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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. [PMID: 39367831 DOI: 10.1021/acs.accounts.4c00423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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Fernández-Solís KG, Domínguez-Fonseca E, Martínez BMG, Becerra AG, Ochoa EF, Mendizábal E, Toriz G, Loyer P, Rosselgong J, Bravo-Anaya LM. Synthesis, characterization and stability of crosslinked chitosan-maltodextrin pH-sensitive nanogels. Int J Biol Macromol 2024; 274:133277. [PMID: 38908642 DOI: 10.1016/j.ijbiomac.2024.133277] [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: 02/25/2024] [Revised: 04/20/2024] [Accepted: 06/18/2024] [Indexed: 06/24/2024]
Abstract
Polysaccharide-based nanogels offer a wide range of chemical compositions and are of great interest due to their biodegradability, biocompatibility, non-toxicity, and their ability to display pH, temperature, or enzymatic response. In this work, we synthesized monodisperse and tunable pH-sensitive nanogels by crosslinking, through reductive amination, chitosan and partially oxidized maltodextrins, by keeping the concentration of chitosan close to its overlap concentration, i.e. in the dilute and semi-dilute regime. The chitosan/maltodextrin nanogels presented sizes ranging from 63 ± 9 to 279 ± 16 nm, showed quasi-spherical and cauliflower-like morphology, reached a ζ-potential of +36 ± 2 mV and maintained a colloidal stability for up to 7 weeks. It was found that the size and surface charge of nanogels depended both on the oxidation degree of maltodextrins and chitosan concentration, as well as on its degree of acetylation and protonation, the latter tuned by pH. The pH-responsiveness of the nanogels was evidenced by an increased size, owed to swelling, and ζ-potential when pH was lowered. Finally, maltodextrin-chitosan biocompatible nanogels were assessed by cell viability assay performed using the HEK293T cell line.
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Affiliation(s)
- Karla Gricelda Fernández-Solís
- Universidad de Guadalajara, Departamento de Química, Blvd. M. García Barragán #1451, C.P. 44430 Guadalajara, Jalisco, Mexico; Université de Rennes, CNRS, ISCR - UMR 6226, F-35000 Rennes, France
| | - Estefanía Domínguez-Fonseca
- Université de Rennes, CNRS, ISCR - UMR 6226, F-35000 Rennes, France; CUTonalá, Departamento de Ciencias Básicas y Aplicadas, Universidad de Guadalajara, Nuevo Periférico # 555, C.P.45425 Ejido San José Tatepozco, Jalisco, Mexico
| | - Brianda María González Martínez
- CUTonalá, Departamento de Ciencias Básicas y Aplicadas, Universidad de Guadalajara, Nuevo Periférico # 555, C.P.45425 Ejido San José Tatepozco, Jalisco, Mexico
| | - Alberto Gutiérrez Becerra
- CUTonalá, Departamento de Ciencias Básicas y Aplicadas, Universidad de Guadalajara, Nuevo Periférico # 555, C.P.45425 Ejido San José Tatepozco, Jalisco, Mexico
| | - Edgar Figueroa Ochoa
- Universidad de Guadalajara, Departamento de Química, Blvd. M. García Barragán #1451, C.P. 44430 Guadalajara, Jalisco, Mexico
| | - Eduardo Mendizábal
- Universidad de Guadalajara, Departamento de Química, Blvd. M. García Barragán #1451, C.P. 44430 Guadalajara, Jalisco, Mexico
| | - Guillermo Toriz
- Departamento de Madera, Celulosa y Papel, Universidad de Guadalajara, Camino R. Padilla Sánchez, 2100, Nextipac, 45200 Zapopan, Jalisco, Mexico
| | - Pascal Loyer
- Université de Rennes, Inserm, INRAE, Institut NUMECAN, UMR-A 1341, UMR-S 1317, Plateforme SynNanoVect, Rennes, France
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3
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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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Tang D, Ji G, Wang J, Liang Z, Chen W, Ji H, Ma J, Liu S, Zhuang Z, Zhou G. A Multifunctional Amino Acid Enables Direct Recycling of Spent LiFePO 4 Cathode Material. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2309722. [PMID: 38010273 DOI: 10.1002/adma.202309722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/22/2023] [Indexed: 11/29/2023]
Abstract
Lithium iron phosphate (LiFePO4 , LFP) batteries are extensively used in electric vehicles and energy storage due to their good cycling stability and safety. However, the finite service life of lithium-ion batteries leads to significant amounts of retired LFP batteries, urgently required to be recycled by environmentally friendly and effective methods. Here, a direct regeneration strategy using natural and low-cost L-threonine as a multifunctional reductant is proposed. The hydroxyl groups and amino groups in L-threonine act as electron donors and nitrogen sources, respectively. The reductive environment created by L-threonine not only aids in converting the degraded FePO4 phase back to a single LFP phase but also facilitates the elimination of detrimental Li-Fe anti-site defects; thus, reconstructing fast Li+ diffusion channels. Meanwhile, N atoms derived from amino groups are able to dope into carbon layers, generating more active sites and enhancing the conductive properties of LFP particles. The regenerated LFP shows great electrochemical performance with a discharge capacity of 147.9 mAh g-1 at 1 C and a capacity retention of 86% after 500 cycles at 5 C. Further, this approach is also feasible for LFP black mass sourced from practical industrial dismantling lines, providing considerable prospects for the large-scale recycling of LFP batteries.
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Affiliation(s)
- Di Tang
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Guanjun Ji
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Junxiong Wang
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zheng Liang
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wen Chen
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Haocheng Ji
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Jun Ma
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Song Liu
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Zhaofeng Zhuang
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Guangmin Zhou
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
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Kong L, Yue Y, Li J, Yang B, Chen B, Liu J, Lu Z. Transcriptomics and metabolomics reveal improved performance of Hu sheep on hybridization with Southdown sheep. Food Res Int 2023; 173:113240. [PMID: 37803553 DOI: 10.1016/j.foodres.2023.113240] [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: 04/11/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 10/08/2023]
Abstract
Consumers are increasingly demanding high-quality mutton. Cross breeding can improve meat quality and is widely used in sheep breeding. However, little is known about the molecular mechanism of cross breeding sheep meat quality. In this study, male Southdown and female Hu sheep were hybridized. The slaughter performance and longissimus dorsi quality of the 6-month-old hybrid offspring were measured, and the longissimus dorsi of the hybrid offspring was analyzed by transcriptomics and metabolomics to explore the effect of cross breeding on meat quality. The results showed that the production performance of Southdown × Hu F1 sheep was significantly improved, the carcass fat content was significantly decreased, and the eating quality of Southdown × Hu F1 sheep were better. Compared with the HS group (Hu × Hu), the NH group (Southdown × Hu) had 538 differentially expressed genes and 166 differentially expressed metabolites (P < 0.05), which were significantly enriched in amino acid metabolism and other related pathways. Up-regulated genes METTL21C, PPARGC1A and down-regulated gene WFIKKN2 are related to muscle growth and development. Among them, the METTL21C gene, which is related to muscle development, was highly correlated with carnosine, a metabolite related to meat quality (correlation > 0.6 and P < 0.05). Our results provide further understanding of the molecular mechanism of cross breeding for sheep muscle growth and meat quality optimization.
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Affiliation(s)
- Lingying Kong
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yaojing Yue
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Jianye Li
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Bohui Yang
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Bowen Chen
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Jianbin Liu
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.
| | - Zengkui Lu
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.
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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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Gómez-Suárez A, Neumann CN. Stereochemistry in All Its Shapes and Forms: The 56 th Bürgenstock Conference. Angew Chem Int Ed Engl 2023; 62:e202309468. [PMID: 37590448 DOI: 10.1002/anie.202309468] [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: 07/04/2023] [Indexed: 08/19/2023]
Abstract
Acknowledging the crucial role of stereochemistry in fields as diverse as total synthesis, synthetic methodology, spectroscopy, and the study of the origin of life, the 56th SCS Conference on Stereochemistry, better known as the BÃ1/4rgenstock Conference, brought together a diverse range of chemistry expertise in Brunnen, Switzerland.
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Affiliation(s)
- Adrián Gómez-Suárez
- Organic Chemistry, Bergische Universität Wuppertal, Gaußstr. 20, 42119, Wuppertal, Germany
| | - Constanze N Neumann
- Department of Heterogeneous Catalysis, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
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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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9
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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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10
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Paczelt V, Wende RC, Schreiner PR, Eckhardt AK. Glycine Imine-The Elusive α-Imino Acid Intermediate in the Reductive Amination of Glyoxylic Acid. Angew Chem Int Ed Engl 2023; 62:e202218548. [PMID: 36656102 DOI: 10.1002/anie.202218548] [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: 12/15/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 01/20/2023]
Abstract
Simple unhindered aldimines tend to hydrolyze or oligomerize and are therefore spectroscopically not well characterized. Herein we report the formation and spectroscopic characterization of the simplest imino acid, namely glycine imine, by cryogenic matrix isolation IR and UV/Vis spectroscopy. Glycine imine forms after UV irradiation of 2-azidoacetic acid by N2 extrusion in anti-(E,E)- and anti-(Z,Z)-conformation that can be photochemically interconverted. In matrix isolation pyrolysis experiments with 2-azidoacetic acid, glycine imine cannot be trapped as it further decarboxylates to aminomethylene. In aqueous solution glycine imine is hydrolyzed to hydroxy glycine and hydrated glyoxylic acid. At higher concentrations or in the presence of FeII SO4 as a reducing agent glycine imine undergoes self-reduction by oxidative decarboxylation chemistry. Glycine imine may be seen as one of the key reaction intermediates connecting prebiotic amino acid and sugar formation chemistry.
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Affiliation(s)
- Viktor Paczelt
- Lehrstuhl für Organische Chemie II, Ruhr-Universität Bochum, Universitätsstraße 150, 44801, Bochum, Germany
| | - Raffael C Wende
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - André K Eckhardt
- Lehrstuhl für Organische Chemie II, Ruhr-Universität Bochum, Universitätsstraße 150, 44801, Bochum, Germany
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