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Sebastianelli L, Kaur H, Chen Z, Krishnamurthy R, Mansy SS. A Magnesium Binding Site And The Anomeric Effect Regulate The Abiotic Redox Chemistry Of Nicotinamide Nucleotides. Chemistry 2024; 30:e202400411. [PMID: 38640109 DOI: 10.1002/chem.202400411] [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: 01/30/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 04/21/2024]
Abstract
Nicotinamide adenine dinucleotide (NAD+) is a redox active molecule that is universally found in biology. Despite the importance and simplicity of this molecule, few reports exist that investigate which molecular features are important for the activity of this ribodinucleotide. By exploiting the nonenzymatic reduction and oxidation of NAD+ by pyruvate and methylene blue, respectively, we were able to identify key molecular features necessary for the intrinsic activity of NAD+ through kinetic analysis. Such features may explain how NAD+ could have been selected early during the emergence of life. Simpler molecules, such as nicotinamide, that lack an anomeric carbon are incapable of accepting electrons from pyruvate. The phosphate moiety inhibits activity in the absence of metal ions but facilitates activity at physiological pH and model prebiotic conditions by recruiting catalytic Mg2+. Reduction proceeds through consecutive single electron transfer events. Of the derivatives tested, including nicotinamide mononucleotide, nicotinamide riboside, 3-(aminocarbonyl)-1-(2,3-dihydroxypropyl)pyridinium, 1-methylnicotinamide, and nicotinamide, only NAD+ and nicotinamide mononucleotide would be capable of efficiently accepting and donating electrons within a nonenzymatic electron transport chain. The data are consistent with early metabolic chemistry exploiting NAD+ or nicotinamide mononucleotide and not simpler molecules.
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Affiliation(s)
- Lorenzo Sebastianelli
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, T6G 2G2, Alberta, Canada
| | - Harpreet Kaur
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, T6G 2G2, Alberta, Canada
| | - Ziniu Chen
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, T6G 2G2, Alberta, Canada
| | - Ramanarayanan Krishnamurthy
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Sheref S Mansy
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, T6G 2G2, Alberta, Canada
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Goldman AD, Weber JM, LaRowe DE, Barge LM. Electron transport chains as a window into the earliest stages of evolution. Proc Natl Acad Sci U S A 2023; 120:e2210924120. [PMID: 37579147 PMCID: PMC10451490 DOI: 10.1073/pnas.2210924120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2023] Open
Abstract
The origin and early evolution of life is generally studied under two different paradigms: bottom up and top down. Prebiotic chemistry and early Earth geochemistry allow researchers to explore possible origin of life scenarios. But for these "bottom-up" approaches, even successful experiments only amount to a proof of principle. On the other hand, "top-down" research on early evolutionary history is able to provide a historical account about ancient organisms, but is unable to investigate stages that occurred during and just after the origin of life. Here, we consider ancient electron transport chains (ETCs) as a potential bridge between early evolutionary history and a protocellular stage that preceded it. Current phylogenetic evidence suggests that ancestors of several extant ETC components were present at least as late as the last universal common ancestor of life. In addition, recent experiments have shown that some aspects of modern ETCs can be replicated by minerals, protocells, or organic cofactors in the absence of biological proteins. Here, we discuss the diversity of ETCs and other forms of chemiosmotic energy conservation, describe current work on the early evolution of membrane bioenergetics, and advocate for several lines of research to enhance this understanding by pairing top-down and bottom-up approaches.
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Affiliation(s)
- Aaron D. Goldman
- Department of Biology, Oberlin College, Oberlin, OH44074
- Blue Marble Space Institute of Science, Seattle, WA98154
| | - Jessica M. Weber
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA91109
| | - Douglas E. LaRowe
- Department of Earth Sciences, University of Southern California, Los Angeles, CA90089
| | - Laura M. Barge
- Blue Marble Space Institute of Science, Seattle, WA98154
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA91109
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3
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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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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: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [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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Aleksandrova M, Bonfio C. Bioenergetics of early life. EMBO Rep 2022; 23:e55679. [PMID: 35861330 PMCID: PMC9346476 DOI: 10.15252/embr.202255679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 07/06/2022] [Indexed: 11/25/2022] Open
Affiliation(s)
- Maiia Aleksandrova
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), CNRS UMR 7006 Université de Strasbourg Strasbourg France
| | - Claudia Bonfio
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), CNRS UMR 7006 Université de Strasbourg Strasbourg France
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Nader S, Sebastianelli L, Mansy SS. Protometabolism as out-of-equilibrium chemistry. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2022; 380:20200423. [PMID: 35599565 PMCID: PMC9125230 DOI: 10.1098/rsta.2020.0423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/24/2021] [Indexed: 05/06/2023]
Abstract
It is common to compare life with machines. Both consume fuel and release waste to run. In biology, the engine that drives the living system is referred to as metabolism. However, attempts at deciphering the origins of metabolism do not focus on this energetic relationship that sustains life but rather concentrate on nonenzymatic reactions that produce all the intermediates of an extant metabolic pathway. Such an approach is akin to studying the molecules produced from the burning of coal instead of deciphering how the released energy drives the movement of pistons and ultimately the train when investigating the mechanisms behind locomotion. Theories that do explicitly invoke geological chemical gradients to drive metabolism most frequently feature hydrothermal vent conditions, but hydrothermal vents are not the only regions of the early Earth that could have provided the fuel necessary to sustain the Earth's first (proto)cells. Here, we give examples of prior reports on protometabolism and highlight how more recent investigations of out-of-equilibrium systems may point to alternative scenarios more consistent with the majority of prebiotic chemistry data accumulated thus far. This article is part of the theme issue 'Emergent phenomena in complex physical and socio-technical systems: from cells to societies'.
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Affiliation(s)
- Serge Nader
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB, Canada T6G 2G2
| | - Lorenzo Sebastianelli
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB, Canada T6G 2G2
| | - Sheref S. Mansy
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB, Canada T6G 2G2
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Barge LM, Rodriguez LE, Weber JM, Theiling BP. Determining the "Biosignature Threshold" for Life Detection on Biotic, Abiotic, or Prebiotic Worlds. ASTROBIOLOGY 2022; 22:481-493. [PMID: 34898272 DOI: 10.1089/ast.2021.0079] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The field of prebiotic chemistry has demonstrated that complex organic chemical systems that exhibit various life-like properties can be produced abiotically in the laboratory. Understanding these chemical systems is important for astrobiology and life detection since we do not know the extent to which prebiotic chemistry might exist or have existed on other worlds. Nor do we know what signatures are diagnostic of an extant or "failed" prebiotic system. On Earth, biology has suppressed most abiotic organic chemistry and overprints geologic records of prebiotic chemistry; therefore, it is difficult to validate whether chemical signatures from future planetary missions are remnant or extant prebiotic systems. The "biosignature threshold" between whether a chemical signature is more likely to be produced by abiotic versus biotic chemistry on a given world could vary significantly, depending on the particular environment, and could change over time, especially if life were to emerge and diversify on that world. To interpret organic signatures detected during a planetary mission, we advocate for (1) gaining a more complete understanding of prebiotic/abiotic chemical possibilities in diverse planetary environments and (2) involving experimental prebiotic samples as analogues when generating comparison libraries for "life-detection" mission instruments.
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Affiliation(s)
- Laura M Barge
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Laura E Rodriguez
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Jessica M Weber
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
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Smokers IBA, van Haren MHI, Lu T, Spruijt E. Complex coacervation and compartmentalized conversion of prebiotically relevant metabolites. CHEMSYSTEMSCHEM 2022. [DOI: 10.1002/syst.202200004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Iris B. A. Smokers
- Radboud University Nijmegen: Radboud Universiteit Institute for Molecules and Materials NETHERLANDS
| | | | - Tiemei Lu
- Radboud University Nijmegen: Radboud Universiteit Institute for Molecules and Materials NETHERLANDS
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Weber JM, Henderson BL, LaRowe DE, Goldman AD, Perl SM, Billings K, Barge LM. Testing Abiotic Reduction of NAD + Directly Mediated by Iron/Sulfur Minerals. ASTROBIOLOGY 2022; 22:25-34. [PMID: 34591607 DOI: 10.1089/ast.2021.0035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Life emerged in a geochemical context, possibly in the midst of mineral substrates. However, it is not known to what extent minerals and dissolved inorganic ions could have facilitated the evolution of biochemical reactions. Herein, we have experimentally shown that iron sulfide minerals can act as electron transfer agents for the reduction of the ubiquitous biological protein cofactor nicotinamide adenine dinucleotide (NAD+) under anaerobic prebiotic conditions, observing the NAD+/NADH redox transition by using ultraviolet-visible spectroscopy and 1H nuclear magnetic resonance. This reaction was mediated with iron sulfide minerals, which were likely abundant on early Earth in seafloor and hydrothermal settings; and the NAD+/NADH redox reaction occurred in the absence of UV light, peptide ligand(s), or dissolved mediators. To better understand this reaction, thermodynamic modeling was also performed. The ability of an iron sulfide mineral to transfer electrons to a biochemical cofactor that is found in every living cell demonstrates how geologic materials could have played a direct role in the evolution of certain cofactor-driven metabolic pathways.
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Affiliation(s)
- Jessica M Weber
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Bryana L Henderson
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Douglas E LaRowe
- Department of Earth Sciences, University of Southern California, Los Angeles, California, USA
| | - Aaron D Goldman
- Blue Marble Space Institute of Science, Seattle, Washington, United States of America
- Department of Biology, Oberlin College, Oberlin, Ohio, USA
| | - Scott M Perl
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Keith Billings
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Laura M Barge
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
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Mu X, Feng X, Wu T, Zhou F, Nie Y, Xu Y. Transamination-Like Reaction Catalyzed by Leucine Dehydrogenase for Efficient Co-Synthesis of α-Amino Acids and α-Keto Acids. Molecules 2021; 26:molecules26237287. [PMID: 34885864 PMCID: PMC8658789 DOI: 10.3390/molecules26237287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/25/2021] [Accepted: 11/27/2021] [Indexed: 11/17/2022] Open
Abstract
α-Amino acids and α-keto acids are versatile building blocks for the synthesis of several commercially valuable products in the food, agricultural, and pharmaceutical industries. In this study, a novel transamination-like reaction catalyzed by leucine dehydrogenase was successfully constructed for the efficient enzymatic co-synthesis of α-amino acids and α-keto acids. In this reaction mode, the α-keto acid substrate was reduced and the α-amino acid substrate was oxidized simultaneously by the enzyme, without the need for an additional coenzyme regeneration system. The thermodynamically unfavorable oxidation reaction was driven by the reduction reaction. The efficiency of the biocatalytic reaction was evaluated using 12 different substrate combinations, and a significant variation was observed in substrate conversion, which was subsequently explained by the differences in enzyme kinetics parameters. The reaction with the selected model substrates 2-oxobutanoic acid and L-leucine reached 90.3% conversion with a high total turnover number of 9.0 × 106 under the optimal reaction conditions. Furthermore, complete conversion was achieved by adjusting the ratio of addition of the two substrates. The constructed reaction mode can be applied to other amino acid dehydrogenases in future studies to synthesize a wider range of valuable products.
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Affiliation(s)
- Xiaoqing Mu
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (X.F.); (T.W.); (F.Z.); (Y.N.); (Y.X.)
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Institute of Industrial Technology, Suqian Jiangnan University, Suqian 223800, China
- Correspondence:
| | - Xian Feng
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (X.F.); (T.W.); (F.Z.); (Y.N.); (Y.X.)
| | - Tao Wu
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (X.F.); (T.W.); (F.Z.); (Y.N.); (Y.X.)
| | - Feng Zhou
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (X.F.); (T.W.); (F.Z.); (Y.N.); (Y.X.)
| | - Yao Nie
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (X.F.); (T.W.); (F.Z.); (Y.N.); (Y.X.)
| | - Yan Xu
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi 214122, China; (X.F.); (T.W.); (F.Z.); (Y.N.); (Y.X.)
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Deal AM, Rapf RJ, Vaida V. Water-Air Interfaces as Environments to Address the Water Paradox in Prebiotic Chemistry: A Physical Chemistry Perspective. J Phys Chem A 2021; 125:4929-4942. [PMID: 33979519 DOI: 10.1021/acs.jpca.1c02864] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The asymmetric water-air interface provides a dynamic aqueous environment with properties that are often very different than bulk aqueous or gaseous phases and promotes reactions that are thermodynamically, kinetically, or otherwise unfavorable in bulk water. Prebiotic chemistry faces a key challenge: water is necessary for life yet reduces the efficiency of many biomolecular synthesis reactions. This perspective considers water-air interfaces as auspicious reaction environments for abiotic synthesis. We discuss recent evidence that (1) water-air interfaces promote condensation reactions including peptide synthesis, phosphorylation, and oligomerization; (2) photochemistry at water-air interfaces may have been a significant source of prebiotic molecular complexity, given the lack of oxygen and increased availability of near-ultraviolet radiation on early Earth; and (3) water-air interfaces can promote spontaneous reduction and oxidation reactions, potentially providing protometabolic pathways. Life likely began within a relatively short time frame, and water-air interfaces offer promising environments for simultaneous and efficient biomolecule production.
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Affiliation(s)
- Alexandra M Deal
- Department of Chemistry and Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Rebecca J Rapf
- Department of Chemistry, Trinity University, 1 Trinity Place, San Antonio, Texas 78212, United States
| | - Veronica Vaida
- Department of Chemistry and Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, Colorado 80309, United States
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