but also has profound implications for fields ranging from astrobiology to synthetic biology.This research employs a multidisciplinary approach, combining a diverse array of techniques, from space missions to wet laboratory experiments to theoretical modeling. Investigations into the formation of the first proto-biomolecules are tailored to explore both the complex molecular processes that underpin life and the geological contexts in which these processes may have occurred. While laboratory experiments are aimed at mimicking the processes of early planets, not every process and sample is attainable. To this end, we demonstrate the use of molecular modeling techniques to complement experimental efforts and extraterrestrial missions. The simulations enable researchers to test hypotheses and explore scenarios that are difficult or impossible to replicate in the laboratory, bridging gaps in our understanding of prebiotic processes across vast time and space scales.Minerals, particularly layered structures like clays and hydrotalcites, play diverse and pivotal roles in the origin of life. They concentrate organic species, catalyze polymerization reactions (such as peptide formation), and provide protective environments for the molecules. Minerals have also been suggested to have acted as primitive genetic materials. Nevertheless, they may lack the ability for long-term information replication. Instead, we suggest that minerals may act as transcribers of information encoded in environmental cyclic phenomena, such as tidal or seasonal changes. We argue that extensive protection of the produced polymer will immobilize it, making it inactive for any further function. Therefore, in order to generate a functional polymer, it is essential that it remains mobile and chemically active. Furthermore, we suggest a route to the identification of pseudobiosignatures, a polymer that was polymerized on the same mineral surface and consequently retained through overprotection.This Account presents a comprehensive evaluation of the current understanding of the role of layered mineral surfaces on life's origin and biosignature preservation. It highlights the complexity of mineral-organic interactions and proposes pathways for proto-biomolecule emergence and methods for identifying and interpreting potential biosignatures. Ultimately, the quest to uncover the origin of life continues to drive scientific exploration and innovation, offering profound insights into the fundamental nature of existence and our place in the universe.
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Affiliation(s)
- Sarah V Stewart
- School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, United Kingdom
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Valentina Erastova
- School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, United Kingdom
- UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
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6
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Mrnjavac N, Schwander L, Brabender M, Martin WF. Chemical Antiquity in Metabolism. Acc Chem Res 2024; 57:2267-2278. [PMID: 39083571 PMCID: PMC11339923 DOI: 10.1021/acs.accounts.4c00226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 07/04/2024] [Accepted: 07/05/2024] [Indexed: 08/02/2024]
Abstract
ConspectusLife is an exergonic chemical reaction. The same was true when the very first cells emerged at life's origin. In order to live, all cells need a source of carbon, energy, and electrons to drive their overall reaction network (metabolism). In most cells, these are separate pathways. There is only one biochemical pathway that serves all three needs simultaneously: the acetyl-CoA pathway of CO2 fixation. In the acetyl-CoA pathway, electrons from H2 reduce CO2 to pyruvate for carbon supply, while methane or acetate synthesis are coupled to energy conservation as ATP. This simplicity and thermodynamic favorability prompted Georg Fuchs and Erhard Stupperich to propose in 1985 that the acetyl-CoA pathway might mark the origin of metabolism, at the same time that Steve Ragsdale and Harland Wood were uncovering catalytic roles for Fe, Co, and Ni in the enzymes of the pathway. Subsequent work has provided strong support for those proposals.In the presence of Fe, Co, and Ni in their native metallic state as catalysts, aqueous H2 and CO2 react specifically to formate, acetate, methane, and pyruvate overnight at 100 °C. These metals (and their alloys) thus replace the function of over 120 enzymes required for the conversion of H2 and CO2 to pyruvate via the pathway and its cofactors, an unprecedented set of findings in the study of biochemical evolution. The reactions require alkaline conditions, which promote hydrogen oxidation by proton removal and are naturally generated in serpentinizing (H2-producing) hydrothermal vents. Serpentinizing hydrothermal vents furthermore produce natural deposits of native Fe, Co, Ni, and their alloys. These are precisely the metals that reduce CO2 with H2 in the laboratory; they are also the metals found at the active sites of enzymes in the acetyl-CoA pathway. Iron, cobalt and nickel are relicts of the environments in which metabolism arose, environments that still harbor ancient methane- and acetate-producing autotrophs today. This convergence indicates bedrock-level antiquity for the acetyl-CoA pathway. In acetogens and methanogens growing on H2 as reductant, the acetyl-CoA pathway requires flavin-based electron bifurcation as a source of reduced ferredoxin (a 4Fe4S cluster-containing protein) in order to function. Recent findings show that H2 can reduce the 4Fe4S clusters of ferredoxin in the presence of native iron, uncovering an evolutionary precursor of flavin-based electron bifurcation and suggesting an origin of FeS-dependent electron transfer in proteins. Traditionally discussed as catalysts in early evolution, the most common function of FeS clusters in metabolism is one-electron transfer, also in radical SAM enzymes, a large and ancient enzyme family. The cofactors and active sites in enzymes of the acetyl-CoA pathway uncover chemical antiquity in metabolism involving metals, methyl groups, methyl transfer reactions, cobamides, pterins, GTP, S-adenosylmethionine, radical SAM enzymes, and carbon-metal bonds. The reaction sequence from H2 and CO2 to pyruvate on naturally deposited native metals is maximally simple. It requires neither nitrogen, sulfur, phosphorus, RNA, ion gradients, nor light. Solid-state metal catalysts tether the origin of metabolism to a H2-producing, serpentinizing hydrothermal vent.
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Affiliation(s)
- Natalia Mrnjavac
- Institute
of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Loraine Schwander
- Institute
of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Max Brabender
- Institute
of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - William F. Martin
- Institute
of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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7
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Song Y, Tüysüz H. CO 2 Fixation to Prebiotic Intermediates over Heterogeneous Catalysts. Acc Chem Res 2024; 57:2038-2047. [PMID: 39024180 PMCID: PMC11308370 DOI: 10.1021/acs.accounts.4c00151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 05/24/2024] [Accepted: 07/03/2024] [Indexed: 07/20/2024]
Abstract
ConspectusThe study of the origin of life requires a multifaceted approach to understanding where and how life arose on Earth. One of the most compelling hypotheses is the chemosynthetic origin of life at hydrothermal vents, as this condition has been considered viable for early forms of life. The continuous production of H2 and heat by serpentinization generates reductive conditions at hydrothermal vents, in which CO2 can be used to build large biomolecules. Although this involves surface catalysis and an autocatalytic process, in which solid minerals act as catalysts in the conversion of CO2 to metabolically important organic molecules, the systematic investigation of heterogeneous catalysis to comprehend prebiotic chemistry at hydrothermal vents has not been undertaken.In this Account, we discuss geochemical CO2 fixation to metabolic intermediates by synthetic minerals at hydrothermal vents from the perspective of heterogeneous catalysis. Ni and Fe are the most abundant transition metals at hydrothermal vents and occur in the active site of the enzymes carbon monoxide dehydrogenases/acetyl coenzyme A synthases (CODH/ACS). Synthetic free-standing NiFe alloy nanoparticles can convert CO2 to acetyl coenzyme A pathway intermediates such as formate, acetate, and pyruvate. The same alloy can further convert pyruvate to citramalate, which is essential in the biological citramalate pathway. Thermal treatment of Ni3Fe nanoparticles under NH3, which can occur in hydrothermal vents, results in Ni3FeN/Ni3Fe heterostructures. This catalyst has been demonstrated to produce prebiotic formamide and acetamide from CO2 and H2O using Ni3FeN/Ni3Fe as both substrate and catalyst. In the process of serpentinization, Co can be reduced in the vicinity of olivine, a Mg-Fe silicate mineral. This produces CoFe and CoFe2 with serpentine in nature, representing SiO2-supported CoFe alloys. In mimicking these natural minerals, synthetic SiO2-supported CoFe alloys demonstrate the same liquid products as NiFe alloys, namely, formate, acetate, and pyruvate under mild hydrothermal vent conditions. In contrast to the NiFe system, hydrocarbons up to C6 were detected in the gas phase, which is also present in hydrothermal vents. The addition of alkali and alkaline-earth metals to the catalysts results in enhanced formate concentration, playing a promotional role in CO2 reduction. Finally, Co was loaded onto ordered mesoporous SiO2 after modification with cations to simulate the minerals found in hydrothermal vents. These catalysts were then investigated under diminished H2O concentration, revealing the conversion of CO2 to CO, CH4, methanol, and acetate. Notably, the selectivity to metabolically relevant methanol was enhanced in the presence of cations that could generate and stabilize the methoxy intermediate. Calculation using the machine learning approach revealed the possibility of predicting the selectivity of CO2 fixation when modifying mesoporous SiO2 supports with heterocations. Our research demonstrates that minerals at hydrothermal vents can convert CO2 into metabolites under a variety of prebiotic conditions, potentially paving the way for modern biological CO2 fixation processes.
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Affiliation(s)
- Youngdong Song
- Department of Heterogeneous
Catalysis, Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Harun Tüysüz
- Department of Heterogeneous
Catalysis, Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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8
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Lingam M, Nichols R, Balbi A. A Bayesian Analysis of the Probability of the Origin of Life Per Site Conducive to Abiogenesis. ASTROBIOLOGY 2024; 24:813-823. [PMID: 39159441 DOI: 10.1089/ast.2024.0037] [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: 08/21/2024]
Abstract
The emergence of life from nonlife, or abiogenesis, remains a fundamental question in scientific inquiry. In this article, we investigate the probability of the origin of life (per conducive site) by leveraging insights from Earth's environments. If life originated endogenously on Earth, its existence is indeed endowed with informative value, although the interpretation of the attendant significance hinges critically upon prior assumptions. By adopting a Bayesian framework, for an agnostic prior, we establish a direct connection between the number of potential locations for abiogenesis on Earth and the probability of life's emergence per site. Our findings suggest that constraints on the availability of suitable environments for the origin(s) of life on Earth may offer valuable insights into the probability of abiogenesis and the frequency of life in the universe.
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Affiliation(s)
- Manasvi Lingam
- Department of Aerospace, Physics and Space Sciences, Florida Institute of Technology, Melbourne, Florida, USA
- Department of Physics, The University of Texas at Austin, Austin, Texas, USA
| | - Ruth Nichols
- Department of Aerospace, Physics and Space Sciences, Florida Institute of Technology, Melbourne, Florida, USA
| | - Amedeo Balbi
- Dipartimento di Fisica, Università di Roma "Tor Vergata," Roma, Italy
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9
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Suzuki S, Ishii S, Chadwick GL, Tanaka Y, Kouzuma A, Watanabe K, Inagaki F, Albertsen M, Nielsen PH, Nealson KH. A non-methanogenic archaeon within the order Methanocellales. Nat Commun 2024; 15:4858. [PMID: 38871712 DOI: 10.1038/s41467-024-48185-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 04/22/2024] [Indexed: 06/15/2024] Open
Abstract
Serpentinization, a geochemical process found on modern and ancient Earth, provides an ultra-reducing environment that can support microbial methanogenesis and acetogenesis. Several groups of archaea, such as the order Methanocellales, are characterized by their ability to produce methane. Here, we generate metagenomic sequences from serpentinized springs in The Cedars, California, and construct a circularized metagenome-assembled genome of a Methanocellales archaeon, termed Met12, that lacks essential methanogenesis genes. The genome includes genes for an acetyl-CoA pathway, but lacks genes encoding methanogenesis enzymes such as methyl-coenzyme M reductase, heterodisulfide reductases and hydrogenases. In situ transcriptomic analyses reveal high expression of a multi-heme c-type cytochrome, and heterologous expression of this protein in a model bacterium demonstrates that it is capable of accepting electrons. Our results suggest that Met12, within the order Methanocellales, is not a methanogen but a CO2-reducing, electron-fueled acetogen without electron bifurcation.
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Affiliation(s)
- Shino Suzuki
- Geobiology and Astrobiology Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan.
- Institute of Space and Astronautical Science (ISAS), Japan Aerospace Exploration Agency (JAXA), Sagamihara, Kanagawa, Japan.
- School of Physical Sciences, SOKENDAI (Graduate University for Advanced Studies), Sagamihara, Kanagawa, Japan.
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine and Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan.
| | - Shun'ichi Ishii
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine and Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan.
| | - Grayson L Chadwick
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Yugo Tanaka
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Atsushi Kouzuma
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Kazuya Watanabe
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo, Japan
| | - Fumio Inagaki
- Advanced Institute for Marine Ecosystem Change (WPI-AIMEC), JAMSTEC, Yokohama, Kanagawa, Japan
- Department of Earth Science, Graduate School of Science, Tohoku University, Sendai, Miyagi, Japan
| | - Mads Albertsen
- Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Per H Nielsen
- Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Kenneth H Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, USA
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10
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Belthle KS, Martin WF, Tüysüz H. Synergistic Effects of Silica-Supported Iron-Cobalt Catalysts for CO 2 Reduction to Prebiotic Organics. ChemCatChem 2024; 16:cctc.202301218. [PMID: 39363906 PMCID: PMC7616659 DOI: 10.1002/cctc.202301218] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Indexed: 10/05/2024]
Abstract
To test the ability of geochemical surfaces in serpentinizing hydrothermal systems to catalyze reactions from which metabolism arose, we investigated H2-dependent CO2 reduction toward metabolic intermediates over silica-supported Co-Fe catalysts. Supported catalysts converted CO2 to various products at 180 °C and 2.0 MPa. The liquid product phase included formate, acetate, and ethanol, while the gaseous product phase consisted of CH4, CO, methanol, and C2-C7 linear hydrocarbons. The 1/1 ratio CoFe alloy with the same composition as the natural mineral wairauite yielded the highest concentrations of formate (6.0 mM) and acetate (0.8 mM), which are key intermediates in the acetyl-coenzyme A (acetyl-CoA) pathway of CO2 fixation. While Co-rich catalysts were proficient at hydrogenation, yielding mostly CH4, Fe-rich catalysts favored the formation of CO and methanol. Mechanistic studies indicated intermediate hydrogenation and C-C coupling activities of alloyed CoFe, in contrast to physical mixtures of both metals. Co in the active site of Co-Fe catalysts performed a similar reaction as tetrapyrrole-coordinated Co in the corrinoid iron-sulfur (CoFeS) methyl transferase in the acetyl-CoA pathway. In a temperature range characteristic for deeper regions of serpentinizing systems, oxygenate product formation was favored at lower, more biocompatible temperatures.
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Affiliation(s)
- Kendra S Belthle
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - William F Martin
- Institute of Molecular Evolution, University of Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Harun Tüysüz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
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11
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Kaur H, Rauscher SA, Werner E, Song Y, Yi J, Kazöne W, Martin WF, Tüysüz H, Moran J. A prebiotic Krebs cycle analog generates amino acids with H 2 and NH 3 over nickel. Chem 2024; 10:1528-1540. [PMID: 38803519 PMCID: PMC7616004 DOI: 10.1016/j.chempr.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Hydrogen (H2) has powered microbial metabolism for roughly 4 billion years. The recent discovery that it also fuels geochemical analogs of the most ancient biological carbon fixation pathway sheds light on the origin of metabolism. However, it remains unclear whether H2 can sustain more complex nonenzymatic reaction networks. Here, we show that H2 drives the nonenzymatic reductive amination of six biological ketoacids and glyoxylate to give the corresponding amino acids in good yields using ammonium concentrations ranging from 6 to 150 mM. Catalytic amounts of nickel or ground meteorites enable these reactions at 22°C and pH 8. The same conditions promote an H2-dependent ketoacid-forming reductive aldol chemistry that co-occurs with reductive amination, producing a continuous reaction network resembling amino acid synthesis in the metabolic core of ancient microbes. The results support the hypothesis that the earliest biochemical networks could have emerged without enzymes or RNA.
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Affiliation(s)
- Harpreet Kaur
- Institut de Science et d’Ingénierie Supramoléculaires (ISIS), CNRS UMR 7006, Université de Strasbourg, 8 alleé Gaspard Monge, 67000 Strasbourg, France
| | - Sophia A. Rauscher
- Institut de Science et d’Ingénierie Supramoléculaires (ISIS), CNRS UMR 7006, Université de Strasbourg, 8 alleé Gaspard Monge, 67000 Strasbourg, France
| | - Emilie Werner
- Institut de Science et d’Ingénierie Supramoléculaires (ISIS), CNRS UMR 7006, Université de Strasbourg, 8 alleé Gaspard Monge, 67000 Strasbourg, France
| | - Youngdong Song
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Jing Yi
- Institut de Science et d’Ingénierie Supramoléculaires (ISIS), CNRS UMR 7006, Université de Strasbourg, 8 alleé Gaspard Monge, 67000 Strasbourg, France
| | - Wahnyalo Kazöne
- Institut de Science et d’Ingénierie Supramoléculaires (ISIS), CNRS UMR 7006, Université de Strasbourg, 8 alleé Gaspard Monge, 67000 Strasbourg, France
| | - William F. Martin
- Institute for Molecular Evolution, Heinrich-Heine-University of Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Harun Tüysüz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Joseph Moran
- Institut de Science et d’Ingénierie Supramoléculaires (ISIS), CNRS UMR 7006, Université de Strasbourg, 8 alleé Gaspard Monge, 67000 Strasbourg, France
- Institut Universitaire de France, 75005 Paris, France
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
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12
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Williamson MP. Autocatalytic Selection as a Driver for the Origin of Life. Life (Basel) 2024; 14:590. [PMID: 38792611 PMCID: PMC11122578 DOI: 10.3390/life14050590] [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: 04/03/2024] [Revised: 04/29/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024] Open
Abstract
Darwin's theory of evolution by natural selection was revolutionary because it provided a mechanism by which variation could be selected. This mechanism can only operate on living systems and thus cannot be applied to the origin of life. Here, we propose a viable alternative mechanism for prebiotic systems: autocatalytic selection, in which molecules catalyze reactions and processes that lead to increases in their concentration. Crucially, this provides a driver for increases in concentrations of molecules to a level that permits prebiotic metabolism. We show how this can produce high levels of amino acids, sugar phosphates, nucleotides and lipids and then lead on to polymers. Our outline is supported by a set of guidelines to support the identification of the most likely prebiotic routes. Most of the steps in this pathway are already supported by experimental results. These proposals generate a coherent and viable set of pathways that run from established Hadean geochemistry to the beginning of life.
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Affiliation(s)
- Mike P Williamson
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
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13
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Matreux T, Aikkila P, Scheu B, Braun D, Mast CB. Heat flows enrich prebiotic building blocks and enhance their reactivity. Nature 2024; 628:110-116. [PMID: 38570715 PMCID: PMC10990939 DOI: 10.1038/s41586-024-07193-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/09/2024] [Indexed: 04/05/2024]
Abstract
The emergence of biopolymer building blocks is a crucial step during the origins of life1-6. However, all known formation pathways rely on rare pure feedstocks and demand successive purification and mixing steps to suppress unwanted side reactions and enable high product yields. Here we show that heat flows through thin, crack-like geo-compartments could have provided a widely available yet selective mechanism that separates more than 50 prebiotically relevant building blocks from complex mixtures of amino acids, nucleobases, nucleotides, polyphosphates and 2-aminoazoles. Using measured thermophoretic properties7,8, we numerically model and experimentally prove the advantageous effect of geological networks of interconnected cracks9,10 that purify the previously mixed compounds, boosting their concentration ratios by up to three orders of magnitude. The importance for prebiotic chemistry is shown by the dimerization of glycine11,12, in which the selective purification of trimetaphosphate (TMP)13,14 increased reaction yields by five orders of magnitude. The observed effect is robust under various crack sizes, pH values, solvents and temperatures. Our results demonstrate how geologically driven non-equilibria could have explored highly parallelized reaction conditions to foster prebiotic chemistry.
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Affiliation(s)
- Thomas Matreux
- Systems Biophysics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Paula Aikkila
- Systems Biophysics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Bettina Scheu
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Dieter Braun
- Systems Biophysics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Christof B Mast
- Systems Biophysics, Ludwig-Maximilians-Universität München, Munich, Germany.
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14
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Brabender M, Henriques Pereira DP, Mrnjavac N, Schlikker ML, Kimura ZI, Sucharitakul J, Kleinermanns K, Tüysüz H, Buckel W, Preiner M, Martin WF. Ferredoxin reduction by hydrogen with iron functions as an evolutionary precursor of flavin-based electron bifurcation. Proc Natl Acad Sci U S A 2024; 121:e2318969121. [PMID: 38513105 PMCID: PMC7615787 DOI: 10.1073/pnas.2318969121] [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: 10/31/2023] [Accepted: 02/14/2024] [Indexed: 03/23/2024] Open
Abstract
Autotrophic theories for the origin of metabolism posit that the first cells satisfied their carbon needs from CO2 and were chemolithoautotrophs that obtained their energy and electrons from H2. The acetyl-CoA pathway of CO2 fixation is central to that view because of its antiquity: Among known CO2 fixing pathways it is the only one that is i) exergonic, ii) occurs in both bacteria and archaea, and iii) can be functionally replaced in full by single transition metal catalysts in vitro. In order to operate in cells at a pH close to 7, however, the acetyl-CoA pathway requires complex multi-enzyme systems capable of flavin-based electron bifurcation that reduce low potential ferredoxin-the physiological donor of electrons in the acetyl-CoA pathway-with electrons from H2. How can the acetyl-CoA pathway be primordial if it requires flavin-based electron bifurcation? Here, we show that native iron (Fe0), but not Ni0, Co0, Mo0, NiFe, Ni2Fe, Ni3Fe, or Fe3O4, promotes the H2-dependent reduction of aqueous Clostridium pasteurianum ferredoxin at pH 8.5 or higher within a few hours at 40 °C, providing the physiological function of flavin-based electron bifurcation, but without the help of enzymes or organic redox cofactors. H2-dependent ferredoxin reduction by iron ties primordial ferredoxin reduction and early metabolic evolution to a chemical process in the Earth's crust promoted by solid-state iron, a metal that is still deposited in serpentinizing hydrothermal vents today.
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Affiliation(s)
- Max Brabender
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf40225, Germany
| | - Delfina P. Henriques Pereira
- Microcosm Earth Center, Research Group for Geochemical Protozymes, Max Planck Institute for Terrestrial Microbiology and Philipps University, Marburg35032, Germany
| | - Natalia Mrnjavac
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf40225, Germany
| | - Manon Laura Schlikker
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf40225, Germany
| | - Zen-Ichiro Kimura
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf40225, Germany
- Department of Civil and Environmental Engineering, National Institute of Technology, Kure College, Kure, Hiroshima737-8506, Japan
| | - Jeerus Sucharitakul
- Department of Biochemistry, Chulalongkorn University, Patumwan, Bangkok10330, Thailand
| | - Karl Kleinermanns
- Institute for Physical Chemistry, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf40225, Germany
| | - Harun Tüysüz
- Max Planck Institute for Coal Research, Department of Heterogeneous Catalysis, Mülheim an der Ruhr45470, Germany
| | - Wolfgang Buckel
- Max Planck Institute for Terrestrial Microbiology, Marburg35043, Germany
- Laboratory for Microbiology, Department of Biology, Philipps University, Marburg35043, Germany
- Center for Synthetic Microbiology SYNMIKRO, Philipps University, Marburg35043, Germany
| | - Martina Preiner
- Microcosm Earth Center, Research Group for Geochemical Protozymes, Max Planck Institute for Terrestrial Microbiology and Philipps University, Marburg35032, Germany
| | - William F. Martin
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf40225, Germany
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15
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Barge LM, Fournier GP. Considerations for Detecting Organic Indicators of Metabolism on Enceladus. ASTROBIOLOGY 2024; 24:328-338. [PMID: 38507694 DOI: 10.1089/ast.2023.0074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Enceladus is of interest to astrobiology and the search for life since it is thought to host active hydrothermal activity and habitable conditions. It is also possible that the organics detected on Enceladus may indicate an active prebiotic or biotic system; in particular, the conditions on Enceladus may favor mineral-driven protometabolic reactions. When including metabolism-related biosignatures in Enceladus mission concepts, it is necessary to base these in a clearer understanding of how these signatures could also be produced prebiotically. In addition, postulating which biological metabolisms to look for on Enceladus requires a non-Earth-centric approach since the details of biological metabolic pathways are heavily shaped by adaptation to geochemical conditions over the planet's history. Creating metabolism-related organic detection objectives for Enceladus missions, therefore, requires consideration of how metabolic systems may operate differently on another world, while basing these speculations on observed Earth-specific microbial processes. In addition, advances in origin-of-life research can play a critical role in distinguishing between interpretations of any future organic detections on Enceladus, and the discovery of an extant prebiotic system would be a transformative astrobiological event in its own right.
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Affiliation(s)
- Laura M Barge
- Planetary Science Section, NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Gregory P Fournier
- Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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16
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Song Y, Beyazay T, Tüysüz H. Effect of Alkali- and Alkaline-Earth-Metal Promoters on Silica-Supported Co-Fe Alloy for Autocatalytic CO 2 Fixation. Angew Chem Int Ed Engl 2024; 63:e202316110. [PMID: 38127486 DOI: 10.1002/anie.202316110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 12/23/2023]
Abstract
Hydrothermal vents harbor numerous microbial communities rich in reduced carbon species such as formate, acetate, and hydrocarbons. Such essential chemicals for life are produced by H2 -dependent CO2 reduction, where serpentinization provides continuous H2 and thermal energy. Here, we show that silica-supported bimetallic Co-Fe alloys, naturally occurring minerals around serpentinite, can convert CO2 and H2 O to key metabolic intermediates of the acetyl coenzyme A pathway such as formate (up to 72 mM), acetate, and pyruvate under mild hydrothermal vent conditions. Long-chain hydrocarbons up to C6 including propene are also detected, just as in the Lost City hydrothermal field. The effects of promoters on structural properties and catalytic functionalities of the Co-Fe alloy are systematically investigated by incorporating a series of alkali and alkaline earth metals including Na, Mg, K, and Ca. Alkali and alkaline earth metals resulted in higher formate concentrations when dissolved in water and increased reaction pH, while alkaline earth metals also favored the formation of insoluble hydroxides and carbonates similar to the constituent minerals of the chimneys at the Lost City hydrothermal fields.
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Affiliation(s)
- Youngdong Song
- Department of Heterogeneous Catalysis, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Tuğçe Beyazay
- Department of Heterogeneous Catalysis, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Harun Tüysüz
- Department of Heterogeneous Catalysis, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
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17
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Brunk CF, Marshall CR. Opinion: The Key Steps in the Origin of Life to the Formation of the Eukaryotic Cell. Life (Basel) 2024; 14:226. [PMID: 38398735 PMCID: PMC10890422 DOI: 10.3390/life14020226] [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: 11/02/2023] [Revised: 01/16/2024] [Accepted: 01/29/2024] [Indexed: 02/25/2024] Open
Abstract
The path from life's origin to the emergence of the eukaryotic cell was long and complex, and as such it is rarely treated in one publication. Here, we offer a sketch of this path, recognizing that there are points of disagreement and that many transitions are still shrouded in mystery. We assume life developed within microchambers of an alkaline hydrothermal vent system. Initial simple reactions were built into more sophisticated reflexively autocatalytic food-generated networks (RAFs), laying the foundation for life's anastomosing metabolism, and eventually for the origin of RNA, which functioned as a genetic repository and as a catalyst (ribozymes). Eventually, protein synthesis developed, leading to life's biology becoming dominated by enzymes and not ribozymes. Subsequent enzymatic innovation included ATP synthase, which generates ATP, fueled by the proton gradient between the alkaline vent flux and the acidic sea. This gradient was later internalized via the evolution of the electron transport chain, a preadaptation for the subsequent emergence of the vent creatures from their microchamber cradles. Differences between bacteria and archaea suggests cellularization evolved at least twice. Later, the bacterial development of oxidative phosphorylation and the archaeal development of proteins to stabilize its DNA laid the foundation for the merger that led to the formation of eukaryotic cells.
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Affiliation(s)
- Clifford F. Brunk
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, CA 90095-1606, USA
| | - Charles R. Marshall
- Department of Integrative Biology and Museum of Paleontology, University of California, Berkeley, CA 94720-4780, USA
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18
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Lane N, Xavier JC. To unravel the origin of life, treat findings as pieces of a bigger puzzle. Nature 2024; 626:948-951. [PMID: 38409541 DOI: 10.1038/d41586-024-00544-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
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19
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Zimmermann J, Mayer RJ, Moran J. A single phosphorylation mechanism in early metabolism - the case of phosphoenolpyruvate. Chem Sci 2023; 14:14100-14108. [PMID: 38098731 PMCID: PMC10717536 DOI: 10.1039/d3sc04116f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/22/2023] [Indexed: 12/17/2023] Open
Abstract
Phosphorylation is thought to be one of the fundamental reactions for the emergence of metabolism. Nearly all enzymatic phosphorylation reactions in the anabolic core of microbial metabolism act on carboxylates to give acyl phosphates, with a notable exception - the phosphorylation of pyruvate to phosphoenolpyruvate (PEP), which involves an enolate. We wondered whether an ancestral mechanism for the phosphorylation of pyruvate to PEP could also have involved carboxylate phosphorylation rather than the modern enzymatic form. The phosphorylation of pyruvate with P4O10 as a model phosphorylating agent was found to indeed occur via carboxylate phosphorylation, as verified by mechanistic studies using model substrates, time course experiments, liquid and solid-state NMR spectroscopy, and DFT calculations. The in situ generated acyl phosphate subsequently undergoes an intramolecular phosphoryl transfer to yield PEP. A single phosphorylation mechanism acting on carboxylates appears sufficient to initiate metabolic networks that include PEP, strengthening the case that metabolism emerged from self-organized chemistry.
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Affiliation(s)
- Joris Zimmermann
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), CNRS UMR 7006, Université de Strasbourg 8 Allée Gaspard Monge 67000 Strasbourg France
| | - Robert J Mayer
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), CNRS UMR 7006, Université de Strasbourg 8 Allée Gaspard Monge 67000 Strasbourg France
| | - Joseph Moran
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), CNRS UMR 7006, Université de Strasbourg 8 Allée Gaspard Monge 67000 Strasbourg France
- Institut Universitaire de France (IUF) France
- Department of Chemistry and Biomolecular Sciences, University of Ottawa Ottawa Ontario K1N 6N5 Canada
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20
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Fisk M, Popa R. Decorated Vesicles as Prebiont Systems (a Hypothesis). ORIGINS LIFE EVOL B 2023; 53:187-203. [PMID: 38072914 DOI: 10.1007/s11084-023-09643-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/20/2023] [Indexed: 12/31/2023]
Abstract
Decorated vesicles in deep, seafloor basalts form abiotically, but show at least four life-analogous features, which makes them a candidate for origin of life research. These features are a physical enclosure, carbon-assimilatory catalysts, semi-permeable boundaries, and a source of usable energy. The nanometer-to-micron-sized spherules on the inner walls of decorated vesicles are proposed to function as mineral proto-enzymes. Chemically, these structures resemble synthetic FeS clusters shown to convert CO2, CO and H2 into methane, formate, and acetate. Secondary phyllosilicate minerals line the vesicles' inner walls and can span openings in the vesicles and thus can act as molecular sieves between the vesicles' interior and the surrounding aquifer. Lastly, basalt glass in the vesicle walls takes up protons, which replace cations in the silicate framework. This results in an inward proton flux, reciprocal outward flux of metal cations, more alkaline pH inside the vesicle than outside, and production of more phyllosilicates. Such life-like features could have been exploited to move decorated vesicles toward protolife systems. Decorated vesicles are proposed as study models of prebiotic systems that are expected to have existed on the early Earth and Earth-like exoplanets. Their analysis can lead to better understanding of changes in planetary geocycles during the origin of life.
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Affiliation(s)
- Martin Fisk
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, 97330, USA.
| | - Radu Popa
- River Road Research, Tonawanda, NY, 14150, USA
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21
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Ju Y, Zhang H, Jiang Y, Wang W, Kan G, Yu K, Wang X, Liu J, Jiang J. Aqueous microdroplets promote C-C bond formation and sequences in the reverse tricarboxylic acid cycle. Nat Ecol Evol 2023; 7:1892-1902. [PMID: 37679455 DOI: 10.1038/s41559-023-02193-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 08/08/2023] [Indexed: 09/09/2023]
Abstract
The reverse tricarboxylic acid cycle (rTCA) is a central anabolic network that uses carbon dioxide (CO2) and may have provided complex carbon substrates for life before the advent of RNA or enzymes. However, non-enzymatic promotion of the rTCA cycle, in particular carbon fixation, remains challenging, even with primordial metal catalysis. Here, we report that the fixation of CO2 by reductive carboxylation of succinate and α-ketoglutarate was achieved in aqueous microdroplets under ambient conditions without the use of catalysts. Under identical conditions, the aqueous microdroplets also facilitated the sequences in the rTCA cycle, including reduction, hydration, dehydration and retro-aldol cleavage and linked with the glyoxylate cycle. These reactions of the rTCA cycle were compatible with the aqueous microdroplets, as demonstrated with two-reaction and four-reaction sequences. A higher selectivity giving higher product yields was also observed. Our results suggest that the microdroplets provide an energetically favourable microenvironment and facilitate a non-enzymatic version of the rTCA cycle in prebiotic carbon anabolism.
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Affiliation(s)
- Yun Ju
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, PR China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, PR China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, PR China
| | - Hong Zhang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, PR China.
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, PR China.
| | - Yanxiao Jiang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, PR China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, PR China
| | - Wenxin Wang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, PR China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, PR China
| | - Guangfeng Kan
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, PR China
| | - Kai Yu
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, PR China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, PR China
| | - Xiaofei Wang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, PR China
| | - Jilin Liu
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, PR China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, PR China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, PR China
| | - Jie Jiang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, PR China.
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, PR China.
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, PR China.
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22
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Mrnjavac N, Wimmer JLE, Brabender M, Schwander L, Martin WF. The Moon-Forming Impact and the Autotrophic Origin of Life. Chempluschem 2023; 88:e202300270. [PMID: 37812146 PMCID: PMC7615287 DOI: 10.1002/cplu.202300270] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/29/2023] [Accepted: 10/03/2023] [Indexed: 10/10/2023]
Abstract
The Moon-forming impact vaporized part of Earth's mantle, and turned the rest into a magma ocean, from which carbon dioxide degassed into the atmosphere, where it stayed until water rained out to form the oceans. The rain dissolved CO2 and made it available to react with transition metal catalysts in the Earth's crust so as to ultimately generate the organic compounds that form the backbone of microbial metabolism. The Moon-forming impact was key in building a planet with the capacity to generate life in that it converted carbon on Earth into a homogeneous and accessible substrate for organic synthesis. Today all ecosystems, without exception, depend upon primary producers, organisms that fix CO2 . According to theories of autotrophic origin, it has always been that way, because autotrophic theories posit that the first forms of life generated all the molecules needed to build a cell from CO2 , forging a direct line of continuity between Earth's initial CO2 -rich atmosphere and the first microorganisms. By modern accounts these were chemolithoautotrophic archaea and bacteria that initially colonized the crust and still inhabit that environment today.
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Affiliation(s)
- Natalia Mrnjavac
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
| | - Jessica L. E. Wimmer
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
| | - Max Brabender
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
| | - Loraine Schwander
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
| | - William F. Martin
- Department of Biology Institute for Molecular Evolution Heinrich Heine University Duesseldorf Universitaetsstr. 1, 40225 Düsseldorf (Germany)
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23
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Nogal N, Sanz-Sánchez M, Vela-Gallego S, Ruiz-Mirazo K, de la Escosura A. The protometabolic nature of prebiotic chemistry. Chem Soc Rev 2023; 52:7359-7388. [PMID: 37855729 PMCID: PMC10614573 DOI: 10.1039/d3cs00594a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Indexed: 10/20/2023]
Abstract
The field of prebiotic chemistry has been dedicated over decades to finding abiotic routes towards the molecular components of life. There is nowadays a handful of prebiotically plausible scenarios that enable the laboratory synthesis of most amino acids, fatty acids, simple sugars, nucleotides and core metabolites of extant living organisms. The major bottleneck then seems to be the self-organization of those building blocks into systems that can self-sustain. The purpose of this tutorial review is having a close look, guided by experimental research, into the main synthetic pathways of prebiotic chemistry, suggesting how they could be wired through common intermediates and catalytic cycles, as well as how recursively changing conditions could help them engage in self-organized and dissipative networks/assemblies (i.e., systems that consume chemical or physical energy from their environment to maintain their internal organization in a dynamic steady state out of equilibrium). In the article we also pay attention to the implications of this view for the emergence of homochirality. The revealed connectivity between those prebiotic routes should constitute the basis for a robust research program towards the bottom-up implementation of protometabolic systems, taken as a central part of the origins-of-life problem. In addition, this approach should foster further exploration of control mechanisms to tame the combinatorial explosion that typically occurs in mixtures of various reactive precursors, thus regulating the functional integration of their respective chemistries into self-sustaining protocellular assemblies.
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Affiliation(s)
- Noemí Nogal
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
| | - Marcos Sanz-Sánchez
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
| | - Sonia Vela-Gallego
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
| | - Kepa Ruiz-Mirazo
- Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, Leioa, Spain
- Department of Philosophy, University of the Basque Country, Leioa, Spain
| | - Andrés de la Escosura
- Department of Organic Chemistry, Universidad Autónoma de Madrid, Campus Cantoblanco, 28049, Madrid, Spain.
- Institute for Advanced Research in Chemistry (IAdChem), Campus de Cantoblanco, 28049, Madrid, Spain
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Werner E, Pinna S, Mayer RJ, Moran J. Metal/ADP Complexes Promote Phosphorylation of Ribonucleotides. J Am Chem Soc 2023; 145:21630-21637. [PMID: 37750669 DOI: 10.1021/jacs.3c08047] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Under enzyme catalysis, adenosine triphosphate (ATP) transfers a phosphoryl group to canonical ribonucleotide diphosphates (NDPs) to form ribonucleotide triphosphates (NTPs), the direct biosynthetic precursors to RNA. However, it remains unclear whether the phosphorylation of NDPs could have occurred in water before enzymes existed and why an adenosine derivative, rather than another canonical NTP, typically performs this function. Here, we show that adenosine diphosphate (ADP) in the presence of Fe3+ or Al3+ promotes phosphoryl transfer from acetyl phosphate to all canonical NDPs to produce their corresponding NTP in water at room temperature and in the absence of enzymes. No other NDPs were found to promote phosphorylation, giving insight into why adenosine derivatives specifically became used for this purpose in biology. The metal-ADP complexes also promote phosphoryl transfer to ribonucleoside monophosphates (NMPs) to form a mixture of the corresponding NDPs and NTPs, albeit less efficiently. This work represents a rare example in which a single nucleotide carries out a function critical to biology without enzymes. ADP-metal complexes may have played an important role in nucleotide phosphorylation in prebiotic chemistry.
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Affiliation(s)
- Emilie Werner
- ISIS UMR 7006, University of Strasbourg, CNRS, 67000 Strasbourg, France
| | - Silvana Pinna
- ISIS UMR 7006, University of Strasbourg, CNRS, 67000 Strasbourg, France
| | - Robert J Mayer
- ISIS UMR 7006, University of Strasbourg, CNRS, 67000 Strasbourg, France
| | - Joseph Moran
- ISIS UMR 7006, University of Strasbourg, CNRS, 67000 Strasbourg, France
- Institut Universitaire de France (IUF), 75005 Paris, France
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
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25
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Schwander L, Brabender M, Mrnjavac N, Wimmer JLE, Preiner M, Martin WF. Serpentinization as the source of energy, electrons, organics, catalysts, nutrients and pH gradients for the origin of LUCA and life. Front Microbiol 2023; 14:1257597. [PMID: 37854333 PMCID: PMC10581274 DOI: 10.3389/fmicb.2023.1257597] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 09/04/2023] [Indexed: 10/20/2023] Open
Abstract
Serpentinization in hydrothermal vents is central to some autotrophic theories for the origin of life because it generates compartments, reductants, catalysts and gradients. During the process of serpentinization, water circulates through hydrothermal systems in the crust where it oxidizes Fe (II) in ultramafic minerals to generate Fe (III) minerals and H2. Molecular hydrogen can, in turn, serve as a freely diffusible source of electrons for the reduction of CO2 to organic compounds, provided that suitable catalysts are present. Using catalysts that are naturally synthesized in hydrothermal vents during serpentinization H2 reduces CO2 to formate, acetate, pyruvate, and methane. These compounds represent the backbone of microbial carbon and energy metabolism in acetogens and methanogens, strictly anaerobic chemolithoautotrophs that use the acetyl-CoA pathway of CO2 fixation and that inhabit serpentinizing environments today. Serpentinization generates reduced carbon, nitrogen and - as newer findings suggest - reduced phosphorous compounds that were likely conducive to the origins process. In addition, it gives rise to inorganic microcompartments and proton gradients of the right polarity and of sufficient magnitude to support chemiosmotic ATP synthesis by the rotor-stator ATP synthase. This would help to explain why the principle of chemiosmotic energy harnessing is more conserved (older) than the machinery to generate ion gradients via pumping coupled to exergonic chemical reactions, which in the case of acetogens and methanogens involve H2-dependent CO2 reduction. Serpentinizing systems exist in terrestrial and deep ocean environments. On the early Earth they were probably more abundant than today. There is evidence that serpentinization once occurred on Mars and is likely still occurring on Saturn's icy moon Enceladus, providing a perspective on serpentinization as a source of reductants, catalysts and chemical disequilibrium for life on other worlds.
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Affiliation(s)
- Loraine Schwander
- Institute of Molecular Evolution, Biology Department, Math. -Nat. Faculty, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Max Brabender
- Institute of Molecular Evolution, Biology Department, Math. -Nat. Faculty, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Natalia Mrnjavac
- Institute of Molecular Evolution, Biology Department, Math. -Nat. Faculty, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Jessica L. E. Wimmer
- Institute of Molecular Evolution, Biology Department, Math. -Nat. Faculty, Heinrich-Heine-Universität, Düsseldorf, Germany
| | - Martina Preiner
- Microcosm Earth Center, Max Planck Institute for Terrestrial Microbiology and Philipps-Universität, Marburg, Germany
| | - William F. Martin
- Institute of Molecular Evolution, Biology Department, Math. -Nat. Faculty, Heinrich-Heine-Universität, Düsseldorf, Germany
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26
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Weingart M, Chen S, Donat C, Helmbrecht V, Orsi WD, Braun D, Alim K. Alkaline vents recreated in two dimensions to study pH gradients, precipitation morphology, and molecule accumulation. SCIENCE ADVANCES 2023; 9:eadi1884. [PMID: 37774032 PMCID: PMC10541008 DOI: 10.1126/sciadv.adi1884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/30/2023] [Indexed: 10/01/2023]
Abstract
Alkaline vents (AVs) are hypothesized to have been a setting for the emergence of life, by creating strong gradients across inorganic membranes within chimney structures. In the past, three-dimensional chimney structures were formed under laboratory conditions; however, no in situ visualization or testing of the gradients was possible. We develop a quasi-two-dimensional microfluidic model of AVs that allows spatiotemporal visualization of mineral precipitation in low-volume experiments. Upon injection of an alkaline fluid into an acidic, iron-rich solution, we observe a diverse set of precipitation morphologies, mainly controlled by flow rate and ion concentration. Using microscope imaging and pH-dependent dyes, we show that finger-like precipitates can facilitate formation and maintenance of microscale pH gradients and accumulation of dispersed particles in confined geometries. Our findings establish a model to investigate the potential of gradients across a semipermeable boundary for early compartmentalization, accumulation, and chemical reactions at the origins of life.
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Affiliation(s)
- Maximilian Weingart
- Systems Biophysics and Center for NanoScience (CeNS), Ludwig-Maximilians University Munich, Amalienstraße 54, 80799 München, Germany
| | - Siyu Chen
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany
| | - Clara Donat
- TUM School of Natural Sciences, Department of Bioscience; Center for Protein Assemblies (CPA), Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748 Garching b. München, Germany
| | - Vanessa Helmbrecht
- Department of Earth and Environmental Sciences, Ludwig-Maximilians University Munich, Richard-Wagner Straße 10, 80333 München, Germany
| | - William D. Orsi
- Department of Earth and Environmental Sciences, Ludwig-Maximilians University Munich, Richard-Wagner Straße 10, 80333 München, Germany
- GeoBio-CenterLMU, Ludwig-Maximilians University Munich, Richard-Wagner Straße 10, 80333 München, Germany
| | - Dieter Braun
- Systems Biophysics and Center for NanoScience (CeNS), Ludwig-Maximilians University Munich, Amalienstraße 54, 80799 München, Germany
| | - Karen Alim
- Max Planck Institute for Dynamics and Self-Organization, Am Faßberg 17, 37077 Göttingen, Germany
- TUM School of Natural Sciences, Department of Bioscience; Center for Protein Assemblies (CPA), Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748 Garching b. München, Germany
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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: 6] [Impact Index Per Article: 6.0] [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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28
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Beyazay T, Martin WF, Tüysüz H. Direct Synthesis of Formamide from CO 2 and H 2O with Nickel-Iron Nitride Heterostructures under Mild Hydrothermal Conditions. J Am Chem Soc 2023; 145:19768-19779. [PMID: 37642297 PMCID: PMC7615090 DOI: 10.1021/jacs.3c05412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Formamide can serve as a key building block for the synthesis of organic molecules relevant to premetabolic processes. Natural pathways for its synthesis from CO2 under early earth conditions are lacking. Here, we report the thermocatalytic conversion of CO2 and H2O to formate and formamide over Ni-Fe nitride heterostructures in the absence of synthetic H2 and N2 under mild hydrothermal conditions. While water molecules act as both a solvent and hydrogen source, metal nitrides serve as nitrogen sources to produce formamide in the temperature range of 25-100 °C under 5-50 bar. Longer reaction times promote the C-C bond coupling and formation of acetate and acetamide as additional products. Besides liquid products, methane and ethane are also produced as gas-phase products. Postreaction characterization of Ni-Fe nitride particles reveals structural alteration and provides insights into the potential reaction mechanism. The findings indicate that gaseous CO2 can serve as a carbon source for the formation of C-N bonds in formamide and acetamide over the Ni-Fe nitride heterostructure under simulated hydrothermal vent conditions.
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Affiliation(s)
- Tuğçe Beyazay
- Max-Planck-Institut fur Kohlenforschung, 45470 Mulheim an der Ruhr, Germany
| | - William F. Martin
- Institute of Molecular Evolution, University of Dusseldorf, 40225 Dusseldorf, Germany
| | - Harun Tüysüz
- Max-Planck-Institut fur Kohlenforschung, 45470 Mulheim an der Ruhr, Germany
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29
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Nicholls JWF, Chin JP, Williams TA, Lenton TM, O’Flaherty V, McGrath JW. On the potential roles of phosphorus in the early evolution of energy metabolism. Front Microbiol 2023; 14:1239189. [PMID: 37601379 PMCID: PMC10433651 DOI: 10.3389/fmicb.2023.1239189] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 07/20/2023] [Indexed: 08/22/2023] Open
Abstract
Energy metabolism in extant life is centered around phosphate and the energy-dense phosphoanhydride bonds of adenosine triphosphate (ATP), a deeply conserved and ancient bioenergetic system. Yet, ATP synthesis relies on numerous complex enzymes and has an autocatalytic requirement for ATP itself. This implies the existence of evolutionarily simpler bioenergetic pathways and potentially primordial alternatives to ATP. The centrality of phosphate in modern bioenergetics, coupled with the energetic properties of phosphorylated compounds, may suggest that primordial precursors to ATP also utilized phosphate in compounds such as pyrophosphate, acetyl phosphate and polyphosphate. However, bioavailable phosphate may have been notably scarce on the early Earth, raising doubts about the roles that phosphorylated molecules might have played in the early evolution of life. A largely overlooked phosphorus redox cycle on the ancient Earth might have provided phosphorus and energy, with reduced phosphorus compounds potentially playing a key role in the early evolution of energy metabolism. Here, we speculate on the biological phosphorus compounds that may have acted as primordial energy currencies, sources of environmental energy, or sources of phosphorus for the synthesis of phosphorylated energy currencies. This review encompasses discussions on the evolutionary history of modern bioenergetics, and specifically those pathways with primordial relevance, and the geochemistry of bioavailable phosphorus on the ancient Earth. We highlight the importance of phosphorus, not only in the form of phosphate, to early biology and suggest future directions of study that may improve our understanding of the early evolution of bioenergetics.
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Affiliation(s)
- Jack W. F. Nicholls
- School of Biological Sciences, Queen’s University of Belfast, Belfast, United Kingdom
| | - Jason P. Chin
- School of Biological Sciences, Queen’s University of Belfast, Belfast, United Kingdom
| | - Tom A. Williams
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Timothy M. Lenton
- Global Systems Institute, University of Exeter, Exeter, United Kingdom
| | | | - John W. McGrath
- School of Biological Sciences, Queen’s University of Belfast, Belfast, United Kingdom
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30
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Wang J, Qu YN, Evans PN, Guo Q, Zhou F, Nie M, Jin Q, Zhang Y, Zhai X, Zhou M, Yu Z, Fu QL, Xie YG, Hedlund BP, Li WJ, Hua ZS, Wang Z, Wang Y. Evidence for nontraditional mcr-containing archaea contributing to biological methanogenesis in geothermal springs. SCIENCE ADVANCES 2023; 9:eadg6004. [PMID: 37379385 DOI: 10.1126/sciadv.adg6004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 05/24/2023] [Indexed: 06/30/2023]
Abstract
Recent discoveries of methyl-coenzyme M reductase-encoding genes (mcr) in uncultured archaea beyond traditional euryarchaeotal methanogens have reshaped our view of methanogenesis. However, whether any of these nontraditional archaea perform methanogenesis remains elusive. Here, we report field and microcosm experiments based on 13C-tracer labeling and genome-resolved metagenomics and metatranscriptomics, revealing that nontraditional archaea are predominant active methane producers in two geothermal springs. Archaeoglobales performed methanogenesis from methanol and may exhibit adaptability in using methylotrophic and hydrogenotrophic pathways based on temperature/substrate availability. A five-year field survey found Candidatus Nezhaarchaeota to be the predominant mcr-containing archaea inhabiting the springs; genomic inference and mcr expression under methanogenic conditions strongly suggested that this lineage mediated hydrogenotrophic methanogenesis in situ. Methanogenesis was temperature-sensitive , with a preference for methylotrophic over hydrogenotrophic pathways when incubation temperatures increased from 65° to 75°C. This study demonstrates an anoxic ecosystem wherein methanogenesis is primarily driven by archaea beyond known methanogens, highlighting diverse nontraditional mcr-containing archaea as previously unrecognized methane sources.
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Affiliation(s)
- Jiajia Wang
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Yan-Ni Qu
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Paul N Evans
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia 4072, QLD, Australia
| | - Qinghai Guo
- MOE Key Laboratory of Groundwater Quality and Health, State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, School of Environmental Studies, China University of Geosciences, Wuhan 430078, China
| | - Fengwu Zhou
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
- College of Geography Science, Nanjing Normal University, Nanjing 210023, China
| | - Ming Nie
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai 200438, China
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Fudan University, Shanghai 200433, China
| | - Qusheng Jin
- Department of Earth Sciences, University of Oregon, Eugene, OR 97403, USA
| | - Yan Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science and Institute of Eco-Chongming, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiangmei Zhai
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Ming Zhou
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
| | - Zhiguo Yu
- School of Hydrology and Water Resources, Nanjing University of Information Science and Technology, Nanjing 210044, China
| | - Qing-Long Fu
- MOE Key Laboratory of Groundwater Quality and Health, State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, School of Environmental Studies, China University of Geosciences, Wuhan 430078, China
| | - Yuan-Guo Xie
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, Las Vegas, NV 89154, USA
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Zheng-Shuang Hua
- Chinese Academy of Sciences Key Laboratory of Urban Pollutant Conversion, Department of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
| | - Zimeng Wang
- Department of Environmental Science and Engineering, Fudan University, Shanghai 200433, China
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Fudan University, Shanghai 200433, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China
| | - Yanxin Wang
- MOE Key Laboratory of Groundwater Quality and Health, State Environmental Protection Key Laboratory of Source Apportionment and Control of Aquatic Pollution, School of Environmental Studies, China University of Geosciences, Wuhan 430078, China
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31
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Lin Z, Tan J, Xiong Z, Fu Z, Chen J, Xie T, Zheng J, Zhang Y, Li P. Regulation of the autochthonous microbial community in excess sludge for the bioconversion of carbon dioxide to acetate without exogenic hydrogen. BIORESOURCE TECHNOLOGY 2023; 378:129011. [PMID: 37011841 DOI: 10.1016/j.biortech.2023.129011] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/26/2023] [Accepted: 03/31/2023] [Indexed: 06/19/2023]
Abstract
The autochthonous microbial community from excess sludge was regulated for enhanced conversion of CO2 to acetate without exogenic H2. It was interesting that the acetate-fed system exhibited a surprising performance to regulate the microbial community for a high acetate yield and selectivity. As a result, some hydrogen-producing bacteria (e.g., Proteiniborus) and acetogenic bacteria with the ability of CO2 reduction were enriched by acetate feeding, 2-bromoethanesulfonate (BES) addition and CO2 stress. When the selected microbial community was applied to convert CO2, the accumulation of acetate was positively correlated to the concentration of yeast extract. Finally, the acetate yield reached up to 67.24 mM with a high product selectivity of 84 % in the presence of yeast extract (2 g/L) and sufficient CO2 in semi-continuous culture for 10 days. This work should help get new insights into the regulation of microbial community for the efficient acetate production from CO2.
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Affiliation(s)
- Zhiwen Lin
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, PR China
| | - Jinan Tan
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, PR China
| | - Zhihan Xiong
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, PR China
| | - Zisen Fu
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, PR China
| | - Jing Chen
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, PR China
| | - Tonghui Xie
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, PR China
| | - Jia Zheng
- Key Laboratory of Wuliangye-flavor Liquor Solid-state Fermentation, China National Light Industry, Yibin, Sichuan 644007, PR China
| | - Yongkui Zhang
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, PR China
| | - Panyu Li
- Department of Pharmaceutical & Biological Engineering, School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, PR China.
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32
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Harrison SA, Webb WL, Rammu H, Lane N. Prebiotic Synthesis of Aspartate Using Life's Metabolism as a Guide. Life (Basel) 2023; 13:life13051177. [PMID: 37240822 DOI: 10.3390/life13051177] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 04/29/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
A protometabolic approach to the origins of life assumes that the conserved biochemistry of metabolism has direct continuity with prebiotic chemistry. One of the most important amino acids in modern biology is aspartic acid, serving as a nodal metabolite for the synthesis of many other essential biomolecules. Aspartate's prebiotic synthesis is complicated by the instability of its precursor, oxaloacetate. In this paper, we show that the use of the biologically relevant cofactor pyridoxamine, supported by metal ion catalysis, is sufficiently fast to offset oxaloacetate's degradation. Cu2+-catalysed transamination of oxaloacetate by pyridoxamine achieves around a 5% yield within 1 h, and can operate across a broad range of pH, temperature, and pressure. In addition, the synthesis of the downstream product β-alanine may also take place in the same reaction system at very low yields, directly mimicking an archaeal synthesis route. Amino group transfer supported by pyridoxal is shown to take place from aspartate to alanine, but the reverse reaction (alanine to aspartate) shows a poor yield. Overall, our results show that the nodal metabolite aspartate and related amino acids can indeed be synthesised via protometabolic pathways that foreshadow modern metabolism in the presence of the simple cofactor pyridoxamine and metal ions.
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Affiliation(s)
- Stuart A Harrison
- Centre for Life's Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - William L Webb
- Centre for Life's Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Hanadi Rammu
- Centre for Life's Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Nick Lane
- Centre for Life's Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
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33
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Halpern A, Bartsch LR, Ibrahim K, Harrison SA, Ahn M, Christodoulou J, Lane N. Biophysical Interactions Underpin the Emergence of Information in the Genetic Code. Life (Basel) 2023; 13:1129. [PMID: 37240774 PMCID: PMC10221087 DOI: 10.3390/life13051129] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 04/25/2023] [Accepted: 04/30/2023] [Indexed: 05/28/2023] Open
Abstract
The genetic code conceals a 'code within the codons', which hints at biophysical interactions between amino acids and their cognate nucleotides. Yet, research over decades has failed to corroborate systematic biophysical interactions across the code. Using molecular dynamics simulations and NMR, we have analysed interactions between the 20 standard proteinogenic amino acids and 4 RNA mononucleotides in 3 charge states. Our simulations show that 50% of amino acids bind best with their anticodonic middle base in the -1 charge state common to the backbone of RNA, while 95% of amino acids interact most strongly with at least 1 of their codonic or anticodonic bases. Preference for the cognate anticodonic middle base was greater than 99% of randomised assignments. We verify a selection of our results using NMR, and highlight challenges with both techniques for interrogating large numbers of weak interactions. Finally, we extend our simulations to a range of amino acids and dinucleotides, and corroborate similar preferences for cognate nucleotides. Despite some discrepancies between the predicted patterns and those observed in biology, the existence of weak stereochemical interactions means that random RNA sequences could template non-random peptides. This offers a compelling explanation for the emergence of genetic information in biology.
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Affiliation(s)
- Aaron Halpern
- UCL Centre for Life’s Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Lilly R. Bartsch
- UCL Centre for Life’s Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Kaan Ibrahim
- UCL Centre for Life’s Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Stuart A. Harrison
- UCL Centre for Life’s Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Minkoo Ahn
- Department of Structural and Molecular Biology, Institute of Structural and Molecular Biology (ISMB), University College London, London WC1E 6BT, UK
| | - John Christodoulou
- Department of Structural and Molecular Biology, Institute of Structural and Molecular Biology (ISMB), University College London, London WC1E 6BT, UK
| | - Nick Lane
- UCL Centre for Life’s Origins and Evolution (CLOE), Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
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34
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Duan Y, Sun J. Preparation of Iron-Based Sulfides and Their Applications in Biomedical Fields. Biomimetics (Basel) 2023; 8:biomimetics8020177. [PMID: 37218763 DOI: 10.3390/biomimetics8020177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/14/2023] [Accepted: 04/21/2023] [Indexed: 05/24/2023] Open
Abstract
Recently, iron-based sulfides, including iron sulfide minerals and biological iron sulfide clusters, have attracted widespread interest, owing to their excellent biocompatibility and multi-functionality in biomedical applications. As such, controlled synthesized iron sulfide nanomaterials with elaborate designs, enhanced functionality and unique electronic structures show numerous advantages. Furthermore, iron sulfide clusters produced through biological metabolism are thought to possess magnetic properties and play a crucial role in balancing the concentration of iron in cells, thereby affecting ferroptosis processes. The electrons in the Fenton reaction constantly transfer between Fe2+ and Fe3+, participating in the production and reaction process of reactive oxygen species (ROS). This mechanism is considered to confer advantages in various biomedical fields such as the antibacterial field, tumor treatment, biosensing and the treatment of neurodegenerative diseases. Thus, we aim to systematically introduce recent advances in common iron-based sulfides.
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Affiliation(s)
- Yefan Duan
- State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory of Biomaterials and Devices, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210009, China
| | - Jianfei Sun
- State Key Laboratory of Bioelectronics, Jiangsu Key Laboratory of Biomaterials and Devices, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210009, China
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35
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Aithal A, Dagar S, Rajamani S. Metals in Prebiotic Catalysis: A Possible Evolutionary Pathway for the Emergence of Metalloproteins. ACS OMEGA 2023; 8:5197-5208. [PMID: 36816708 PMCID: PMC9933472 DOI: 10.1021/acsomega.2c07635] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 01/12/2023] [Indexed: 06/07/2023]
Abstract
Proteinaceous catalysts found in extant biology are products of life that were potentially derived through prolonged periods of evolution. Given their complexity, it is reasonable to assume that they were not accessible to prebiotic chemistry as such. Nevertheless, the dependence of many enzymes on metal ions or metal-ligand cores suggests that catalysis relevant to biology could also be possible with just the metal centers. Given their availability on the Hadean/Archean Earth, it is fair to conjecture that metal ions could have constituted the first forms of catalysts. A slow increase of complexity that was facilitated through the provision of organic ligands and amino acids/peptides possibly allowed for further evolution and diversification, eventually demarcating them into specific functions. Herein, we summarize some key experimental developments and observations that support the possible roles of metal catalysts in shaping the origins of life. Further, we also discuss how they could have evolved into modern-day enzymes, with some suggestions for what could be the imminent next steps that researchers can pursue, to delineate the putative sequence of catalyst evolution during the early stages of life.
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Affiliation(s)
- Anuraag Aithal
- Department
of Biology, Indian Institute of Science
Education and Research, Pune, Maharashtra 411008, India
| | - Shikha Dagar
- Department
of Biology, Indian Institute of Science
Education and Research, Pune, Maharashtra 411008, India
| | - Sudha Rajamani
- Department
of Biology, Indian Institute of Science
Education and Research, Pune, Maharashtra 411008, India
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36
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Beyazay T, Belthle KS, Farès C, Preiner M, Moran J, Martin WF, Tüysüz H. Ambient temperature CO 2 fixation to pyruvate and subsequently to citramalate over iron and nickel nanoparticles. Nat Commun 2023; 14:570. [PMID: 36732515 PMCID: PMC9894855 DOI: 10.1038/s41467-023-36088-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 01/16/2023] [Indexed: 02/04/2023] Open
Abstract
The chemical reactions that formed the building blocks of life at origins required catalysts, whereby the nature of those catalysts influenced the type of products that accumulated. Recent investigations have shown that at 100 °C awaruite, a Ni3Fe alloy that naturally occurs in serpentinizing systems, is an efficient catalyst for CO2 conversion to formate, acetate, and pyruvate. These products are identical with the intermediates and products of the acetyl-CoA pathway, the most ancient CO2 fixation pathway and the backbone of carbon metabolism in H2-dependent autotrophic microbes. Here, we show that Ni3Fe nanoparticles prepared via the hard-templating method catalyze the conversion of H2 and CO2 to formate, acetate and pyruvate at 25 °C under 25 bar. Furthermore, the 13C-labeled pyruvate can be further converted to acetate, parapyruvate, and citramalate over Ni, Fe, and Ni3Fe nanoparticles at room temperature within one hour. These findings strongly suggest that awaruite can catalyze both the formation of citramalate, the C5 product of pyruvate condensation with acetyl-CoA in microbial carbon metabolism, from pyruvate and the formation of pyruvate from CO2 at very moderate reaction conditions without organic catalysts. These results align well with theories for an autotrophic origin of microbial metabolism under hydrothermal vent conditions.
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Affiliation(s)
- Tuğçe Beyazay
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | - Kendra S Belthle
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | - Christophe Farès
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | - Martina Preiner
- Faculty of Geosciences, Utrecht University, Department of Ocean Systems, Royal Netherlands Institute for Sea Research (NIOZ), Yerseke, The Netherlands
| | - Joseph Moran
- Université de Strasbourg, CNRS, ISIS UMR 7006, Strasbourg, France
| | - William F Martin
- Institute of Molecular Evolution, University of Düsseldorf, Düsseldorf, Germany.
| | - Harun Tüysüz
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany.
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Cohen ZR, Todd ZR, Wogan N, Black RA, Keller SL, Catling DC. Plausible Sources of Membrane-Forming Fatty Acids on the Early Earth: A Review of the Literature and an Estimation of Amounts. ACS EARTH & SPACE CHEMISTRY 2023; 7:11-27. [PMID: 36704178 PMCID: PMC9869395 DOI: 10.1021/acsearthspacechem.2c00168%20] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
The first cells were plausibly bounded by membranes assembled from fatty acids with at least 8 carbons. Although the presence of fatty acids on the early Earth is widely assumed within the astrobiology community, there is no consensus regarding their origin and abundance. In this Review, we highlight three possible sources of fatty acids: (1) delivery by carbonaceous meteorites, (2) synthesis on metals delivered by impactors, and (3) electrochemical synthesis by spark discharges. We also discuss fatty acid synthesis by UV or particle irradiation, gas-phase ion-molecule reactions, and aqueous redox reactions. We compare estimates for the total mass of fatty acids supplied to Earth by each source during the Hadean eon after an extremely massive asteroid impact that would have reset Earth's fatty acid inventory. We find that synthesis on iron-rich surfaces derived from the massive impactor in contact with an impact-generated reducing atmosphere could have contributed ∼102 times more total mass of fatty acids than subsequent delivery by either carbonaceous meteorites or electrochemical synthesis. Additionally, we estimate that a single carbonaceous meteorite would not deliver a high enough concentration of fatty acids (∼15 mM for decanoic acid) into an existing body of water on the Earth's surface to spontaneously form membranes unless the fatty acids were further concentrated by another mechanism, such as subsequent evaporation of the water. Our estimates rely heavily on various assumptions, leading to significant uncertainties; nevertheless, these estimates provide rough order-of-magnitude comparisons of various sources of fatty acids on the early Earth. We also suggest specific experiments to improve future estimates. Our calculations support the view that fatty acids would have been available on the early Earth. Further investigation is needed to assess the mechanisms by which fatty acids could have been concentrated sufficiently to assemble into membranes during the origin of life.
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Affiliation(s)
- Zachary R. Cohen
- Department
of Chemistry, Department of Earth and Space Sciences, and Astrobiology Program, University of Washington, Seattle, Washington 98195, United States
| | - Zoe R. Todd
- Department
of Chemistry, Department of Earth and Space Sciences, and Astrobiology Program, University of Washington, Seattle, Washington 98195, United States
| | - Nicholas Wogan
- Department
of Chemistry, Department of Earth and Space Sciences, and Astrobiology Program, University of Washington, Seattle, Washington 98195, United States
| | - Roy A. Black
- Department
of Chemistry, Department of Earth and Space Sciences, and Astrobiology Program, University of Washington, Seattle, Washington 98195, United States
| | - Sarah L. Keller
- Department
of Chemistry, Department of Earth and Space Sciences, and Astrobiology Program, University of Washington, Seattle, Washington 98195, United States
| | - David C. Catling
- Department
of Chemistry, Department of Earth and Space Sciences, and Astrobiology Program, University of Washington, Seattle, Washington 98195, United States
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38
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Cohen ZR, Todd ZR, Wogan N, Black RA, Keller SL, Catling DC. Plausible Sources of Membrane-Forming Fatty Acids on the Early Earth: A Review of the Literature and an Estimation of Amounts. ACS EARTH & SPACE CHEMISTRY 2023; 7:11-27. [PMID: 36704178 PMCID: PMC9869395 DOI: 10.1021/acsearthspacechem.2c00168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 06/18/2023]
Abstract
The first cells were plausibly bounded by membranes assembled from fatty acids with at least 8 carbons. Although the presence of fatty acids on the early Earth is widely assumed within the astrobiology community, there is no consensus regarding their origin and abundance. In this Review, we highlight three possible sources of fatty acids: (1) delivery by carbonaceous meteorites, (2) synthesis on metals delivered by impactors, and (3) electrochemical synthesis by spark discharges. We also discuss fatty acid synthesis by UV or particle irradiation, gas-phase ion-molecule reactions, and aqueous redox reactions. We compare estimates for the total mass of fatty acids supplied to Earth by each source during the Hadean eon after an extremely massive asteroid impact that would have reset Earth's fatty acid inventory. We find that synthesis on iron-rich surfaces derived from the massive impactor in contact with an impact-generated reducing atmosphere could have contributed ∼102 times more total mass of fatty acids than subsequent delivery by either carbonaceous meteorites or electrochemical synthesis. Additionally, we estimate that a single carbonaceous meteorite would not deliver a high enough concentration of fatty acids (∼15 mM for decanoic acid) into an existing body of water on the Earth's surface to spontaneously form membranes unless the fatty acids were further concentrated by another mechanism, such as subsequent evaporation of the water. Our estimates rely heavily on various assumptions, leading to significant uncertainties; nevertheless, these estimates provide rough order-of-magnitude comparisons of various sources of fatty acids on the early Earth. We also suggest specific experiments to improve future estimates. Our calculations support the view that fatty acids would have been available on the early Earth. Further investigation is needed to assess the mechanisms by which fatty acids could have been concentrated sufficiently to assemble into membranes during the origin of life.
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Affiliation(s)
- Zachary R. Cohen
- Department
of Chemistry, Department of Earth and Space Sciences, and Astrobiology Program, University of Washington, Seattle, Washington 98195, United States
| | - Zoe R. Todd
- Department
of Chemistry, Department of Earth and Space Sciences, and Astrobiology Program, University of Washington, Seattle, Washington 98195, United States
| | - Nicholas Wogan
- Department
of Chemistry, Department of Earth and Space Sciences, and Astrobiology Program, University of Washington, Seattle, Washington 98195, United States
| | - Roy A. Black
- Department
of Chemistry, Department of Earth and Space Sciences, and Astrobiology Program, University of Washington, Seattle, Washington 98195, United States
| | - Sarah L. Keller
- Department
of Chemistry, Department of Earth and Space Sciences, and Astrobiology Program, University of Washington, Seattle, Washington 98195, United States
| | - David C. Catling
- Department
of Chemistry, Department of Earth and Space Sciences, and Astrobiology Program, University of Washington, Seattle, Washington 98195, United States
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39
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Malvoisin B, Brunet F. Barren ground depressions, natural H 2 and orogenic gold deposits: Spatial link and geochemical model. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 856:158969. [PMID: 36162584 DOI: 10.1016/j.scitotenv.2022.158969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/19/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
A review of the localities in continental rocks where H2-rich gases have been reported, showed that they are mainly located near orogenic gold deposits. Two types of geomorphological features known as markers of gas venting in sedimentary basins were also systematically observed near orogenic gold deposits on satellite images. They consist in both barren ground depressions and high densities of small (<20 m in diameter) circular- and comet-shaped white spots in 32 and 7 localities, respectively. Point pattern analysis revealed that the white spots are self-organized, and similar to previously described vegetation patterns associated with termite mounds and fairy circles. We proposed a geochemical model to account for this relationship between orogenic gold deposits, H2 emanations and geomorphological features. Fe‑carbonates are ubiquitous mineral products associated with gold mineralization. They can further dissolve in the presence of aqueous fluid due to their high reactivity below 200 °C to produce magnetite and up to ∼1 mol H2 per kg of rock along with ∼3 mol/kg CO2. This process induces a solid volume decrease of 50 %. Therefore, we propose that Fe‑carbonate dissolution is (1) the primary source of H2 in orogenic gold deposit areas, and (2) involved in the formation of the geomorphological structures reported here, providing a new framework to understand their seemingly complex formation. Ground depressions and white spots are possible tools for gold exploration. Actually, we identified four new areas where we suspect possible orogenic gold deposits. The association between H2-rich gas and ground depressions was also made near other formations containing Fe‑carbonates such as iron formations and carbonatites. This suggests that H2 production through Fe‑carbonate dissolution is not restricted to gold deposits. The global H2 production in crustal rocks associated with Fe‑carbonate alteration is estimated to 3 × 105 mol/yr.
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Affiliation(s)
- Benjamin Malvoisin
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, IRD, Univ. Gustave Eiffel, ISTerre, 38000 Grenoble, France.
| | - Fabrice Brunet
- Univ. Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, IRD, Univ. Gustave Eiffel, ISTerre, 38000 Grenoble, France
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40
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Unique H 2-utilizing lithotrophy in serpentinite-hosted systems. THE ISME JOURNAL 2023; 17:95-104. [PMID: 36207493 PMCID: PMC9751293 DOI: 10.1038/s41396-022-01197-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 01/08/2022] [Accepted: 01/17/2022] [Indexed: 11/08/2022]
Abstract
Serpentinization of ultramafic rocks provides molecular hydrogen (H2) that can support lithotrophic metabolism of microorganisms, but also poses extremely challenging conditions, including hyperalkalinity and limited electron acceptor availability. Investigation of two serpentinization-active systems reveals that conventional H2-/CO2-dependent homoacetogenesis is thermodynamically unfavorable in situ due to picomolar CO2 levels. Through metagenomics and thermodynamics, we discover unique taxa capable of metabolism adapted to the habitat. This included a novel deep-branching phylum, "Ca. Lithacetigenota", that exclusively inhabits serpentinite-hosted systems and harbors genes encoding alternative modes of H2-utilizing lithotrophy. Rather than CO2, these putative metabolisms utilize reduced carbon compounds detected in situ presumably serpentinization-derived: formate and glycine. The former employs a partial homoacetogenesis pathway and the latter a distinct pathway mediated by a rare selenoprotein-the glycine reductase. A survey of microbiomes shows that glycine reductases are diverse and nearly ubiquitous in serpentinite-hosted environments. "Ca. Lithacetigenota" glycine reductases represent a basal lineage, suggesting that catabolic glycine reduction is an ancient bacterial innovation by Terrabacteria for gaining energy from geogenic H2 even under hyperalkaline, CO2-poor conditions. Unique non-CO2-reducing metabolisms presented here shed light on potential strategies that extremophiles may employ for overcoming a crucial obstacle in serpentinization-associated environments, features potentially relevant to primordial lithotrophy in early Earth.
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41
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Bauwe H. Photorespiration - Rubisco's repair crew. JOURNAL OF PLANT PHYSIOLOGY 2023; 280:153899. [PMID: 36566670 DOI: 10.1016/j.jplph.2022.153899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/11/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
The photorespiratory repair pathway (photorespiration in short) was set up from ancient metabolic modules about three billion years ago in cyanobacteria, the later ancestors of chloroplasts. These prokaryotes developed the capacity for oxygenic photosynthesis, i.e. the use of water as a source of electrons and protons (with O2 as a by-product) for the sunlight-driven synthesis of ATP and NADPH for CO2 fixation in the Calvin cycle. However, the CO2-binding enzyme, ribulose 1,5-bisphosphate carboxylase (known under the acronym Rubisco), is not absolutely selective for CO2 and can also use O2 in a side reaction. It then produces 2-phosphoglycolate (2PG), the accumulation of which would inhibit and potentially stop the Calvin cycle and subsequently photosynthetic electron transport. Photorespiration removes the 2-PG and in this way prevents oxygenic photosynthesis from poisoning itself. In plants, the core of photorespiration consists of ten enzymes distributed over three different types of organelles, requiring interorganellar transport and interaction with several auxiliary enzymes. It goes together with the release and to some extent loss of freshly fixed CO2. This disadvantageous feature can be suppressed by CO2-concentrating mechanisms, such as those that evolved in C4 plants thirty million years ago, which enhance CO2 fixation and reduce 2PG synthesis. Photorespiration itself provided a pioneer variant of such mechanisms in the predecessors of C4 plants, C3-C4 intermediate plants. This article is a review and update particularly on the enzyme components of plant photorespiration and their catalytic mechanisms, on the interaction of photorespiration with other metabolism and on its impact on the evolution of photosynthesis. This focus was chosen because a better knowledge of the enzymes involved and how they are embedded in overall plant metabolism can facilitate the targeted use of the now highly advanced methods of metabolic network modelling and flux analysis. Understanding photorespiration more than before as a process that enables, rather than reduces, plant photosynthesis, will help develop rational strategies for crop improvement.
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Affiliation(s)
- Hermann Bauwe
- University of Rostock, Plant Physiology, Albert-Einstein-Straße 3, D-18051, Rostock, Germany.
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42
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Boyd ES, Spietz RL, Kour M, Colman DR. A naturalist perspective of microbiology: Examples from methanogenic archaea. Environ Microbiol 2023; 25:184-198. [PMID: 36367391 DOI: 10.1111/1462-2920.16285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 11/09/2022] [Indexed: 11/13/2022]
Abstract
Storytelling has been the primary means of knowledge transfer over human history. The effectiveness and reach of stories are improved when the message is appropriate for the target audience. Oftentimes, the stories that are most well received and recounted are those that have a clear purpose and that are told from a variety of perspectives that touch on the varied interests of the target audience. Whether scientists realize or not, they are accustomed to telling stories of their own scientific discoveries through the preparation of manuscripts, presentations, and lectures. Perhaps less frequently, scientists prepare review articles or book chapters that summarize a body of knowledge on a given subject matter, meant to be more holistic recounts of a body of literature. Yet, by necessity, such summaries are often still narrow in their scope and are told from the perspective of a particular discipline. In other words, interdisciplinary reviews or book chapters tend to be the rarity rather than the norm. Here, we advocate for and highlight the benefits of interdisciplinary perspectives on microbiological subjects.
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Affiliation(s)
- Eric S Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Rachel L Spietz
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Manjinder Kour
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Daniel R Colman
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
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43
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Zhao W, Zhong B, Zheng L, Tan P, Wang Y, Leng H, de Souza N, Liu Z, Hong L, Xiao X. Proteome-wide 3D structure prediction provides insights into the ancestral metabolism of ancient archaea and bacteria. Nat Commun 2022; 13:7861. [PMID: 36543797 PMCID: PMC9772386 DOI: 10.1038/s41467-022-35523-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Ancestral metabolism has remained controversial due to a lack of evidence beyond sequence-based reconstructions. Although prebiotic chemists have provided hints that metabolism might originate from non-enzymatic protometabolic pathways, gaps between ancestral reconstruction and prebiotic processes mean there is much that is still unknown. Here, we apply proteome-wide 3D structure predictions and comparisons to investigate ancestorial metabolism of ancient bacteria and archaea, to provide information beyond sequence as a bridge to the prebiotic processes. We compare representative bacterial and archaeal strains, which reveal surprisingly similar physiological and metabolic characteristics via microbiological and biophysical experiments. Pairwise comparison of protein structures identify the conserved metabolic modules in bacteria and archaea, despite interference from overly variable sequences. The conserved modules (for example, middle of glycolysis, partial TCA, proton/sulfur respiration, building block biosynthesis) constitute the basic functions that possibly existed in the archaeal-bacterial common ancestor, which are remarkably consistent with the experimentally confirmed protometabolic pathways. These structure-based findings provide a new perspective to reconstructing the ancestral metabolism and understanding its origin, which suggests high-throughput protein 3D structure prediction is a promising approach, deserving broader application in future ancestral exploration.
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Affiliation(s)
- Weishu Zhao
- State Key Laboratory of Microbial Metabolism, International Center for Deep Life Investigation (IC-DLI), School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Bozitao Zhong
- State Key Laboratory of Microbial Metabolism, International Center for Deep Life Investigation (IC-DLI), School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China
- Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center) and MOE-LSC, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Lirong Zheng
- Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center) and MOE-LSC, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Pan Tan
- Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center) and MOE-LSC, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, International Center for Deep Life Investigation (IC-DLI), School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Hao Leng
- State Key Laboratory of Microbial Metabolism, International Center for Deep Life Investigation (IC-DLI), School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Nicolas de Souza
- Australian Nuclear Science and Technology (ANSTO), Locked Bag 2001, Kirrawee DC, Sydney, NSW, 2232, Australia
| | - Zhuo Liu
- Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center) and MOE-LSC, Shanghai Jiao Tong University, 200240, Shanghai, China
- Shanghai Artificial Intelligence Laboratory, 200232, Shanghai, China
- School of Physics and Astronomy, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Liang Hong
- Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center) and MOE-LSC, Shanghai Jiao Tong University, 200240, Shanghai, China.
- Shanghai Artificial Intelligence Laboratory, 200232, Shanghai, China.
- School of Physics and Astronomy, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, 200240, Shanghai, China.
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, International Center for Deep Life Investigation (IC-DLI), School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China.
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44
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Rauscher SA, Moran J. Hydrogen Drives Part of the Reverse Krebs Cycle under Metal or Meteorite Catalysis. Angew Chem Int Ed Engl 2022; 61:e202212932. [PMID: 36251920 PMCID: PMC10100321 DOI: 10.1002/anie.202212932] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Indexed: 11/24/2022]
Abstract
Hydrogen (H2 ) is a geological source of reducing electrons that is thought to have powered the metabolism of the last universal common ancestor to all extant life, and that is still metabolized by various modern organisms. It has been suggested that H2 drove a geochemical analogue of some or all of the reverse Krebs cycle at the emergence of the metabolic network, catalyzed by metals, but this has yet to be demonstrated experimentally. Herein, we show that three consecutive steps of the reverse Krebs cycle, converting oxaloacetate into succinate, can be driven without enzymes and in one-pot by H2 as the reducing agent under mild conditions compatible with biological chemistry. Low catalytic amounts of nickel (10-20 mol %) or platinum group metals (0.1-1 mol %) or even small amounts of ground meteorites were found to promote the reductive chemistry at temperatures between 5 and 60 °C and over a wide pH range, including pH 7. These results lend additional support to the hypothesis that geologically produced hydrogen and metal catalysts could have initiated early metabolic networks.
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Affiliation(s)
- Sophia A Rauscher
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), CNRS UMR 7006, University of Strasbourg, 8 Allée Gaspard Monge, 67000, Strasbourg, France
| | - Joseph Moran
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), CNRS UMR 7006, University of Strasbourg, 8 Allée Gaspard Monge, 67000, Strasbourg, France.,Institut Universitaire de France (IUF), France
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45
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Bowker M, DeBeer S, Dummer NF, Hutchings GJ, Scheffler M, Schüth F, Taylor SH, Tüysüz H. Advancing Critical Chemical Processes for a Sustainable Future: Challenges for Industry and the Max Planck-Cardiff Centre on the Fundamentals of Heterogeneous Catalysis (FUNCAT). Angew Chem Int Ed Engl 2022; 61:e202209016. [PMID: 36351240 PMCID: PMC10099920 DOI: 10.1002/anie.202209016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Indexed: 11/11/2022]
Abstract
Catalysis is involved in around 85 % of manufacturing industry and contributes an estimated 25 % to the global domestic product, with the majority of the processes relying on heterogeneous catalysis. Despite the importance in different global segments, the fundamental understanding of heterogeneously catalysed processes lags substantially behind that achieved in other fields. The newly established Max Planck-Cardiff Centre on the Fundamentals of Heterogeneous Catalysis (FUNCAT) targets innovative concepts that could contribute to the scientific developments needed in the research field to achieve net zero greenhouse gas emissions in the chemical industries. This Viewpoint Article presents some of our research activities and visions on the current and future challenges of heterogeneous catalysis regarding green industry and the circular economy by focusing explicitly on critical processes. Namely, hydrogen production, ammonia synthesis, and carbon dioxide reduction, along with new aspects of acetylene chemistry.
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Affiliation(s)
- Michael Bowker
- Max Planck–Cardiff Centre on the Fundamentals of Heterogeneous CatalysisCardiff Catalysis InstituteSchool of ChemistryCardiff UniversityCardiffCF10 3ATUK
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy ConversionGermany
| | - Nicholas F. Dummer
- Max Planck–Cardiff Centre on the Fundamentals of Heterogeneous CatalysisCardiff Catalysis InstituteSchool of ChemistryCardiff UniversityCardiffCF10 3ATUK
| | - Graham J. Hutchings
- Max Planck–Cardiff Centre on the Fundamentals of Heterogeneous CatalysisCardiff Catalysis InstituteSchool of ChemistryCardiff UniversityCardiffCF10 3ATUK
| | - Matthias Scheffler
- The NOMAD Laboratory at the FHI of the Max-Planck-Gesellschaft and IRIS Adlershof of the Humboldt Universität zu BerlinGermany
| | | | - Stuart H. Taylor
- Max Planck–Cardiff Centre on the Fundamentals of Heterogeneous CatalysisCardiff Catalysis InstituteSchool of ChemistryCardiff UniversityCardiffCF10 3ATUK
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Narrowing gaps between Earth and life. Proc Natl Acad Sci U S A 2022; 119:e2216017119. [PMID: 36288265 PMCID: PMC9674954 DOI: 10.1073/pnas.2216017119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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47
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Bowker M, DeBeer S, Dummer NF, Hutchings GJ, Scheffler M, Schüth F, Taylor SH, Tüysüz H. Advancing Critical Chemical Processes for a Sustainable Future: Challenges for Industry and the Max Planck–Cardiff Centre on the Fundamentals of Heterogeneous Catalysis (FUNCAT). Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202209016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Michael Bowker
- Max Planck–Cardiff Centre on the Fundamentals of Heterogeneous Catalysis Cardiff Catalysis Institute School of Chemistry Cardiff University Cardiff CF10 3AT UK
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion Germany
| | - Nicholas F. Dummer
- Max Planck–Cardiff Centre on the Fundamentals of Heterogeneous Catalysis Cardiff Catalysis Institute School of Chemistry Cardiff University Cardiff CF10 3AT UK
| | - Graham J. Hutchings
- Max Planck–Cardiff Centre on the Fundamentals of Heterogeneous Catalysis Cardiff Catalysis Institute School of Chemistry Cardiff University Cardiff CF10 3AT UK
| | - Matthias Scheffler
- The NOMAD Laboratory at the FHI of the Max-Planck-Gesellschaft and IRIS Adlershof of the Humboldt Universität zu Berlin Germany
| | | | - Stuart H. Taylor
- Max Planck–Cardiff Centre on the Fundamentals of Heterogeneous Catalysis Cardiff Catalysis Institute School of Chemistry Cardiff University Cardiff CF10 3AT UK
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48
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Belthle KS, Beyazay T, Ochoa-Hernández C, Miyazaki R, Foppa L, Martin WF, Tüysüz H. Effects of Silica Modification (Mg, Al, Ca, Ti, and Zr) on Supported Cobalt Catalysts for H 2-Dependent CO 2 Reduction to Metabolic Intermediates. J Am Chem Soc 2022; 144:21232-21243. [DOI: 10.1021/jacs.2c08845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kendra S. Belthle
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Tuğçe Beyazay
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Cristina Ochoa-Hernández
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Ray Miyazaki
- The NOMAD Laboratory at the FHI of the Max-Planck-Gesellschaft and IRIS-Adlershof of the Humboldt-Universität zu Berlin, Faradayweg 4-6, 14195 Berlin, Germany
| | - Lucas Foppa
- The NOMAD Laboratory at the FHI of the Max-Planck-Gesellschaft and IRIS-Adlershof of the Humboldt-Universität zu Berlin, Faradayweg 4-6, 14195 Berlin, Germany
| | - William F. Martin
- Institute of Molecular Evolution, University of Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Harun Tüysüz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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49
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Nunes Palmeira R, Colnaghi M, Harrison SA, Pomiankowski A, Lane N. The limits of metabolic heredity in protocells. Proc Biol Sci 2022; 289:20221469. [PMID: 36350219 PMCID: PMC9653231 DOI: 10.1098/rspb.2022.1469] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The universal core of metabolism could have emerged from thermodynamically favoured prebiotic pathways at the origin of life. Starting with H
2
and CO
2
, the synthesis of amino acids and mixed fatty acids, which self-assemble into protocells, is favoured under warm anoxic conditions. Here, we address whether it is possible for protocells to evolve greater metabolic complexity, through positive feedbacks involving nucleotide catalysis. Using mathematical simulations to model metabolic heredity in protocells, based on branch points in protometabolic flux, we show that nucleotide catalysis can indeed promote protocell growth. This outcome only occurs when nucleotides directly catalyse CO
2
fixation. Strong nucleotide catalysis of other pathways (e.g. fatty acids and amino acids) generally unbalances metabolism and slows down protocell growth, and when there is competition between catalytic functions cell growth collapses. Autocatalysis of nucleotide synthesis can promote growth but only if nucleotides also catalyse CO
2
fixation; autocatalysis alone leads to the accumulation of nucleotides at the expense of CO
2
fixation and protocell growth rate. Our findings offer a new framework for the emergence of greater metabolic complexity, in which nucleotides catalyse broad-spectrum processes such as CO
2
fixation, hydrogenation and phosphorylation important to the emergence of genetic heredity at the origin of life.
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Affiliation(s)
- Raquel Nunes Palmeira
- Department of Computer Science, Engineering Building, Malet Place, University College London, WC1E 7JG, UK
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Marco Colnaghi
- Department of Computer Science, Engineering Building, Malet Place, University College London, WC1E 7JG, UK
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Stuart A. Harrison
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Andrew Pomiankowski
- Department of Computer Science, Engineering Building, Malet Place, University College London, WC1E 7JG, UK
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Nick Lane
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
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Harrison SA, Palmeira RN, Halpern A, Lane N. A biophysical basis for the emergence of the genetic code in protocells. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148597. [PMID: 35868450 DOI: 10.1016/j.bbabio.2022.148597] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/27/2022] [Accepted: 07/13/2022] [Indexed: 11/17/2022]
Abstract
The origin of the genetic code is an abiding mystery in biology. Hints of a 'code within the codons' suggest biophysical interactions, but these patterns have resisted interpretation. Here, we present a new framework, grounded in the autotrophic growth of protocells from CO2 and H2. Recent work suggests that the universal core of metabolism recapitulates a thermodynamically favoured protometabolism right up to nucleotide synthesis. Considering the genetic code in relation to an extended protometabolism allows us to predict most codon assignments. We show that the first letter of the codon corresponds to the distance from CO2 fixation, with amino acids encoded by the purines (G followed by A) being closest to CO2 fixation. These associations suggest a purine-rich early metabolism with a restricted pool of amino acids. The second position of the anticodon corresponds to the hydrophobicity of the amino acid encoded. We combine multiple measures of hydrophobicity to show that this correlation holds strongly for early amino acids but is weaker for later species. Finally, we demonstrate that redundancy at the third position is not randomly distributed around the code: non-redundant amino acids can be assigned based on size, specifically length. We attribute this to additional stereochemical interactions at the anticodon. These rules imply an iterative expansion of the genetic code over time with codon assignments depending on both distance from CO2 and biophysical interactions between nucleotide sequences and amino acids. In this way the earliest RNA polymers could produce non-random peptide sequences with selectable functions in autotrophic protocells.
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Affiliation(s)
- Stuart A Harrison
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, United Kingdom of Great Britain and Northern Ireland
| | - Raquel Nunes Palmeira
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, United Kingdom of Great Britain and Northern Ireland
| | - Aaron Halpern
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, United Kingdom of Great Britain and Northern Ireland
| | - Nick Lane
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, United Kingdom of Great Britain and Northern Ireland.
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