1
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de Jong TJ, Demertzi AD, Robinson WE, Huck WTS. Environmental History is Transferred via Minerals Altering Formose Reaction Pathways. Angew Chem Int Ed Engl 2025; 64:e202504659. [PMID: 40116706 PMCID: PMC12124346 DOI: 10.1002/anie.202504659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2025] [Revised: 03/20/2025] [Accepted: 03/20/2025] [Indexed: 03/23/2025]
Abstract
It is generally accepted that minerals were an important source of prebiotic catalysis. In this work we demonstrate how the prebiotic sugar forming formose reaction is guided to unique reaction compositions in the presence of a variety of minerals. When the same mineral is transferred between multiple sequential batch reactions, a new reaction composition is obtained after each reaction cycle. We attribute this effect to the adsorption of catalytic Ca(OH)2 to mineral surfaces. Further exploration shows that first exposing the mineral surface to the aqueous catalyst allows the mineral to subsequently produce formose outputs without the need for any additional catalyst to be present. As such, the mineral surface functions as storage of the preceding environmental conditions. Our work supports the development of chemical complexity through the transfer of information between sequences of chemical environments.
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Affiliation(s)
- Thijs J. de Jong
- Department of Physical Organic ChemistryInstitute for Molecules and Materials (IMM)Radboud UniversityNijmegenNetherlands
| | - Astra D. Demertzi
- Department of Physical Organic ChemistryInstitute for Molecules and Materials (IMM)Radboud UniversityNijmegenNetherlands
| | - William E. Robinson
- Department of Physical Organic ChemistryInstitute for Molecules and Materials (IMM)Radboud UniversityNijmegenNetherlands
| | - Wilhelm T. S. Huck
- Department of Physical Organic ChemistryInstitute for Molecules and Materials (IMM)Radboud UniversityNijmegenNetherlands
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2
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Matange K, Rajaei V, Capera-Aragones P, Costner JT, Robertson A, Kim JS, Petrov AS, Bowman JC, Williams LD, Frenkel-Pinter M. Evolution of complex chemical mixtures reveals combinatorial compression and population synchronicity. Nat Chem 2025; 17:590-597. [PMID: 39939341 DOI: 10.1038/s41557-025-01734-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/06/2025] [Indexed: 02/14/2025]
Abstract
Many open questions about the origins of life are centred on the generation of complex chemical species. Past work has characterized specific chemical reactions that might lead to biological molecules. Here we establish an experimental model of chemical evolution to investigate general processes by which chemical systems continuously change. We used water as a chemical reactant, product and medium. We leveraged oscillating water activity at near-ambient temperatures to cause ratcheting of near-equilibrium reactions in mixtures of organic molecules containing carboxylic acids, amines, thiols and hydroxyl groups. Our system (1) undergoes continuous change with transitions to new chemical spaces while not converging throughout the experiment; (2) demonstrates combinatorial compression with stringent chemical selection; and (3) displays synchronicity of molecular populations. Our results suggest that chemical evolution and selection can be observed in organic mixtures and might ultimately be adapted to produce a broad array of molecules with novel structures and functions.
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Affiliation(s)
- Kavita Matange
- NASA Center for Integration of the Origins of Life, Atlanta, GA, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Vahab Rajaei
- NASA Center for Integration of the Origins of Life, Atlanta, GA, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Pau Capera-Aragones
- NASA Center for Integration of the Origins of Life, Atlanta, GA, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - John T Costner
- NASA Center for Integration of the Origins of Life, Atlanta, GA, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Adelaide Robertson
- NASA Center for Integration of the Origins of Life, Atlanta, GA, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jennifer Seoyoung Kim
- NASA Center for Integration of the Origins of Life, Atlanta, GA, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Anton S Petrov
- NASA Center for Integration of the Origins of Life, Atlanta, GA, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- NSF-NASA Center of Chemical Evolution, Atlanta, GA, USA
| | - Jessica C Bowman
- NASA Center for Integration of the Origins of Life, Atlanta, GA, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- NSF-NASA Center of Chemical Evolution, Atlanta, GA, USA
| | - Loren Dean Williams
- NASA Center for Integration of the Origins of Life, Atlanta, GA, USA.
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA.
- NSF-NASA Center of Chemical Evolution, Atlanta, GA, USA.
| | - Moran Frenkel-Pinter
- NASA Center for Integration of the Origins of Life, Atlanta, GA, USA.
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, Israel.
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3
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Xu HX, Zhao ZR, Wang X. A selective non-enzymatic synthesis of ribose simply from formaldehyde, metal salts and clays. Chem Commun (Camb) 2025; 61:1701-1704. [PMID: 39749890 DOI: 10.1039/d4cc03981e] [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: 01/04/2025]
Abstract
This study demonstrates that metal-doped-clay (MDC) can be a selective platform for ribose produced from formaldehyde under abiotic conditions. Ribose exhibits superior retention compared with other carbohydrates on naturally occurring minerals on the early Earth in the presence of divalent cations. This finding offers an insight into the necessity of the emergence of ribose as the backbone of extant RNA.
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Affiliation(s)
- Hao-Xing Xu
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China.
| | - Ze-Run Zhao
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China.
| | - Xiao Wang
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China.
- Frontiers Science Center for Critical Earth Material Cycling, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
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4
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Hashidzume A. The second wave of formose research. BBA ADVANCES 2025; 7:100141. [PMID: 39974666 PMCID: PMC11835704 DOI: 10.1016/j.bbadva.2025.100141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2024] [Revised: 01/09/2025] [Accepted: 01/13/2025] [Indexed: 02/21/2025] Open
Abstract
This review article highlights key developments in the second wave of formose research (from approximately 2000), summarizing approximately 100 relevant studies. Section 1 introduces the basics of formose reaction and its historical context. Section 2 provides a brief overview of the pioneering works from the first wave of formose research (from 1970 to 1990). Section 3 then overviews the second wave of formose research, in which formose reactions under various conditions, mechanistic studies of the formose reaction, formose reactions and the origin of life, and applications of formose reactions are described. Finally, Section 4 offers summary and outlook.
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Affiliation(s)
- Akihito Hashidzume
- Department of Macromolecular Science, Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
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5
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Kua J, Peña MT, Cotter SN, Leca J. Sulfur Analogs of the Core Formose Cycle: A Free Energy Map. Life (Basel) 2024; 15:1. [PMID: 39859941 PMCID: PMC11766735 DOI: 10.3390/life15010001] [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: 11/26/2024] [Revised: 12/16/2024] [Accepted: 12/19/2024] [Indexed: 01/27/2025] Open
Abstract
Using computational methods, we examine if the presence of H2S can tame the unruly formose reaction by generating a free energy map of the reaction thermodynamics and kinetics of sulfur analogs within the core cycle. With mercaptoaldehyde as the linchpin C2 species, and feeding the cycle with CH2O, selected aldol additions and enolizations are kinetically more favorable. Thione formation is thermodynamically less favored compared to aldehydes and ketones, but all these species can be connected by enolization reactions. In some sulfur analogs, the retroaldol transformation of a C4 species back into linchpin species is thermodynamically favorable, and we have found one route incorporating where incorporating sulfur selects for a specific pathway over others. However, as CH2O diminishes, the aldol addition of larger species is less favorable for the sulfur analogs. Our results also suggest that competing Cannizzaro side reactions are kinetically less favored and thermodynamically disfavored when H2S is abundant.
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Affiliation(s)
- Jeremy Kua
- Department of Chemistry & Biochemistry, University of San Diego, San Diego, CA 92110, USA
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6
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Kurpik G, Walczak A, Dydio P, Stefankiewicz AR. Multi-Stimuli-Responsive Network of Multicatalytic Reactions using a Single Palladium/Platinum Catalyst. Angew Chem Int Ed Engl 2024; 63:e202404684. [PMID: 38877818 DOI: 10.1002/anie.202404684] [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: 03/07/2024] [Revised: 06/13/2024] [Accepted: 06/14/2024] [Indexed: 06/16/2024]
Abstract
Given her unrivalled proficiency in the synthesis of all molecules of life, nature has been an endless source of inspiration for developing new strategies in organic chemistry and catalysis. However, one feature that remains thus far beyond chemists' grasp is her unique ability to adapt the productivity of metabolic processes in response to triggers that indicate the temporary need for specific metabolites. To demonstrate the remarkable potential of such stimuli-responsive systems, we present a metabolism-inspired network of multicatalytic processes capable of selectively synthesising a range of products from simple starting materials. Specifically, the network is built of four classes of distinct catalytic reactions-cross-couplings, substitutions, additions, and reductions, involving three organic starting materials-terminal alkyne, aryl iodide, and hydrosilane. All starting materials are either introduced sequentially or added to the system at the same time, with no continuous influx of reagents or efflux of products. All processes in the system are catalysed by a multifunctional heteronuclear PdII/PtII complex, whose performance can be controlled by specific additives and external stimuli. The reaction network exhibits a substantial degree of orthogonality between different pathways, enabling the controllable synthesis of ten distinct products with high efficiency and selectivity through simultaneous triggering and suppression mechanisms.
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Affiliation(s)
- Gracjan Kurpik
- Center for Advanced Technologies, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 10, 61-614, Poznań, Poland
- Faculty of Chemistry, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 8, 61-614, Poznań, Poland
| | - Anna Walczak
- Center for Advanced Technologies, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 10, 61-614, Poznań, Poland
- Faculty of Chemistry, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 8, 61-614, Poznań, Poland
| | - Paweł Dydio
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, Cambridge, UK
- University of Strasbourg, CNRS, ISIS UMR 7006, 8 Allée Gaspard Monge, 67000, Strasbourg, France
| | - Artur R Stefankiewicz
- Center for Advanced Technologies, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 10, 61-614, Poznań, Poland
- Faculty of Chemistry, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 8, 61-614, Poznań, Poland
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7
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Gentili PL, Stano P. Living cells and biological mechanisms as prototypes for developing chemical artificial intelligence. Biochem Biophys Res Commun 2024; 720:150060. [PMID: 38754164 DOI: 10.1016/j.bbrc.2024.150060] [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: 10/26/2023] [Revised: 03/25/2024] [Accepted: 05/06/2024] [Indexed: 05/18/2024]
Abstract
Artificial Intelligence (AI) is having a revolutionary impact on our societies. It is helping humans in facing the global challenges of this century. Traditionally, AI is developed in software or through neuromorphic engineering in hardware. More recently, a brand-new strategy has been proposed. It is the so-called Chemical AI (CAI), which exploits molecular, supramolecular, and systems chemistry in wetware to mimic human intelligence. In this work, two promising approaches for boosting CAI are described. One regards designing and implementing neural surrogates that can communicate through optical or chemical signals and give rise to networks for computational purposes and to develop micro/nanorobotics. The other approach concerns "bottom-up synthetic cells" that can be exploited for applications in various scenarios, including future nano-medicine. Both topics are presented at a basic level, mainly to inform the broader audience of non-specialists, and so favour the rise of interest in these frontier subjects.
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Affiliation(s)
- Pier Luigi Gentili
- Department of Chemistry, Biology, and Biotechnology, Università degli Studi di Perugia, Perugia, Italy.
| | - Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy.
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8
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Kua J, Tripoli LP. Exploring the Core Formose Cycle: Catalysis and Competition. Life (Basel) 2024; 14:933. [PMID: 39202675 PMCID: PMC11355428 DOI: 10.3390/life14080933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 07/10/2024] [Accepted: 07/19/2024] [Indexed: 09/03/2024] Open
Abstract
The core autocatalytic cycle of the formose reaction may be enhanced or eroded by the presence of simple molecules at life's origin. Utilizing quantum chemistry, we calculate the thermodynamics and kinetics of reactions both within the core cycle and those that deplete the reactants and intermediates, such as the Cannizzaro reaction. We find that via disproportionation of aldehydes into carboxylic acids and alcohols, the Cannizzaro reaction furnishes simple catalysts for a variety of reactions. We also find that ammonia can catalyze both in-cycle and Cannizzaro reactions while hydrogen sulfide does not; both, however, play a role in sequestering reactants and intermediates in the web of potential reactions.
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Affiliation(s)
- Jeremy Kua
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, CA 92110, USA
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9
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Baltussen MG, de Jong TJ, Duez Q, Robinson WE, Huck WTS. Chemical reservoir computation in a self-organizing reaction network. Nature 2024; 631:549-555. [PMID: 38926572 PMCID: PMC11254755 DOI: 10.1038/s41586-024-07567-x] [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: 10/24/2023] [Accepted: 05/14/2024] [Indexed: 06/28/2024]
Abstract
Chemical reaction networks, such as those found in metabolism and signalling pathways, enable cells to process information from their environment1,2. Current approaches to molecular information processing and computation typically pursue digital computation models and require extensive molecular-level engineering3. Despite considerable advances, these approaches have not reached the level of information processing capabilities seen in living systems. Here we report on the discovery and implementation of a chemical reservoir computer based on the formose reaction4. We demonstrate how this complex, self-organizing chemical reaction network can perform several nonlinear classification tasks in parallel, predict the dynamics of other complex systems and achieve time-series forecasting. This in chemico information processing system provides proof of principle for the emergent computational capabilities of complex chemical reaction networks, paving the way for a new class of biomimetic information processing systems.
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Affiliation(s)
- Mathieu G Baltussen
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Thijs J de Jong
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Quentin Duez
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - William E Robinson
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands.
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10
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Venturini A, González J. Prebiotic Synthesis of Glycolaldehyde and Glyceraldehyde from Formaldehyde: A Computational Study on the Initial Steps of the Formose Reaction. Chempluschem 2024; 89:e202300388. [PMID: 37932034 DOI: 10.1002/cplu.202300388] [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: 07/25/2023] [Revised: 10/10/2023] [Indexed: 11/08/2023]
Abstract
In this work, the initial steps of the mechanism of the Formose reaction (FR) is computationally studied using DFT methods. The FR has been considered to be a relevant process in the prebiotic evolution leading to several types of sugars or carbohydrates. These molecules are some of the basic building blocks of the life. The dimerization of formaldehyde was found to take place via an intramolecular deprotonation reaction, leading to the formation of an intermediate which, after an isomerization, forms a Ca-complex of the cis-enediol tautomer of glycolaldehyde. The aldol reaction of this complex with additional formaldehyde gave glyceraldehyde, the simplest aldotriose. The catalyst Ca(OH)2 plays a dual role in the reaction, acting as a base (in the intramolecular deprotonation) and as Lewis acid (activating the carbonyl group) in the aldol addition.
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Affiliation(s)
- Alessandro Venturini
- Institute of Organic Synthesis and Photoreactivity (ISOF), National Research Council of Italy, Via P. Gobetti 101, 40129, -Bologna, Italy
| | - Javier González
- Departamento de Química Orgánica e Inorgánica, Universidad de Oviedo, c/ Julián Clavería 8, 33006-, Oviedo, Spain
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11
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Briš A, Baltussen MG, Tripodi GL, Huck WTS, Franceschi P, Roithová J. Direct Analysis of Complex Reaction Mixtures: Formose Reaction. Angew Chem Int Ed Engl 2024; 63:e202316621. [PMID: 38100204 DOI: 10.1002/anie.202316621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Indexed: 12/31/2023]
Abstract
Complex reaction mixtures, like those postulated on early Earth, present an analytical challenge because of the number of components, their similarity, and vastly different concentrations. Interpreting the reaction networks is typically based on simplified or partial data, limiting our insight. We present a new approach based on online monitoring of reaction mixtures formed by the formose reaction by ion-mobility-separation mass-spectrometry. Monitoring the reaction mixtures led to large data sets that we analyzed by non-negative matrix factorization, thereby identifying ion-signal groups capturing the time evolution of the network. The groups comprised ≈300 major ion signals corresponding to sugar-calcium complexes formed during the formose reaction. Multivariate analysis of the kinetic profiles of these complexes provided an overview of the interconnected kinetic processes in the solution, highlighting different pathways for sugar growth and the effects of different initiators on the initial kinetics. Reconstructing the network's topology further, we revealed so far unnoticed fast retro-aldol reaction of ketoses, which significantly affects the initial reaction dynamics. We also detected the onset of sugar-backbone branching for C6 sugars and cyclization reactions starting for C5 sugars. This top-down analytical approach opens a new way to analyze complex dynamic mixtures online with unprecedented coverage and time resolution.
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Affiliation(s)
- Anamarija Briš
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525, AJ Nijmegen, The Netherlands
- Laboratory for physical-organic chemistry, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička c. 54, 10000, Zagreb, Croatia
| | - Mathieu G Baltussen
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525, AJ Nijmegen, The Netherlands
| | - Guilherme L Tripodi
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525, AJ Nijmegen, The Netherlands
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525, AJ Nijmegen, The Netherlands
| | - Pietro Franceschi
- Research and innovation Centre, Fondazione E. Mach, Via Edmund Mach, 1, 38098, San Michele All'adige TN, Italy
| | - Jana Roithová
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525, AJ Nijmegen, The Netherlands
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12
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Tabata H, Nishijima H, Yamada Y, Miyake R, Yamamoto K, Kato S, Nakanishi S. Microbial Biomanufacturing Using Chemically Synthesized Non-Natural Sugars as the Substrate. Chembiochem 2024; 25:e202300760. [PMID: 38063314 DOI: 10.1002/cbic.202300760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/02/2023] [Indexed: 12/20/2023]
Abstract
The bioproduction of valuable materials using biomass sugars is attracting attention as an environmentally friendly technology. However, its ability to fulfil the enormous demand to produce fuels and chemical products is limited. With a view towards the future development of a novel bioproduction process that addresses these concerns, this study investigated the feasibility of bioproduction of valuable substances using Corynebacterium glutamicum (C. glutamicum) with a chemically synthesized non-natural sugar solution. Cells were grown using the synthesized sugar solution as the sole carbon source and they produced lactate under oxygen-limited conditions. It was also found that some of the sugars produced by the series of chemical reactions inhibited cell growth since prior removal of these sugars increased the cell growth rate. The results obtained in this study indicate that chemically synthesized sugars have the potential to resolve the concerns regarding future biomass sugar supply in microbial biomanufacturing.
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Affiliation(s)
- Hiro Tabata
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan
| | - Hiroaki Nishijima
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan
| | - Yuki Yamada
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan
| | - Rika Miyake
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan
| | - Keisuke Yamamoto
- Green Earth Research Centre, Green Earth Institute Co., Ltd., 2-5-9 Kazusakamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Souichiro Kato
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-17-2-1 Tsukisamu higashi, Toyohira, Sapporo, Hokkaido, 062-8517, Japan
| | - Shuji Nakanishi
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan
- Innovative Catalysis Science Division, Institute for Open and Transdisciplinary Research Initiatives (ICS-OTRI), Osaka University, 2-1 Yamada-oka, Suita, Osaka, 565-0871, Japan
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13
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Tabata H, Chikatani G, Nishijima H, Harada T, Miyake R, Kato S, Igarashi K, Mukouyama Y, Shirai S, Waki M, Hase Y, Nakanishi S. Construction of an autocatalytic reaction cycle in neutral medium for synthesis of life-sustaining sugars. Chem Sci 2023; 14:13475-13484. [PMID: 38033894 PMCID: PMC10685314 DOI: 10.1039/d3sc03377e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/09/2023] [Indexed: 12/02/2023] Open
Abstract
Autocatalytic mechanisms in carbon metabolism, such as the Calvin cycle, are responsible for the biological assimilation of CO2 to form organic compounds with complex structures, including sugars. Compounds that form C-C bonds with CO2 are regenerated in these autocatalytic reaction cycles, and the products are concurrently released. The formose reaction in basic aqueous solution has attracted attention as a nonbiological reaction involving an autocatalytic reaction cycle that non-enzymatically synthesizes sugars from the C1 compound formaldehyde. However, formaldehyde and sugars, which are the substrate and products of the formose reaction, respectively, are consumed in Cannizzaro reactions, particularly under basic aqueous conditions, which makes the formose reaction a fragile sugar-production system. Here, we constructed an autocatalytic reaction cycle for sugar synthesis under neutral conditions. We focused on the weak Brønsted basicity of oxometalate anions such as tungstates and molybdates as catalysts, thereby enabling the aldol reaction, retro-aldol reaction, and aldose-ketose transformation, which collectively constitute the autocatalytic reaction cycle. These bases acted on sugar molecules of substrates together with sodium ions of a Lewis acid to promote deprotonation under neutral conditions, which is the initiation step of the reactions forming an autocatalytic cycle, whereas the Cannizzaro reaction was inhibited. The autocatalytic reaction cycle established using this abiotic approach is a robust sugar production system. Furthermore, we found that the synthesized sugars work as energy storage substances that sustain microbial growth despite their absence in nature.
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Affiliation(s)
- Hiro Tabata
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University Toyonaka Osaka 560-8531 Japan
| | - Genta Chikatani
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University Toyonaka Osaka 560-8531 Japan
| | - Hiroaki Nishijima
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University Toyonaka Osaka 560-8531 Japan
| | - Takashi Harada
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University Toyonaka Osaka 560-8531 Japan
| | - Rika Miyake
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University Toyonaka Osaka 560-8531 Japan
| | - Souichiro Kato
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University Toyonaka Osaka 560-8531 Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) 2-17-2-1, Tsukisamu higashi, Toyohira Sapporo 062-8517 Japan
| | - Kensuke Igarashi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) 2-17-2-1, Tsukisamu higashi, Toyohira Sapporo 062-8517 Japan
| | - Yoshiharu Mukouyama
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University Toyonaka Osaka 560-8531 Japan
- Division of Science, College of Science and Engineering, Tokyo Denki University Hatoyama Saitama 350-0394 Japan
| | - Soichi Shirai
- Toyota Central R&D Labs., Inc. 41-1 Yokomichi Nagakute Aichi 480-1192 Japan
| | - Minoru Waki
- Toyota Central R&D Labs., Inc. 41-1 Yokomichi Nagakute Aichi 480-1192 Japan
| | - Yoko Hase
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University Toyonaka Osaka 560-8531 Japan
- Toyota Central R&D Labs., Inc. 41-1 Yokomichi Nagakute Aichi 480-1192 Japan
| | - Shuji Nakanishi
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University Toyonaka Osaka 560-8531 Japan
- Innovative Catalysis Science Division, Institute for Open and Transdisciplinary Research Initiatives (ICS-OTRI), Osaka University Suita Osaka 565-0871 Japan
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14
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Sangchai T, Al Shehimy S, Penocchio E, Ragazzon G. Artificial Molecular Ratchets: Tools Enabling Endergonic Processes. Angew Chem Int Ed Engl 2023; 62:e202309501. [PMID: 37545196 DOI: 10.1002/anie.202309501] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 08/08/2023]
Abstract
Non-equilibrium chemical systems underpin multiple domains of contemporary interest, including supramolecular chemistry, molecular machines, systems chemistry, prebiotic chemistry, and energy transduction. Experimental chemists are now pioneering the realization of artificial systems that can harvest energy away from equilibrium. In this tutorial Review, we provide an overview of artificial molecular ratchets: the chemical mechanisms enabling energy absorption from the environment. By focusing on the mechanism type-rather than the application domain or energy source-we offer a unifying picture of seemingly disparate phenomena, which we hope will foster progress in this fascinating domain of science.
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Affiliation(s)
- Thitiporn Sangchai
- University of Strasbourg, CNRS, Institut de Science et d'Ingénierie Supramoléculaires (ISIS) UMR 7006, 8 allée Gaspard Monge, 67000, Strasbourg, France
| | - Shaymaa Al Shehimy
- University of Strasbourg, CNRS, Institut de Science et d'Ingénierie Supramoléculaires (ISIS) UMR 7006, 8 allée Gaspard Monge, 67000, Strasbourg, France
| | - Emanuele Penocchio
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Giulio Ragazzon
- University of Strasbourg, CNRS, Institut de Science et d'Ingénierie Supramoléculaires (ISIS) UMR 7006, 8 allée Gaspard Monge, 67000, Strasbourg, France
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15
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Tran QP, Yi R, Fahrenbach AC. Towards a prebiotic chemoton - nucleotide precursor synthesis driven by the autocatalytic formose reaction. Chem Sci 2023; 14:9589-9599. [PMID: 37712016 PMCID: PMC10498504 DOI: 10.1039/d3sc03185c] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/17/2023] [Indexed: 09/16/2023] Open
Abstract
The formose reaction is often cited as a prebiotic source of sugars and remains one of the most plausible forms of autocatalysis on the early Earth. Herein, we investigated how cyanamide and 2-aminooxazole, molecules proposed to be present on early Earth and precursors for nonenzymatic ribonucleotide synthesis, mediate the formose reaction using HPLC, LC-MS and 1H NMR spectroscopy. Cyanamide was shown to delay the exponential phase of the formose reaction by reacting with formose sugars to form 2-aminooxazole and 2-aminooxazolines thereby diverting some of these sugars from the autocatalytic cycle, which nonetheless remains intact. Masses for tetrose and pentose aminooxazolines, precursors for nucleotide synthesis including TNA and RNA, were also observed. The results of this work in the context of the chemoton model are further discussed. Additionally, we highlight other prebiotically plausible molecules that could have mediated the formose reaction and alternative prebiotic autocatalytic systems.
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Affiliation(s)
- Quoc Phuong Tran
- School of Chemistry, University of New South Wales Sydney NSW 2052 Australia
- Australian Centre for Astrobiology, University of New South Wales Sydney NSW 2052 Australia
| | - Ruiqin Yi
- Earth-Life Science Institute, Tokyo Institute of Technology Tokyo 152-8550 Japan
| | - Albert C Fahrenbach
- School of Chemistry, University of New South Wales Sydney NSW 2052 Australia
- Australian Centre for Astrobiology, University of New South Wales Sydney NSW 2052 Australia
- UNSW RNA Institute, University of New South Wales Sydney NSW 2052 Australia
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