1
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Lee CC, Górecki K, Stang M, Ribbe MW, Hu Y. Cofactor maturase NifEN: A prototype ancient nitrogenase? SCIENCE ADVANCES 2024; 10:eado6169. [PMID: 38865457 PMCID: PMC11168457 DOI: 10.1126/sciadv.ado6169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 05/07/2024] [Indexed: 06/14/2024]
Abstract
Nitrogenase plays a key role in the global nitrogen cycle; yet, the evolutionary history of nitrogenase and, particularly, the sequence of appearance between the homologous, yet distinct NifDK (the catalytic component) and NifEN (the cofactor maturase) of the extant molybdenum nitrogenase, remains elusive. Here, we report the ability of NifEN to reduce N2 at its surface-exposed L-cluster ([Fe8S9C]), a structural/functional homolog of the M-cluster (or cofactor; [(R-homocitrate)MoFe7S9C]) of NifDK. Furthermore, we demonstrate the ability of the L-cluster-bound NifDK to mimic its NifEN counterpart and enable N2 reduction. These observations, coupled with phylogenetic, ecological, and mechanistic considerations, lead to the proposal of a NifEN-like, L-cluster-carrying protein as an ancient nitrogenase, the exploration of which could shed crucial light on the evolutionary origin of nitrogenase and related enzymes.
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Affiliation(s)
- Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697- 3900, USA
| | - Kamil Górecki
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697- 3900, USA
| | - Martin Stang
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
| | - Markus W. Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697- 3900, USA
- Department of Chemistry, University of California, Irvine, CA 92697-2025, USA
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697- 3900, USA
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2
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Williamson MP. Autocatalytic Selection as a Driver for the Origin of Life. Life (Basel) 2024; 14:590. [PMID: 38792611 PMCID: PMC11122578 DOI: 10.3390/life14050590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/29/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024] Open
Abstract
Darwin's theory of evolution by natural selection was revolutionary because it provided a mechanism by which variation could be selected. This mechanism can only operate on living systems and thus cannot be applied to the origin of life. Here, we propose a viable alternative mechanism for prebiotic systems: autocatalytic selection, in which molecules catalyze reactions and processes that lead to increases in their concentration. Crucially, this provides a driver for increases in concentrations of molecules to a level that permits prebiotic metabolism. We show how this can produce high levels of amino acids, sugar phosphates, nucleotides and lipids and then lead on to polymers. Our outline is supported by a set of guidelines to support the identification of the most likely prebiotic routes. Most of the steps in this pathway are already supported by experimental results. These proposals generate a coherent and viable set of pathways that run from established Hadean geochemistry to the beginning of life.
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Affiliation(s)
- Mike P Williamson
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
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3
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Schaible MJ, Szeinbaum N, Bozdag GO, Chou L, Grefenstette N, Colón-Santos S, Rodriguez LE, Styczinski MJ, Thweatt JL, Todd ZR, Vázquez-Salazar A, Adams A, Araújo MN, Altair T, Borges S, Burton D, Campillo-Balderas JA, Cangi EM, Caro T, Catalano E, Chen K, Conlin PL, Cooper ZS, Fisher TM, Fos SM, Garcia A, Glaser DM, Harman CE, Hermis NY, Hooks M, Johnson-Finn K, Lehmer O, Hernández-Morales R, Hughson KHG, Jácome R, Jia TZ, Marlow JJ, McKaig J, Mierzejewski V, Muñoz-Velasco I, Nural C, Oliver GC, Penev PI, Raj CG, Roche TP, Sabuda MC, Schaible GA, Sevgen S, Sinhadc P, Steller LH, Stelmach K, Tarnas J, Tavares F, Trubl G, Vidaurri M, Vincent L, Weber JM, Weng MM, Wilpiszeki RL, Young A. Chapter 1: The Astrobiology Primer 3.0. ASTROBIOLOGY 2024; 24:S4-S39. [PMID: 38498816 DOI: 10.1089/ast.2021.0129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
The Astrobiology Primer 3.0 (ABP3.0) is a concise introduction to the field of astrobiology for students and others who are new to the field of astrobiology. It provides an entry into the broader materials in this supplementary issue of Astrobiology and an overview of the investigations and driving hypotheses that make up this interdisciplinary field. The content of this chapter was adapted from the other 10 articles in this supplementary issue and thus represents the contribution of all the authors who worked on these introductory articles. The content of this chapter is not exhaustive and represents the topics that the authors found to be the most important and compelling in a dynamic and changing field.
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Affiliation(s)
- Micah J Schaible
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Nadia Szeinbaum
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - G Ozan Bozdag
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Luoth Chou
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
- Center for Space Sciences and Technology, University of Maryland, Baltimore, Maryland, USA
- Georgetown University, Washington DC, USA
| | - Natalie Grefenstette
- Santa Fe Institute, Santa Fe, New Mexico, USA
- Blue Marble Space Institute of Science, Seattle, Washington, USA
| | - Stephanie Colón-Santos
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Wisconsin, USA
- Department of Botany, University of Wisconsin-Madison, Wisconsin, USA
| | - Laura E Rodriguez
- Lunar and Planetary Institute, Universities Space Research Association, Houston, Texas, USA
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - M J Styczinski
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- University of Washington, Seattle, Washington, USA
| | - Jennifer L Thweatt
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania, USA
| | - Zoe R Todd
- Department of Earth and Space Sciences, University of Washington, Seattle, Washington, USA
| | - Alberto Vázquez-Salazar
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, California, USA
| | - Alyssa Adams
- Center for Space Sciences and Technology, University of Maryland, Baltimore, Maryland, USA
| | - M N Araújo
- Biochemistry Department, University of São Paulo, São Carlos, Brazil
| | - Thiago Altair
- Institute of Chemistry of São Carlos, Universidade de São Paulo, São Carlos, Brazil
- Department of Chemistry, College of the Atlantic, Bar Harbor, Maine, USA
| | | | - Dana Burton
- Department of Anthropology, George Washington University, Washington DC, USA
| | | | - Eryn M Cangi
- Laboratory for Atmospheric and Space Physics, University of Colorado Boulder, Boulder, Colorado, USA
| | - Tristan Caro
- Department of Geological Sciences, University of Colorado Boulder, Boulder, Colorado, USA
| | - Enrico Catalano
- Sant'Anna School of Advanced Studies, The BioRobotics Institute, Pisa, Italy
| | - Kimberly Chen
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Peter L Conlin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Z S Cooper
- Department of Earth and Space Sciences, University of Washington, Seattle, Washington, USA
| | - Theresa M Fisher
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona, USA
| | - Santiago Mestre Fos
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Amanda Garcia
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin, USA
| | - D M Glaser
- Arizona State University, Tempe, Arizona, USA
| | - Chester E Harman
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ninos Y Hermis
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
- Department of Physics and Space Sciences, University of Granada, Granada, Spain
| | - M Hooks
- NASA Johnson Space Center, Houston, Texas, USA
| | - K Johnson-Finn
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo, Japan
- Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Owen Lehmer
- Department of Earth and Space Sciences, University of Washington, Seattle, Washington, USA
| | - Ricardo Hernández-Morales
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Kynan H G Hughson
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Rodrigo Jácome
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Tony Z Jia
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo, Japan
| | - Jeffrey J Marlow
- Department of Biology, Boston University, Boston, Massachusetts, USA
| | - Jordan McKaig
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Veronica Mierzejewski
- School of Earth and Space Exploration, Arizona State University, Tempe, Arizona, USA
| | - Israel Muñoz-Velasco
- Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Departamento de Biología Celular, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Ceren Nural
- Istanbul Technical University, Istanbul, Turkey
| | - Gina C Oliver
- Department of Geology, San Bernardino Valley College, San Bernardino, California, USA
| | - Petar I Penev
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Chinmayee Govinda Raj
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Tyler P Roche
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Mary C Sabuda
- Department of Earth and Environmental Sciences, University of Minnesota-Twin Cities, Minneapolis, Minnesota, USA
- Biotechnology Institute, University of Minnesota-Twin Cities, St. Paul, Minnesota, USA
| | - George A Schaible
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Serhat Sevgen
- Blue Marble Space Institute of Science, Seattle, Washington, USA
- Institute of Marine Sciences, Middle East Technical University, Erdemli, Mersin, Turkey
| | - Pritvik Sinhadc
- BEYOND: Center For Fundamental Concepts in Science, Arizona State University, Arizona, USA
- Dubai College, Dubai, United Arab Emirates
| | - Luke H Steller
- Australian Centre for Astrobiology, and School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, Australia
| | - Kamil Stelmach
- Department of Chemistry, University of Virginia, Charlottesville, Virginia, USA
| | - J Tarnas
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Frank Tavares
- Space Enabled Research Group, MIT Media Lab, Cambridge, Massachusetts, USA
| | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Monica Vidaurri
- Center for Space Sciences and Technology, University of Maryland, Baltimore, Maryland, USA
- Department of Physics and Astronomy, Howard University, Washington DC, USA
| | - Lena Vincent
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Wisconsin, USA
| | - Jessica M Weber
- NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | | | | | - Amber Young
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
- Northern Arizona University, Flagstaff, Arizona, USA
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4
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Grefenstette N, Chou L, Colón-Santos S, Fisher TM, Mierzejewski V, Nural C, Sinhadc P, Vidaurri M, Vincent L, Weng MM. Chapter 9: Life as We Don't Know It. ASTROBIOLOGY 2024; 24:S186-S201. [PMID: 38498819 DOI: 10.1089/ast.2021.0103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
While Earth contains the only known example of life in the universe, it is possible that life elsewhere is fundamentally different from what we are familiar with. There is an increased recognition in the astrobiology community that the search for life should steer away from terran-specific biosignatures to those that are more inclusive to all life-forms. To start exploring the space of possibilities that life could occupy, we can try to dissociate life from the chemistry that composes it on Earth by envisioning how different life elsewhere could be in composition, lifestyle, medium, and form, and by exploring how the general principles that govern living systems on Earth might be found in different forms and environments across the Solar System. Exotic life-forms could exist on Mars or Venus, or icy moons like Europa and Enceladus, or even as a shadow biosphere on Earth. New perspectives on agnostic biosignature detection have also begun to emerge, allowing for a broader and more inclusive approach to seeking exotic life with unknown chemistry that is distinct from life as we know it on Earth.
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Affiliation(s)
- Natalie Grefenstette
- Santa Fe Institute, Santa Fe, New Mexico, USA
- Blue Marble Space Institute of Science, Seattle, Washington, USA
| | - Luoth Chou
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
- Georgetown University, Washington, DC, USA
| | | | - Theresa M Fisher
- School of Earth and Space Exploration, Arizona State University, Arizona, USA
| | | | - Ceren Nural
- Istanbul Technical University, Istanbul, Turkey
| | - Pritvik Sinhadc
- BEYOND: Center For Fundamental Concepts in Science, Arizona State University, Arizona, USA
- Dubai College, Dubai, United Arab Emirates
| | - Monica Vidaurri
- NASA Goddard Space Flight Center, Greenbelt, Maryland, USA
- Howard University, DC, USA
| | - Lena Vincent
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Wisconsin, USA
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5
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Rojas L, Pardo-Rodriguez D, Urueña C, Lasso P, Arévalo C, Cala MP, Fiorentino S. Effect of Petiveria alliacea Extracts on Metabolism of K562 Myeloid Leukemia Cells. Int J Mol Sci 2023; 24:17418. [PMID: 38139247 PMCID: PMC10743714 DOI: 10.3390/ijms242417418] [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: 10/18/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
Previously, studies have shown that leukemic cells exhibit elevated glycolytic metabolism and oxidative phosphorylation in comparison to hematopoietic stem cells. These metabolic processes play a crucial role in the growth and survival of leukemic cells. Due to the metabolic plasticity of tumor cells, the use of natural products has been proposed as a therapeutic alternative due to their ability to attack several targets in tumor cells, including those that could modulate metabolism. In this study, the potential of Petiveria alliacea to modulate the metabolism of K562 cell lysates was evaluated by non-targeted metabolomics. Initially, in vitro findings showed that P. alliacea reduces K562 cell proliferation; subsequently, alterations were observed in the endometabolome of cell lysates treated with the extract, mainly in glycolytic, phosphorylative, lipid, and amino acid metabolism. Finally, in vitro assays were performed, confirming that P. Alliacea extract decreased the oxygen consumption rate and intracellular ATP. These results suggest that the anti-tumor activity of the aqueous extract on the K562 cell line is attributed to the decrease in metabolites related to cell proliferation and/or growth, such as nucleotides and nucleosides, leading to cell cycle arrest. Our results provide a preliminary part of the mechanism for the anti-tumor and antiproliferative effects of P. alliacea on cancer.
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Affiliation(s)
- Laura Rojas
- Grupo de Inmunobiología y Biología Celular, Pontificia Universidad Javeriana, Bogotá 110211, Colombia; (L.R.); (C.U.); (P.L.); (C.A.)
| | - Daniel Pardo-Rodriguez
- Metabolomics Core Facility—MetCore, Vicepresidency for Research, Universidad de Los Andes, Bogotá 111711, Colombia;
| | - Claudia Urueña
- Grupo de Inmunobiología y Biología Celular, Pontificia Universidad Javeriana, Bogotá 110211, Colombia; (L.R.); (C.U.); (P.L.); (C.A.)
| | - Paola Lasso
- Grupo de Inmunobiología y Biología Celular, Pontificia Universidad Javeriana, Bogotá 110211, Colombia; (L.R.); (C.U.); (P.L.); (C.A.)
| | - Cindy Arévalo
- Grupo de Inmunobiología y Biología Celular, Pontificia Universidad Javeriana, Bogotá 110211, Colombia; (L.R.); (C.U.); (P.L.); (C.A.)
| | - Mónica P. Cala
- Metabolomics Core Facility—MetCore, Vicepresidency for Research, Universidad de Los Andes, Bogotá 111711, Colombia;
| | - Susana Fiorentino
- Grupo de Inmunobiología y Biología Celular, Pontificia Universidad Javeriana, Bogotá 110211, Colombia; (L.R.); (C.U.); (P.L.); (C.A.)
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6
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Ju Y, Zhang H, Jiang Y, Wang W, Kan G, Yu K, Wang X, Liu J, Jiang J. Aqueous microdroplets promote C-C bond formation and sequences in the reverse tricarboxylic acid cycle. Nat Ecol Evol 2023; 7:1892-1902. [PMID: 37679455 DOI: 10.1038/s41559-023-02193-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 08/08/2023] [Indexed: 09/09/2023]
Abstract
The reverse tricarboxylic acid cycle (rTCA) is a central anabolic network that uses carbon dioxide (CO2) and may have provided complex carbon substrates for life before the advent of RNA or enzymes. However, non-enzymatic promotion of the rTCA cycle, in particular carbon fixation, remains challenging, even with primordial metal catalysis. Here, we report that the fixation of CO2 by reductive carboxylation of succinate and α-ketoglutarate was achieved in aqueous microdroplets under ambient conditions without the use of catalysts. Under identical conditions, the aqueous microdroplets also facilitated the sequences in the rTCA cycle, including reduction, hydration, dehydration and retro-aldol cleavage and linked with the glyoxylate cycle. These reactions of the rTCA cycle were compatible with the aqueous microdroplets, as demonstrated with two-reaction and four-reaction sequences. A higher selectivity giving higher product yields was also observed. Our results suggest that the microdroplets provide an energetically favourable microenvironment and facilitate a non-enzymatic version of the rTCA cycle in prebiotic carbon anabolism.
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Affiliation(s)
- Yun Ju
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, PR China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, PR China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, PR China
| | - Hong Zhang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, PR China.
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, PR China.
| | - Yanxiao Jiang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, PR China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, PR China
| | - Wenxin Wang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, PR China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, PR China
| | - Guangfeng Kan
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, PR China
| | - Kai Yu
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, PR China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, PR China
| | - Xiaofei Wang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, PR China
| | - Jilin Liu
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, PR China
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, PR China
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, PR China
| | - Jie Jiang
- School of Marine Science and Technology, Harbin Institute of Technology at Weihai, Weihai, PR China.
- State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, PR China.
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, PR China.
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7
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Ernst L, Barayeu U, Hädeler J, Dick TP, Klatt JM, Keppler F, Rebelein JG. Methane formation driven by light and heat prior to the origin of life and beyond. Nat Commun 2023; 14:4364. [PMID: 37528079 PMCID: PMC10394037 DOI: 10.1038/s41467-023-39917-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 07/03/2023] [Indexed: 08/03/2023] Open
Abstract
Methane is a potent greenhouse gas, which likely enabled the evolution of life by keeping the early Earth warm. Here, we demonstrate routes towards abiotic methane and ethane formation under early-earth conditions from methylated sulfur and nitrogen compounds with prebiotic origin. These compounds are demethylated in Fenton reactions governed by ferrous iron and reactive oxygen species (ROS) produced by light and heat in aqueous environments. After the emergence of life, this phenomenon would have greatly intensified in the anoxic Archean by providing methylated sulfur and nitrogen substrates. This ROS-driven Fenton chemistry can occur delocalized from serpentinization across Earth's humid realm and thereby substantially differs from previously suggested methane formation routes that are spatially restricted. Here, we report that Fenton reactions driven by light and heat release methane and ethane and might have shaped the chemical evolution of the atmosphere prior to the origin of life and beyond.
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Affiliation(s)
- Leonard Ernst
- Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.
- Center for Synthetic Microbiology (SYNMIKRO), 35032, Marburg, Germany.
| | - Uladzimir Barayeu
- Division of Redox Regulation, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Jonas Hädeler
- Institute of Earth Sciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Tobias P Dick
- Division of Redox Regulation, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Judith M Klatt
- Center for Synthetic Microbiology (SYNMIKRO), 35032, Marburg, Germany
- Microcosm Earth Center, Max Planck Institute for Terrestrial Microbiology & Philipps University Marburg, 35032, Marburg, Germany
- Biogeochemistry Group, Department for Chemistry, Philipps University Marburg, 35032, Marburg, Germany
| | - Frank Keppler
- Institute of Earth Sciences, Heidelberg University, 69120, Heidelberg, Germany
- Heidelberg Center for the Environment HCE, Heidelberg University, 69120, Heidelberg, Germany
| | - Johannes G Rebelein
- Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany.
- Center for Synthetic Microbiology (SYNMIKRO), 35032, Marburg, Germany.
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8
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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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Fontecilla-Camps JC. Reflections on the Origin and Early Evolution of the Genetic Code. Chembiochem 2023; 24:e202300048. [PMID: 37052530 DOI: 10.1002/cbic.202300048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/01/2023] [Indexed: 04/14/2023]
Abstract
Examination of the genetic code (GeCo) reveals that amino acids coded by (A/U) codons display a large functional spectrum and bind RNA whereas, except for Arg, those coded by (G/C) codons do not. From a stereochemical viewpoint, the clear preference for (A/U)-rich codons to be located at the GeCo half blocks suggests they were specifically determined. Conversely, the overall lower affinity of cognate amino acids for their (G/C)-rich anticodons points to their late arrival to the GeCo. It is proposed that i) initially the code was composed of the eight (A/U) codons; ii) these codons were duplicated when G/C nucleotides were added to their wobble positions, and three new codons with G/C in their first position were incorporated; and iii) a combination of A/U and G/C nucleotides progressively generated the remaining codons.
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10
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Xenotopic expression of alternative oxidase (AOX) to study mechanisms of mitochondrial disease. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148947. [PMID: 36481273 DOI: 10.1016/j.bbabio.2022.148947] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/17/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022]
Abstract
The mitochondrial respiratory chain or electron transport chain (ETC) facilitates redox reactions which ultimately lead to the reduction of oxygen to water (respiration). Energy released by this process is used to establish a proton electrochemical gradient which drives ATP formation (oxidative phosphorylation, OXPHOS). It also plays an important role in vital processes beyond ATP formation and cellular metabolism, such as heat production, redox and ion homeostasis. Dysfunction of the ETC can thus impair cellular and organismal viability and is thought to be the underlying cause of a heterogeneous group of so-called mitochondrial diseases. Plants, yeasts, and many lower organisms, but not insects and vertebrates, possess an enzymatic mechanism that confers resistance to respiratory stress conditions, i.e., the alternative oxidase (AOX). Even in cells that naturally lack AOX, it is autonomously imported into the mitochondrial compartment upon xenotopic expression, where it refolds and becomes catalytically engaged when the cytochrome segment of the ETC is blocked. AOX was therefore proposed as a tool to study disease etiologies. To this end, AOX has been xenotopically expressed in mammalian cells and disease models of the fruit fly and mouse. Surprisingly, AOX showed remarkable rescue effects in some cases, whilst in others it had no effect or even exacerbated a condition. Here we summarize what has been learnt from the use of AOX in various disease models and discuss issues which still need to be addressed in order to understand the role of the ETC in health and disease.
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11
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Self-Similar Patterns from Abiotic Decarboxylation Metabolism through Chemically Oscillating Reactions: A Prebiotic Model for the Origin of Life. Life (Basel) 2023; 13:life13020551. [PMID: 36836908 PMCID: PMC9960873 DOI: 10.3390/life13020551] [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: 11/26/2022] [Revised: 02/03/2023] [Accepted: 02/11/2023] [Indexed: 02/18/2023] Open
Abstract
The origin of life must have included an abiotic stage of carbon redox reactions that involved electron transport chains and the production of lifelike patterns. Chemically oscillating reactions (COR) are abiotic, spontaneous, out-of-equilibrium, and redox reactions that involve the decarboxylation of carboxylic acids with strong oxidants and strong acids to produce CO2 and characteristic self-similar patterns. Those patterns have circular concentricity, radial geometries, characteristic circular twins, colour gradients, cavity structures, and branching to parallel alignment. We propose that COR played a role during the prebiotic cycling of carboxylic acids, furthering the new model for geology where COR can also explain the patterns of diagenetic spheroids in sediments. The patterns of COR in Petri dishes are first considered and compared to those observed in some eukaryotic lifeforms. The molecular structures and functions of reactants in COR are then compared to key biological metabolic processes. We conclude that the newly recognised similarities in compositions and patterns warrant future research to better investigate the role of halogens in biochemistry; COR in life-forms, including in humans; and the COR-stage of prebiotic carbon cycling on other planets, such as Mars.
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12
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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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13
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Arnold PK, Finley LWS. Regulation and function of the mammalian tricarboxylic acid cycle. J Biol Chem 2023; 299:102838. [PMID: 36581208 PMCID: PMC9871338 DOI: 10.1016/j.jbc.2022.102838] [Citation(s) in RCA: 77] [Impact Index Per Article: 77.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 12/27/2022] Open
Abstract
The tricarboxylic acid (TCA) cycle, otherwise known as the Krebs cycle, is a central metabolic pathway that performs the essential function of oxidizing nutrients to support cellular bioenergetics. More recently, it has become evident that TCA cycle behavior is dynamic, and products of the TCA cycle can be co-opted in cancer and other pathologic states. In this review, we revisit the TCA cycle, including its potential origins and the history of its discovery. We provide a detailed accounting of the requirements for sustained TCA cycle function and the critical regulatory nodes that can stimulate or constrain TCA cycle activity. We also discuss recent advances in our understanding of the flexibility of TCA cycle wiring and the increasingly appreciated heterogeneity in TCA cycle activity exhibited by mammalian cells. Deeper insight into how the TCA cycle can be differentially regulated and, consequently, configured in different contexts will shed light on how this pathway is primed to meet the requirements of distinct mammalian cell states.
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Affiliation(s)
- Paige K Arnold
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA; Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Lydia W S Finley
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA.
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14
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Rauscher SA, Moran J. Hydrogen Drives Part of the Reverse Krebs Cycle under Metal or Meteorite Catalysis. Angew Chem Int Ed Engl 2022; 61:e202212932. [PMID: 36251920 PMCID: PMC10100321 DOI: 10.1002/anie.202212932] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Indexed: 11/24/2022]
Abstract
Hydrogen (H2 ) is a geological source of reducing electrons that is thought to have powered the metabolism of the last universal common ancestor to all extant life, and that is still metabolized by various modern organisms. It has been suggested that H2 drove a geochemical analogue of some or all of the reverse Krebs cycle at the emergence of the metabolic network, catalyzed by metals, but this has yet to be demonstrated experimentally. Herein, we show that three consecutive steps of the reverse Krebs cycle, converting oxaloacetate into succinate, can be driven without enzymes and in one-pot by H2 as the reducing agent under mild conditions compatible with biological chemistry. Low catalytic amounts of nickel (10-20 mol %) or platinum group metals (0.1-1 mol %) or even small amounts of ground meteorites were found to promote the reductive chemistry at temperatures between 5 and 60 °C and over a wide pH range, including pH 7. These results lend additional support to the hypothesis that geologically produced hydrogen and metal catalysts could have initiated early metabolic networks.
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Affiliation(s)
- Sophia A Rauscher
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), CNRS UMR 7006, University of Strasbourg, 8 Allée Gaspard Monge, 67000, Strasbourg, France
| | - Joseph Moran
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), CNRS UMR 7006, University of Strasbourg, 8 Allée Gaspard Monge, 67000, Strasbourg, France.,Institut Universitaire de France (IUF), France
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15
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Nunes Palmeira R, Colnaghi M, Harrison SA, Pomiankowski A, Lane N. The limits of metabolic heredity in protocells. Proc Biol Sci 2022; 289:20221469. [PMID: 36350219 PMCID: PMC9653231 DOI: 10.1098/rspb.2022.1469] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The universal core of metabolism could have emerged from thermodynamically favoured prebiotic pathways at the origin of life. Starting with H
2
and CO
2
, the synthesis of amino acids and mixed fatty acids, which self-assemble into protocells, is favoured under warm anoxic conditions. Here, we address whether it is possible for protocells to evolve greater metabolic complexity, through positive feedbacks involving nucleotide catalysis. Using mathematical simulations to model metabolic heredity in protocells, based on branch points in protometabolic flux, we show that nucleotide catalysis can indeed promote protocell growth. This outcome only occurs when nucleotides directly catalyse CO
2
fixation. Strong nucleotide catalysis of other pathways (e.g. fatty acids and amino acids) generally unbalances metabolism and slows down protocell growth, and when there is competition between catalytic functions cell growth collapses. Autocatalysis of nucleotide synthesis can promote growth but only if nucleotides also catalyse CO
2
fixation; autocatalysis alone leads to the accumulation of nucleotides at the expense of CO
2
fixation and protocell growth rate. Our findings offer a new framework for the emergence of greater metabolic complexity, in which nucleotides catalyse broad-spectrum processes such as CO
2
fixation, hydrogenation and phosphorylation important to the emergence of genetic heredity at the origin of life.
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Affiliation(s)
- Raquel Nunes Palmeira
- Department of Computer Science, Engineering Building, Malet Place, University College London, WC1E 7JG, UK
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Marco Colnaghi
- Department of Computer Science, Engineering Building, Malet Place, University College London, WC1E 7JG, UK
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Stuart A. Harrison
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Andrew Pomiankowski
- Department of Computer Science, Engineering Building, Malet Place, University College London, WC1E 7JG, UK
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Nick Lane
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
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16
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Medina MÁ, García-Ponce ÁL, Blanco-López Á, Quesada AR, Urdiales JL, Fajardo I, Suárez F, Alonso-Carrión FJ. Turning around Cycles: An Approach Based on Selected Problems/Cases to Stimulate Collaborative Learning about Krebs and His Four Metabolic Cycles. JOURNAL OF CHEMICAL EDUCATION 2022; 99:2270-2276. [PMID: 35722632 PMCID: PMC9202563 DOI: 10.1021/acs.jchemed.1c01038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 04/18/2022] [Indexed: 06/15/2023]
Abstract
Metabolism is a challenging subject for bioscience students due to the intrinsic complexity of the metabolic network, as well as that of the overlapping mechanisms of metabolic regulation. Collaborative learning based on a problem-based learning approach can help students to successfully learn and understand metabolism. In the present article, we propose a selection of exercises, problems, and cases aimed to focus students' attention on the scientific work made by Sir Hans Krebs and his collaborators to elucidate four main metabolic cycles, as well as on the study of these cycles, their regulation, and their metabolic integration. The objectives, the tools, and the implementation of this proposal are described, and the results obtained during its first implementation with volunteer students enrolled in two courses on metabolic regulation at our university are presented and discussed. These volunteer students signed a learning contract and were randomly distributed in small groups (3-4 students each). Application of this collaborative learning activity to our classrooms has been very satisfactory, as evidenced by an improvement in the volunteers' academic performance and a very positive perception by most of them, who declared to be "very satisfied" or "satisfied" with their experience and felt that they had learned more.
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Affiliation(s)
- Miguel Ángel Medina
- Department
of Molecular Biology and Biochemistry, Universidad
de Málaga, Andalucía Tech, 29016 Málaga, Spain
| | - Ángel Luis García-Ponce
- Department
of Mathematics Education, Social Sciences Education, and Sciences
Education, Universidad de Málaga,
Andalucía Tech, 29016 Málaga, Spain
| | - Ángel Blanco-López
- Department
of Mathematics Education, Social Sciences Education, and Sciences
Education, Universidad de Málaga,
Andalucía Tech, 29016 Málaga, Spain
| | - Ana R. Quesada
- Department
of Molecular Biology and Biochemistry, Universidad
de Málaga, Andalucía Tech, 29016 Málaga, Spain
| | - José Luis Urdiales
- Department
of Molecular Biology and Biochemistry, Universidad
de Málaga, Andalucía Tech, 29016 Málaga, Spain
| | - Ignacio Fajardo
- Department
of Molecular Biology and Biochemistry, Universidad
de Málaga, Andalucía Tech, 29016 Málaga, Spain
| | - Fernanda Suárez
- Department
of Molecular Biology and Biochemistry, Universidad
de Málaga, Andalucía Tech, 29016 Málaga, Spain
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17
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Koper K, Han SW, Pastor DC, Yoshikuni Y, Maeda HA. Evolutionary Origin and Functional Diversification of Aminotransferases. J Biol Chem 2022; 298:102122. [PMID: 35697072 PMCID: PMC9309667 DOI: 10.1016/j.jbc.2022.102122] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 11/30/2022] Open
Abstract
Aminotransferases (ATs) are pyridoxal 5′-phosphate–dependent enzymes that catalyze the transamination reactions between amino acid donor and keto acid acceptor substrates. Modern AT enzymes constitute ∼2% of all classified enzymatic activities, play central roles in nitrogen metabolism, and generate multitude of primary and secondary metabolites. ATs likely diverged into four distinct AT classes before the appearance of the last universal common ancestor and further expanded to a large and diverse enzyme family. Although the AT family underwent an extensive functional specialization, many AT enzymes retained considerable substrate promiscuity and multifunctionality because of their inherent mechanistic, structural, and functional constraints. This review summarizes the evolutionary history, diverse metabolic roles, reaction mechanisms, and structure–function relationships of the AT family enzymes, with a special emphasis on their substrate promiscuity and multifunctionality. Comprehensive characterization of AT substrate specificity is still needed to reveal their true metabolic functions in interconnecting various branches of the nitrogen metabolic network in different organisms.
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Affiliation(s)
- Kaan Koper
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Sang-Woo Han
- The US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Yasuo Yoshikuni
- The US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Global Center for Food, Land, and Water Resources, Research Faculty of Agriculture, Hokkaido University, Hokkaido 060-8589, Japan
| | - Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA
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18
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Iacometti C, Marx K, Hönick M, Biletskaia V, Schulz-Mirbach H, Dronsella B, Satanowski A, Delmas VA, Berger A, Dubois I, Bouzon M, Döring V, Noor E, Bar-Even A, Lindner SN. Activating Silent Glycolysis Bypasses in Escherichia coli. BIODESIGN RESEARCH 2022; 2022:9859643. [PMID: 37850128 PMCID: PMC10521649 DOI: 10.34133/2022/9859643] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 04/08/2022] [Indexed: 10/19/2023] Open
Abstract
All living organisms share similar reactions within their central metabolism to provide precursors for all essential building blocks and reducing power. To identify whether alternative metabolic routes of glycolysis can operate in E. coli, we complementarily employed in silico design, rational engineering, and adaptive laboratory evolution. First, we used a genome-scale model and identified two potential pathways within the metabolic network of this organism replacing canonical Embden-Meyerhof-Parnas (EMP) glycolysis to convert phosphosugars into organic acids. One of these glycolytic routes proceeds via methylglyoxal and the other via serine biosynthesis and degradation. Then, we implemented both pathways in E. coli strains harboring defective EMP glycolysis. Surprisingly, the pathway via methylglyoxal seemed to immediately operate in a triosephosphate isomerase deletion strain cultivated on glycerol. By contrast, in a phosphoglycerate kinase deletion strain, the overexpression of methylglyoxal synthase was necessary to restore growth of the strain. Furthermore, we engineered the "serine shunt" which converts 3-phosphoglycerate via serine biosynthesis and degradation to pyruvate, bypassing an enolase deletion. Finally, to explore which of these alternatives would emerge by natural selection, we performed an adaptive laboratory evolution study using an enolase deletion strain. Our experiments suggest that the evolved mutants use the serine shunt. Our study reveals the flexible repurposing of metabolic pathways to create new metabolite links and rewire central metabolism.
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Affiliation(s)
- Camillo Iacometti
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Katharina Marx
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Maria Hönick
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Viktoria Biletskaia
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Helena Schulz-Mirbach
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Beau Dronsella
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Ari Satanowski
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Valérie A. Delmas
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry-Courcouronne, France
| | - Anne Berger
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry-Courcouronne, France
| | - Ivan Dubois
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry-Courcouronne, France
| | - Madeleine Bouzon
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry-Courcouronne, France
| | - Volker Döring
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry-Courcouronne, France
| | - Elad Noor
- Institute of Molecular Systems Biology, ETH Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Steffen N. Lindner
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Department of Biochemistry, Charité Universitätsmedizin, Virchowweg 6, 10117 Berlin, Germany
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19
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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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20
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Cyanide as a primordial reductant enables a protometabolic reductive glyoxylate pathway. Nat Chem 2022; 14:170-178. [PMID: 35115655 DOI: 10.1038/s41557-021-00878-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 12/14/2021] [Indexed: 11/08/2022]
Abstract
Investigation of prebiotic metabolic pathways is predominantly based on abiotically replicating the reductive citric acid cycle. While attractive from a parsimony point of view, attempts using metal/mineral-mediated reductions have produced complex mixtures with inefficient and uncontrolled reactions. Here we show that cyanide acts as a mild and efficient reducing agent mediating abiotic transformations of tricarboxylic acid intermediates and derivatives. The hydrolysis of the cyanide adducts followed by their decarboxylation enables the reduction of oxaloacetate to malate and of fumarate to succinate, whereas pyruvate and α-ketoglutarate themselves are not reduced. In the presence of glyoxylate, malonate and malononitrile, alternative pathways emerge that bypass the challenging reductive carboxylation steps to produce metabolic intermediates and compounds found in meteorites. These results suggest a simpler prebiotic forerunner of today's metabolism, involving a reductive glyoxylate pathway without oxaloacetate and α-ketoglutarate-implying that the extant metabolic reductive carboxylation chemistries are an evolutionary invention mediated by complex metalloproteins.
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21
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Carbon dioxide photoreduction in prebiotic environments. Photochem Photobiol Sci 2022; 21:863-878. [PMID: 35107790 DOI: 10.1007/s43630-021-00168-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/27/2021] [Indexed: 10/19/2022]
Abstract
The reduction of carbon dioxide is one of the hottest topics due to the concern of global warming. Carbon dioxide reduction is also an essential step for life's origins as photoautotrophs arose soon after Earth formation. Both the topics are of high general interest, and possibly, there could be a fruitful cross-fertilization of the two fields. Herein, we selected and collected papers related to photoreduction of carbon dioxide using compounds easily available on the Earth and considered of prebiotic relevance. This work might be useful also to scientists interested in carbon dioxide photoreduction and/or to have an overview of the techniques available.
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22
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Computational Analysis of a Prebiotic Amino Acid Synthesis with Reference to Extant Codon-Amino Acid Relationships. Life (Basel) 2021; 11:life11121343. [PMID: 34947874 PMCID: PMC8707928 DOI: 10.3390/life11121343] [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: 10/29/2021] [Revised: 11/26/2021] [Accepted: 11/30/2021] [Indexed: 11/28/2022] Open
Abstract
Novel density functional theory calculations are presented regarding a mechanism for prebiotic amino acid synthesis from alpha-keto acids that was suggested to happen via catalysis by dinucleotide species. Our results were analysed with comparison to the original hypothesis (Copley et al., PNAS, 2005, 102, 4442–4447). It was shown that the keto acid–dinucleotide hypothesis for possible prebiotic amino acid synthesis was plausible based on an initial computational analysis, and details of the structures for the intermediates and transition states showed that there was wide scope for interactions between the keto acid and dinucleotide moieties that could affect the free energy profiles and lead to the required proto-metabolic selectivity.
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23
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Piedrafita G, Varma SJ, Castro C, Messner CB, Szyrwiel L, Griffin JL, Ralser M. Cysteine and iron accelerate the formation of ribose-5-phosphate, providing insights into the evolutionary origins of the metabolic network structure. PLoS Biol 2021; 19:e3001468. [PMID: 34860829 PMCID: PMC8673631 DOI: 10.1371/journal.pbio.3001468] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 12/15/2021] [Accepted: 11/04/2021] [Indexed: 12/21/2022] Open
Abstract
The structure of the metabolic network is highly conserved, but we know little about its evolutionary origins. Key for explaining the early evolution of metabolism is solving a chicken–egg dilemma, which describes that enzymes are made from the very same molecules they produce. The recent discovery of several nonenzymatic reaction sequences that topologically resemble central metabolism has provided experimental support for a “metabolism first” theory, in which at least part of the extant metabolic network emerged on the basis of nonenzymatic reactions. But how could evolution kick-start on the basis of a metal catalyzed reaction sequence, and how could the structure of nonenzymatic reaction sequences be imprinted on the metabolic network to remain conserved for billions of years? We performed an in vitro screening where we add the simplest components of metabolic enzymes, proteinogenic amino acids, to a nonenzymatic, iron-driven reaction network that resembles glycolysis and the pentose phosphate pathway (PPP). We observe that the presence of the amino acids enhanced several of the nonenzymatic reactions. Particular attention was triggered by a reaction that resembles a rate-limiting step in the oxidative PPP. A prebiotically available, proteinogenic amino acid cysteine accelerated the formation of RNA nucleoside precursor ribose-5-phosphate from 6-phosphogluconate. We report that iron and cysteine interact and have additive effects on the reaction rate so that ribose-5-phosphate forms at high specificity under mild, metabolism typical temperature and environmental conditions. We speculate that accelerating effects of amino acids on rate-limiting nonenzymatic reactions could have facilitated a stepwise enzymatization of nonenzymatic reaction sequences, imprinting their structure on the evolving metabolic network. The evolutionary origins of metabolism are largely unknown. This study shows that the prebiotically available proteinogenic amino acid cysteine can promote the metabolism-like rate-limiting formation of ribose-5-phosphate, suggesting that early metabolic pathways could have emerged thought the stepwise enzymatization of non-enzymatic reaction sequences.
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Affiliation(s)
- Gabriel Piedrafita
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, United Kingdom
| | - Sreejith J. Varma
- Department of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Cecilia Castro
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, United Kingdom
| | - Christoph B. Messner
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Lukasz Szyrwiel
- Department of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Julian L. Griffin
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, United Kingdom
- The Rowett Institute, The University of Aberdeen, Aberdeen, United Kingdom
| | - Markus Ralser
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, United Kingdom
- Department of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, United Kingdom
- * E-mail:
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24
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Kang W, Suzuki M, Saito T, Miyado K. Emerging Role of TCA Cycle-Related Enzymes in Human Diseases. Int J Mol Sci 2021; 22:13057. [PMID: 34884868 PMCID: PMC8657694 DOI: 10.3390/ijms222313057] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/27/2021] [Accepted: 11/30/2021] [Indexed: 02/03/2023] Open
Abstract
The tricarboxylic acid (TCA) cycle is the main source of cellular energy and participates in many metabolic pathways in cells. Recent reports indicate that dysfunction of TCA cycle-related enzymes causes human diseases, such as neurometabolic disorders and tumors, have attracted increasing interest in their unexplained roles. The diseases which develop as a consequence of loss or dysfunction of TCA cycle-related enzymes are distinct, suggesting that each enzyme has a unique function. This review aims to provide a comprehensive overview of the relationship between each TCA cycle-related enzyme and human diseases. We also discuss their functions in the context of both mitochondrial and extra-mitochondrial (or cytoplasmic) enzymes.
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Affiliation(s)
- Woojin Kang
- Department of Reproductive Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan; (M.S.); (K.M.)
| | - Miki Suzuki
- Department of Reproductive Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan; (M.S.); (K.M.)
| | - Takako Saito
- Department of Applied Life Sciences, Faculty of Agriculture, Shizuoka University, Shizuoka 422-8529, Japan;
| | - Kenji Miyado
- Department of Reproductive Biology, National Research Institute for Child Health and Development, Tokyo 157-8535, Japan; (M.S.); (K.M.)
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25
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Vincent L, Colón-Santos S, Cleaves HJ, Baum DA, Maurer SE. The Prebiotic Kitchen: A Guide to Composing Prebiotic Soup Recipes to Test Origins of Life Hypotheses. Life (Basel) 2021; 11:life11111221. [PMID: 34833097 PMCID: PMC8618940 DOI: 10.3390/life11111221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/14/2021] [Accepted: 10/30/2021] [Indexed: 01/20/2023] Open
Abstract
“Prebiotic soup” often features in discussions of origins of life research, both as a theoretical concept when discussing abiological pathways to modern biochemical building blocks and, more recently, as a feedstock in prebiotic chemistry experiments focused on discovering emergent, systems-level processes such as polymerization, encapsulation, and evolution. However, until now, little systematic analysis has gone into the design of well-justified prebiotic mixtures, which are needed to facilitate experimental replicability and comparison among researchers. This paper explores principles that should be considered in choosing chemical mixtures for prebiotic chemistry experiments by reviewing the natural environmental conditions that might have created such mixtures and then suggests reasonable guidelines for designing recipes. We discuss both “assembled” mixtures, which are made by mixing reagent grade chemicals, and “synthesized” mixtures, which are generated directly from diversity-generating primary prebiotic syntheses. We discuss different practical concerns including how to navigate the tremendous uncertainty in the chemistry of the early Earth and how to balance the desire for using prebiotically realistic mixtures with experimental tractability and replicability. Examples of two assembled mixtures, one based on materials likely delivered by carbonaceous meteorites and one based on spark discharge synthesis, are presented to illustrate these challenges. We explore alternative procedures for making synthesized mixtures using recursive chemical reaction systems whose outputs attempt to mimic atmospheric and geochemical synthesis. Other experimental conditions such as pH and ionic strength are also considered. We argue that developing a handful of standardized prebiotic recipes may facilitate coordination among researchers and enable the identification of the most promising mechanisms by which complex prebiotic mixtures were “tamed” during the origin of life to give rise to key living processes such as self-propagation, information processing, and adaptive evolution. We end by advocating for the development of a public prebiotic chemistry database containing experimental methods (including soup recipes), results, and analytical pipelines for analyzing complex prebiotic mixtures.
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Affiliation(s)
- Lena Vincent
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA; (L.V.); (S.C.-S.)
| | - Stephanie Colón-Santos
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA; (L.V.); (S.C.-S.)
| | - H. James Cleaves
- Earth and Planets Laboratory, The Carnegie Institution for Science, Washington, DC 20015, USA;
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Blue Marble Space Institute for Science, Seattle, WA 97154, USA
| | - David A. Baum
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA; (L.V.); (S.C.-S.)
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53705, USA
- Correspondence: (D.A.B.); (S.E.M.)
| | - Sarah E. Maurer
- Department of Chemistry and Biochemistry, Central Connecticut State University, New Britain, CT 06050, USA
- Correspondence: (D.A.B.); (S.E.M.)
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26
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Abstract
Tremendous chemical diversity is the hallmark of plants and is supported by highly complex biochemical machinery. Plant metabolic enzymes originated and were transferred from eukaryotic and prokaryotic ancestors and further diversified by the unprecedented rates of gene duplication and functionalization experienced in land plants. Unlike microbes, which have frequent horizontal gene transfer events and multiple inputs of energy and organic carbon, land plants predominantly rely on organic carbon generated from CO2 and have experienced very few, if any, gene transfers during their recent evolutionary history. As such, plant metabolic networks have evolved in a stepwise manner and on existing networks under various evolutionary constraints. This review aims to take a broader view of plant metabolic evolution and lay a framework to further explore evolutionary mechanisms of the complex metabolic network. Understanding the underlying metabolic and genetic constraints is also an empirical prerequisite for rational engineering and redesigning of plant metabolic pathways.
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Affiliation(s)
- Hiroshi A Maeda
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA;
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany;
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27
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Legnani L, Darù A, Jones AX, Blackmond DG. Mechanistic Insight into the Origin of Stereoselectivity in the Ribose-Mediated Strecker Synthesis of Alanine. J Am Chem Soc 2021; 143:7852-7858. [PMID: 33979125 DOI: 10.1021/jacs.1c03552] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enantioenriched amino acids are produced in a hydrolytic kinetic resolution of racemic aminonitriles mediated by chiral pentose sugars. Experimental kinetic and spectroscopic results combined with DFT computational studies and microkinetic modeling help to identify the nature of the intermediate species and provide insight into the stereoselectivity of their hydrolysis in the prebiotically relevant ribose-alanine system. These studies support a synergistic role for sugars and amino acids in the emergence of homochirality in biological molecules.
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Affiliation(s)
- Luca Legnani
- Department of Chemistry, Scripps Research, La Jolla, California 92037, United States
| | - Andrea Darù
- Department of Chemistry, Scripps Research, La Jolla, California 92037, United States
| | - Alexander X Jones
- Department of Chemistry, Scripps Research, La Jolla, California 92037, United States
| | - Donna G Blackmond
- Department of Chemistry, Scripps Research, La Jolla, California 92037, United States
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28
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Freire MÁ. Phosphorylation and acylation transfer reactions: Clues to a dual origin of metabolism. Biosystems 2020; 198:104260. [PMID: 32987142 DOI: 10.1016/j.biosystems.2020.104260] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/23/2020] [Accepted: 09/23/2020] [Indexed: 12/22/2022]
Abstract
Many theories of the origin of life focus on only one primitive polymer as an archetype of a world paradigm. However, life would have emerged within more complex scenarios where a variety of molecules and diverse polymers interconnected by a few similar chemical reactions. Previous work suggested that the ancestors of all major biopolymers would have arisen from abiotic template independent replication processes. They would have been organized in two closed sets of polymerization cycles: polysaccharides, polyribonucleotides and polyphosphates on one site; and peptides, fatty acids and polyhydroxyalkanoates on the other site. Then, these polymerization reaction cycles integrated into a minimal organization closure. Here, the purpose was to explore which kind of reactions could have supported the chemical networks that led to the early (bio)polymers. As a result, the proposed overview suggests that phosphorylation and acylation transfer reactions would have arisen independently and forged two distinct chemical systems that provided the phosphorylated and carboxylated intermediates used for the synthesis of the corresponding polymers. In this sense, modern metabolism may still reflect its dual nature, probably relying on these two reaction networks from the beginnings.
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Affiliation(s)
- Miguel Ángel Freire
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET, Universidad Nacional de Córdoba (UNC). Facultad de Ciencias Exactas, Físicas y Naturales. Av. Vélez Sarsfield 299, CC 495, 5000, Córdoba, Argentina.
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29
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A way to thioacetate esters compatible with non-oxidative prebiotic conditions. Sci Rep 2020; 10:14488. [PMID: 32879403 PMCID: PMC7467925 DOI: 10.1038/s41598-020-71524-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 08/17/2020] [Indexed: 11/22/2022] Open
Abstract
The centrality of pyruvate oxidative decarboxylation into acetyl-CoA in current biochemistry is a strong argument for proposing that a similar reaction have been necessary for the development of an effective protometabolism on the primitive Earth. However, such a decarboxylation requires the use of an oxidant and a catalyst, today enzymatic. Based on the mechanisms of the pyruvate dehydrogenase complex and pyruvate-ferredoxin oxidoreductase, we propose that the initial mechanism involved disulfides and occurred via radicals. A first disulfide is obtained by reacting glyoxylate with hydrogen sulfide. It is then possible to produce a wide variety of other disulfides by exchange reactions. When reacted with pyruvate under UV light they give thioesters. This process requires no oxidant and is therefore compatible with what is known of the redox conditions of the early Earth. Neither does it require any catalyst. It could be the first way to acetyl thioesters, a way that was later improved by the introduction of catalysts, first minerals, then enzymes.
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30
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van Gastel N, Spinelli JB, Sharda A, Schajnovitz A, Baryawno N, Rhee C, Oki T, Grace E, Soled HJ, Milosevic J, Sykes DB, Hsu PP, Vander Heiden MG, Vidoudez C, Trauger SA, Haigis MC, Scadden DT. Induction of a Timed Metabolic Collapse to Overcome Cancer Chemoresistance. Cell Metab 2020; 32:391-403.e6. [PMID: 32763164 PMCID: PMC8397232 DOI: 10.1016/j.cmet.2020.07.009] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 05/26/2020] [Accepted: 07/15/2020] [Indexed: 12/11/2022]
Abstract
Cancer relapse begins when malignant cells pass through the extreme metabolic bottleneck of stress from chemotherapy and the byproducts of the massive cell death in the surrounding region. In acute myeloid leukemia, complete remissions are common, but few are cured. We tracked leukemia cells in vivo, defined the moment of maximal response following chemotherapy, captured persisting cells, and conducted unbiased metabolomics, revealing a metabolite profile distinct from the pre-chemo growth or post-chemo relapse phase. Persisting cells used glutamine in a distinctive manner, preferentially fueling pyrimidine and glutathione generation, but not the mitochondrial tricarboxylic acid cycle. Notably, malignant cell pyrimidine synthesis also required aspartate provided by specific bone marrow stromal cells. Blunting glutamine metabolism or pyrimidine synthesis selected against residual leukemia-initiating cells and improved survival in leukemia mouse models and patient-derived xenografts. We propose that timed cell-intrinsic or niche-focused metabolic disruption can exploit a transient vulnerability and induce metabolic collapse in cancer cells to overcome chemoresistance.
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Affiliation(s)
- Nick van Gastel
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jessica B Spinelli
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Azeem Sharda
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Amir Schajnovitz
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Ninib Baryawno
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Stockholm 17177, Sweden
| | - Catherine Rhee
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Toshihiko Oki
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Eliane Grace
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Heather J Soled
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Jelena Milosevic
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - David B Sykes
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Peggy P Hsu
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Dana-Farber Cancer Institute, Boston, MA 02115, USA; Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Charles Vidoudez
- FAS Small Molecule Mass Spectrometry Facility, Harvard University, Cambridge, MA 02138, USA
| | - Sunia A Trauger
- FAS Small Molecule Mass Spectrometry Facility, Harvard University, Cambridge, MA 02138, USA
| | - Marcia C Haigis
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - David T Scadden
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.
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31
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Muchowska KB, Varma SJ, Moran J. Nonenzymatic Metabolic Reactions and Life's Origins. Chem Rev 2020; 120:7708-7744. [PMID: 32687326 DOI: 10.1021/acs.chemrev.0c00191] [Citation(s) in RCA: 123] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Prebiotic chemistry aims to explain how the biochemistry of life as we know it came to be. Most efforts in this area have focused on provisioning compounds of importance to life by multistep synthetic routes that do not resemble biochemistry. However, gaining insight into why core metabolism uses the molecules, reactions, pathways, and overall organization that it does requires us to consider molecules not only as synthetic end goals. Equally important are the dynamic processes that build them up and break them down. This perspective has led many researchers to the hypothesis that the first stage of the origin of life began with the onset of a primitive nonenzymatic version of metabolism, initially catalyzed by naturally occurring minerals and metal ions. This view of life's origins has come to be known as "metabolism first". Continuity with modern metabolism would require a primitive version of metabolism to build and break down ketoacids, sugars, amino acids, and ribonucleotides in much the same way as the pathways that do it today. This review discusses metabolic pathways of relevance to the origin of life in a manner accessible to chemists, and summarizes experiments suggesting several pathways might have their roots in prebiotic chemistry. Finally, key remaining milestones for the protometabolic hypothesis are highlighted.
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Affiliation(s)
| | - Sreejith J Varma
- University of Strasbourg, CNRS, ISIS UMR 7006, 67000 Strasbourg, France
| | - Joseph Moran
- University of Strasbourg, CNRS, ISIS UMR 7006, 67000 Strasbourg, France
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32
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A Possible Primordial Acetyleno/Carboxydotrophic Core Metabolism. Life (Basel) 2020; 10:life10040035. [PMID: 32272667 PMCID: PMC7235995 DOI: 10.3390/life10040035] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/03/2020] [Accepted: 04/04/2020] [Indexed: 12/04/2022] Open
Abstract
Carbon fixation, in addition to the evolution of metabolism, is a main requirement for the evolution of life. Here, we report a one-pot carbon fixation of acetylene (C2H2) and carbon monoxide (CO) by aqueous nickel sulfide (NiS) under hydrothermal (>100 °C) conditions. A slurry of precipitated NiS converts acetylene and carbon monoxide into a set of C2–4-products that are surprisingly representative for C2–4-segments of all four central CO2-fixation cycles of the domains Bacteria and Archaea, whereby some of the products engage in the same interconversions, as seen in the central CO2-fixation cycles. The results suggest a primordial, chemically predetermined, non-cyclic acetyleno/carboxydotrophic core metabolism. This metabolism is based on aqueous organo–metal chemistry, from which the extant central CO2-fixation cycles based on thioester chemistry would have evolved by piecemeal modifications.
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33
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Scossa F, Fernie AR. The evolution of metabolism: How to test evolutionary hypotheses at the genomic level. Comput Struct Biotechnol J 2020; 18:482-500. [PMID: 32180906 PMCID: PMC7063335 DOI: 10.1016/j.csbj.2020.02.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 02/12/2020] [Accepted: 02/13/2020] [Indexed: 01/21/2023] Open
Abstract
The origin of primordial metabolism and its expansion to form the metabolic networks extant today represent excellent systems to study the impact of natural selection and the potential adaptive role of novel compounds. Here we present the current hypotheses made on the origin of life and ancestral metabolism and present the theories and mechanisms by which the large chemical diversity of plants might have emerged along evolution. In particular, we provide a survey of statistical methods that can be used to detect signatures of selection at the gene and population level, and discuss potential and limits of these methods for investigating patterns of molecular adaptation in plant metabolism.
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Affiliation(s)
- Federico Scossa
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics (CREA-GB), Via Ardeatina 546, 00178 Rome, Italy
| | - Alisdair R. Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
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34
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Maltais TR, VanderVelde D, LaRowe DE, Goldman AD, Barge LM. Reactivity of Metabolic Intermediates and Cofactor Stability under Model Early Earth Conditions. ORIGINS LIFE EVOL B 2020; 50:35-55. [PMID: 31981046 DOI: 10.1007/s11084-019-09590-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 12/30/2019] [Indexed: 01/24/2023]
Abstract
Understanding the emergence of metabolic pathways is key to unraveling the factors that promoted the origin of life. One popular view is that protein cofactors acted as catalysts prior to the evolution of the protein enzymes with which they are now associated. We investigated the stability of acetyl coenzyme A (Acetyl Co-A, the group transfer cofactor in citric acid synthesis in the TCA cycle) under early Earth conditions, as well as whether Acetyl Co-A or its small molecule analogs thioacetate or acetate can catalyze the transfer of an acetyl group onto oxaloacetate in the absence of the citrate synthase enzyme. Several different temperatures, pH ranges, and compositions of aqueous environments were tested to simulate the Earth's early ocean and its possible components; the effect of these variables on oxaloacetate and cofactor chemistry were assessed under ambient and anoxic conditions. The cofactors tested are chemically stable under early Earth conditions, but none of the three compounds (Acetyl Co-A, thioacetate, or acetate) promoted synthesis of citric acid from oxaloacetate under the conditions tested. Oxaloacetate reacted with itself and/or decomposed to form a sequence of other products under ambient conditions, and under anoxic conditions was more stable; under ambient conditions the specific chemical pathways observed depended on the environmental conditions such as pH and presence/absence of bicarbonate or salt ions in early Earth ocean simulants. This work demonstrates the stability of these metabolic intermediates under anoxic conditions. However, even though free cofactors may be stable in a geological environmental setting, an enzyme or other mechanism to promote reaction specificity would likely be necessary for at least this particular reaction to proceed.
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Affiliation(s)
- Thora R Maltais
- NASA Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, CA, 91109, USA
| | - David VanderVelde
- Department of Chemistry, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA, 91125, USA
| | - Douglas E LaRowe
- Department of Earth Sciences, University of Southern California, 3651 Trousdale Pkwy, Los Angeles, CA, 90089, USA
| | - Aaron D Goldman
- Department of Biology, Oberlin College, Science Center K123 119 Woodland St., Oberlin, OH, 44074, USA.,Blue Marble Space Institute for Science, Seattle, Washington, 98154, USA
| | - Laura M Barge
- NASA Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, CA, 91109, USA.
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35
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Vasiliadou R, Dimov N, Szita N, Jordan SF, Lane N. Possible mechanisms of CO 2 reduction by H 2 via prebiotic vectorial electrochemistry. Interface Focus 2019; 9:20190073. [PMID: 31641439 PMCID: PMC6802132 DOI: 10.1098/rsfs.2019.0073] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2019] [Indexed: 02/07/2023] Open
Abstract
Methanogens are putatively ancestral autotrophs that reduce CO2 with H2 to form biomass using a membrane-bound, proton-motive Fe(Ni)S protein called the energy-converting hydrogenase (Ech). At the origin of life, geologically sustained H+ gradients across inorganic barriers containing Fe(Ni)S minerals could theoretically have driven CO2 reduction by H2 through vectorial chemistry in a similar way to Ech. pH modulation of the redox potentials of H2, CO2 and Fe(Ni)S minerals could in principle enable an otherwise endergonic reaction. Here, we analyse whether vectorial electrochemistry can facilitate the reduction of CO2 by H2 under alkaline hydrothermal conditions using a microfluidic reactor. We present pilot data showing that steep pH gradients of approximately 5 pH units can be sustained over greater than 5 h across Fe(Ni)S barriers, with H+-flux across the barrier about two million-fold faster than OH--flux. This high flux produces a calculated 3-pH unit-gradient (equating to 180 mV) across single approximately 25-nm Fe(Ni)S nanocrystals, which is close to that required to reduce CO2. However, the poor solubility of H2 at atmospheric pressure limits CO2 reduction by H2, explaining why organic synthesis has so far proved elusive in our reactor. Higher H2 concentration will be needed in future to facilitate CO2 reduction through prebiotic vectorial electrochemistry.
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Affiliation(s)
- Rafaela Vasiliadou
- Centre for Life's Origin and Evolution, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Nikolay Dimov
- School of Engineering and Computer Science, University of Hertfordshire, College Lane, Hatfield AL10 9AB, UK
| | - Nicolas Szita
- Department of Biochemical Engineering, University College London, Bernard Katz Building, Gower Street, London WC1E 6BT, UK
| | - Sean F. Jordan
- Centre for Life's Origin and Evolution, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
| | - Nick Lane
- Centre for Life's Origin and Evolution, Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
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36
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Goldford JE, Hartman H, Marsland R, Segrè D. Environmental boundary conditions for the origin of life converge to an organo-sulfur metabolism. Nat Ecol Evol 2019; 3:1715-1724. [PMID: 31712697 PMCID: PMC6881557 DOI: 10.1038/s41559-019-1018-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 09/27/2019] [Indexed: 11/30/2022]
Abstract
It has been suggested that a deep memory of early life is hidden in the architecture of metabolic networks, whose reactions could have been catalyzed by small molecules or minerals before genetically encoded enzymes. A major challenge in unravelling these early steps is assessing the plausibility of a connected, thermodynamically consistent proto-metabolism under different geochemical conditions, which are still surrounded by high uncertainty. Here we combine network-based algorithms with physico-chemical constraints on chemical reaction networks to systematically show how different combinations of parameters (temperature, pH, redox potential and availability of molecular precursors) could have affected the evolution of a proto-metabolism. Our analysis of possible trajectories indicates that a subset of boundary conditions converges to an organo-sulfur-based proto-metabolic network fuelled by a thioester- and redox-driven variant of the reductive tricarboxylic acid cycle that is capable of producing lipids and keto acids. Surprisingly, environmental sources of fixed nitrogen and low-potential electron donors are not necessary for the earliest phases of biochemical evolution. We use one of these networks to build a steady-state dynamical metabolic model of a protocell, and find that different combinations of carbon sources and electron donors can support the continuous production of a minimal ancient 'biomass' composed of putative early biopolymers and fatty acids.
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Affiliation(s)
- Joshua E Goldford
- Bioinformatics Program, Boston University, Boston, MA, USA.
- Department of Chemistry, Boston University, Boston, MA, USA.
- Biological Design Center, Boston University, Boston, MA, USA.
| | - Hyman Hartman
- Earth, Atmosphere and Planetary Science Department, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Daniel Segrè
- Bioinformatics Program, Boston University, Boston, MA, USA.
- Biological Design Center, Boston University, Boston, MA, USA.
- Department of Physics, Boston University, Boston, MA, USA.
- Department of Biomedical Engineering, Department of Biology, Boston University, Boston, MA, USA.
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37
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Vincent L, Berg M, Krismer M, Saghafi SS, Cosby J, Sankari T, Vetsigian K, Ii HJC, Baum DA. Chemical Ecosystem Selection on Mineral Surfaces Reveals Long-Term Dynamics Consistent with the Spontaneous Emergence of Mutual Catalysis. Life (Basel) 2019; 9:life9040080. [PMID: 31652727 PMCID: PMC6911371 DOI: 10.3390/life9040080] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 10/14/2019] [Accepted: 10/16/2019] [Indexed: 11/28/2022] Open
Abstract
How did chemicals first become organized into systems capable of self-propagation and adaptive evolution? One possibility is that the first evolvers were chemical ecosystems localized on mineral surfaces and composed of sets of molecular species that could catalyze each other’s formation. We used a bottom-up experimental framework, chemical ecosystem selection (CES), to evaluate this perspective and search for surface-associated and mutually catalytic chemical systems based on the changes in chemistry that they are expected to induce. Here, we report the results of preliminary CES experiments conducted using a synthetic “prebiotic soup” and pyrite grains, which yielded dynamical patterns that are suggestive of the emergence of mutual catalysis. While more research is needed to better understand the specific patterns observed here and determine whether they are reflective of self-propagation, these results illustrate the potential power of CES to test competing hypotheses for the emergence of protobiological chemical systems.
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Affiliation(s)
- Lena Vincent
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA.
| | - Michael Berg
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA.
| | - Mitchell Krismer
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA.
| | - Samuel S Saghafi
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA.
| | - Jacob Cosby
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA.
| | - Talia Sankari
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA.
| | - Kalin Vetsigian
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA.
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - H James Cleaves Ii
- Geophysical Laboratory, The Carnegie Institution for Science, Washington, DC 20015, USA.
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Meguro-ku, Tokyo 152-8550, Japan.
- Blue Marble Space Institute for Science, Seattle, WA 97154, USA.
- Institute for Advanced Study, Princeton, NJ 08540, USA.
| | - David A Baum
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI 53715, USA.
- Department of Botany, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Ślesak I, Kula M, Ślesak H, Miszalski Z, Strzałka K. How to define obligatory anaerobiosis? An evolutionary view on the antioxidant response system and the early stages of the evolution of life on Earth. Free Radic Biol Med 2019; 140:61-73. [PMID: 30862543 DOI: 10.1016/j.freeradbiomed.2019.03.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/01/2019] [Accepted: 03/05/2019] [Indexed: 10/27/2022]
Abstract
One of the former definitions of "obligate anaerobiosis" was based on three main criteria: 1) it occurs in organisms, so-called obligate anaerobes, which live in environments without oxygen (O2), 2) O2-dependent (aerobic) respiration, and 3) antioxidant enzymes are absent in obligate anaerobes. In contrast, aerobes need O2 in order to grow and develop properly. Obligate (or strict) anaerobes belong to prokaryotic microorganisms from two domains, Bacteria and Archaea. A closer look at anaerobiosis covers a wide range of microorganisms that permanently or in a time-dependent manner tolerate different concentrations of O2 in their habitats. On this basis they can be classified as obligate/facultative anaerobes, microaerophiles and nanaerobes. Paradoxically, O2 tolerance in strict anaerobes is usually, as in aerobes, associated with the activity of the antioxidant response system, which involves different antioxidant enzymes responsible for removing excess reactive oxygen species (ROS). In our opinion, the traditional definition of "obligate anaerobiosis" loses its original sense. Strict anaerobiosis should only be restricted to the occurrence of O2-independent pathways involved in energy generation. For that reason, a term better than "obligate anaerobes" would be O2/ROS tolerant anaerobes, where the role of the O2/ROS detoxification system is separated from O2-independent metabolic pathways that supply energy. Ubiquitous key antioxidant enzymes like superoxide dismutase (SOD) and superoxide reductase (SOR) in contemporary obligate anaerobes might suggest that their origin is ancient, maybe even the beginning of the evolution of life on Earth. It cannot be ruled out that c. 3.5 Gyr ago, local microquantities of O2/ROS played a role in the evolution of the last universal common ancestor (LUCA) of all modern organisms. On the basis of data in the literature, the hypothesis that LUCA could be an O2/ROS tolerant anaerobe is discussed together with the question of the abiotic sources of O2/ROS and/or the early evolution of cyanobacteria that perform oxygenic photosynthesis.
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Affiliation(s)
- Ireneusz Ślesak
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239, Krakow, Poland.
| | - Monika Kula
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239, Krakow, Poland.
| | - Halina Ślesak
- Institute of Botany, Jagiellonian University, Gronostajowa 9, 30-387, Krakow, Poland.
| | - Zbigniew Miszalski
- The Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Niezapominajek 21, 30-239, Krakow, Poland.
| | - Kazimierz Strzałka
- Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7A, 30-387, Krakow, Poland; Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland.
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Geisberger T, Diederich P, Steiner T, Eisenreich W, Schmitt-Kopplin P, Huber C. Evolutionary Steps in the Analytics of Primordial Metabolic Evolution. Life (Basel) 2019; 9:E50. [PMID: 31216665 PMCID: PMC6616974 DOI: 10.3390/life9020050] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 06/11/2019] [Accepted: 06/14/2019] [Indexed: 12/22/2022] Open
Abstract
Experimental studies of primordial metabolic evolution are based on multi-component reactions which typically result in highly complex product mixtures. The detection and structural assignment of these products crucially depends on sensitive and selective analytical procedures. Progress in the instrumentation of these methods steadily lowered the detection limits to concentrations in the pico molar range. At the same time, conceptual improvements in chromatography, nuclear magnetic resonance (NMR) and mass spectrometry dramatically increased the resolution power as well as throughput, now, allowing the simultaneous detection and structural determination of hundreds to thousands of compounds in complex mixtures. In retrospective, the development of these analytical methods occurred stepwise in a kind of evolutionary process that is reminiscent of steps occurring in the evolution of metabolism under chemoautotrophic conditions. This can be nicely exemplified in the analytical procedures used in our own studies that are based on Wächtershäuser's theory for metabolic evolution under Fe/Ni-catalyzed volcanic aqueous conditions. At the onset of these studies, gas chromatography (GC) and GC-MS (mass spectrometry) was optimized to detect specific low molecular weight products (<200 Da) in a targeted approach, e.g., methyl thioacetate, amino acids, hydroxy acids, and closely related molecules. Liquid chromatography mass spectrometry (LC-MS) was utilized for the detection of larger molecules including peptides exceeding a molecular weight of 200 Da. Although being less sensitive than GC-MS or LC-MS, NMR spectroscopy benefitted the structural determination of relevant products, such as intermediates involved in a putative primordial peptide cycle. In future, Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) seems to develop as a complementary method to analyze the compositional space of the products and reaction clusters in a non-targeted approach at unprecedented sensitivity and mass resolution (700,000 for m/z 250). Stable isotope labeling was important to differentiate between reaction products and artifacts but also to reveal the mechanisms of product formation. In this review; we summarize some of the developmental steps and key improvements in analytical procedures mainly used in own studies of metabolic evolution.
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Affiliation(s)
- Thomas Geisberger
- Department of Biochemistry, Technical University of Munich, 80333 Munich, Germany.
| | - Philippe Diederich
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany.
| | - Thomas Steiner
- Department of Biochemistry, Technical University of Munich, 80333 Munich, Germany.
| | - Wolfgang Eisenreich
- Department of Biochemistry, Technical University of Munich, 80333 Munich, Germany.
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry, Helmholtz Zentrum München-German Research Center for Environmental Health, 85764 Neuherberg, Germany.
| | - Claudia Huber
- Department of Biochemistry, Technical University of Munich, 80333 Munich, Germany.
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Recreating ancient metabolic pathways before enzymes. Bioorg Med Chem 2019; 27:2292-2297. [DOI: 10.1016/j.bmc.2019.03.012] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 03/02/2019] [Accepted: 03/06/2019] [Indexed: 12/12/2022]
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Kitadai N, Nakamura R, Yamamoto M, Takai K, Yoshida N, Oono Y. Metals likely promoted protometabolism in early ocean alkaline hydrothermal systems. SCIENCE ADVANCES 2019; 5:eaav7848. [PMID: 31223650 PMCID: PMC6584212 DOI: 10.1126/sciadv.aav7848] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 05/15/2019] [Indexed: 06/01/2023]
Abstract
One of the most plausible scenarios of the origin of life assumes the preceding prebiotic autotrophic metabolism in sulfide-rich hydrothermal vent environments. However, geochemical mechanisms to harness the reductive power provided by hydrothermal systems remain to be elucidated. Here, we show that, under a geoelectrochemical condition realizable in the early ocean hydrothermal systems, several metal sulfides (FeS, Ag2S, CuS, and PbS) undergo hour- to day-scale conversion to the corresponding metals at ≤-0.7 V (versus the standard hydrogen electrode). The electrochemically produced FeS-Fe0 assemblage promoted various reactions including certain steps in the reductive tricarboxylic acid cycle with efficiencies far superior to those due to pure FeS. The threshold potential is readily generated in the H2-rich alkaline hydrothermal systems that were probably ubiquitous on the Hadean seafloor. Thus, widespread metal production and metal-sustained primordial metabolism were likely to occur as a natural consequence of the active hydrothermal processes on the Hadean Earth.
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Affiliation(s)
- Norio Kitadai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Ryuhei Nakamura
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Masahiro Yamamoto
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Ken Takai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Naohiro Yoshida
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Department of Environmental Chemistry and Engineering, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, Kanazawa 226-8503, Japan
| | - Yoshi Oono
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 W. Green Street, Urbana, IL 61801-3080, USA
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Synthesis and breakdown of universal metabolic precursors promoted by iron. Nature 2019; 569:104-107. [PMID: 31043728 DOI: 10.1038/s41586-019-1151-1] [Citation(s) in RCA: 163] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 03/05/2019] [Indexed: 02/08/2023]
Abstract
Life builds its molecules from carbon dioxide (CO2) and breaks them back down again through the intermediacy of just five metabolites, which are the universal hubs of biochemistry1. However, it is unclear how core biological metabolism began and why it uses the intermediates, reactions and pathways that it does. Here we describe a purely chemical reaction network promoted by ferrous iron, in which aqueous pyruvate and glyoxylate-two products of abiotic CO2 reduction2-4-build up 9 of the 11 intermediates of the biological Krebs (or tricarboxylic acid) cycle, including all 5 universal metabolic precursors. The intermediates simultaneously break down to CO2 in a life-like regime that resembles biological anabolism and catabolism5. Adding hydroxylamine6-8 and metallic iron into the system produces four biological amino acids in a manner that parallels biosynthesis. The observed network overlaps substantially with the Krebs and glyoxylate cycles9,10, and may represent a prebiotic precursor to these core metabolic pathways.
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Prebiotic chemistry in neutral/reduced-alkaline gas-liquid interfaces. Sci Rep 2019; 9:1916. [PMID: 30760732 PMCID: PMC6374446 DOI: 10.1038/s41598-018-36579-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 11/25/2018] [Indexed: 11/09/2022] Open
Abstract
The conditions for the potential abiotic formation of organic compounds from inorganic precursors have great implications for our understanding of the origin of life on Earth and for its possible detection in other environments of the Solar System. It is known that aerosol-interfaces are effective at enhancing prebiotic chemical reactions, but the roles of salinity and pH have been poorly investigated to date. Here, we experimentally demonstrate the uniqueness of alkaline aerosols as prebiotic reactors that produce an undifferentiated accumulation of a variety of multi-carbon biomolecules resulting from high-energy processes (in our case, electrical discharges). Using simulation experiments, we demonstrate that the detection of important biomolecules in tholins increases when plausible and particular local planetary environmental conditions are simulated. A greater diversity in amino acids, carboxylic acids, N-heterocycles, and ketoacids, such as glyoxylic and pyruvic acid, was identified in tholins synthetized from reduced and neutral atmospheres in the presence of alkaline aqueous aerosols than that from the same atmospheres but using neutral or acidic aqueous aerosols.
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Keller MA, Kampjut D, Harrison SA, Driscoll PC, Ralser M. Reply to ‘Do sulfate radicals really enable a non-enzymatic Krebs cycle precursor?’. Nat Ecol Evol 2019; 3:139-140. [DOI: 10.1038/s41559-018-0792-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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46
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Sutherland J, Ritson D. Do sulfate radicals really enable a non-enzymatic Krebs cycle precursor? Nat Ecol Evol 2019; 3:138. [DOI: 10.1038/s41559-018-0791-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Fontecilla-Camps JC. Geochemical Continuity and Catalyst/Cofactor Replacement in the Emergence and Evolution of Life. Angew Chem Int Ed Engl 2018; 58:42-48. [DOI: 10.1002/anie.201808438] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/27/2018] [Indexed: 12/29/2022]
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48
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Fontecilla-Camps JC. Geochemische Kontinuität und Katalysator/Cofaktor-Austausch für Ursprung und Evolution des Lebens. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201808438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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49
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Conceptual challenges for the emergence of the biological system: Cell theory and self-replication. Med Hypotheses 2018; 119:79-83. [DOI: 10.1016/j.mehy.2018.07.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 07/23/2018] [Accepted: 07/29/2018] [Indexed: 11/20/2022]
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50
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Saovieng S, Wu J, Huang CY, Kao CL, Higgins MF, Chuanchaiyakul R, Kuo CH. Deep Ocean Minerals Minimize Eccentric Exercise-Induced Inflammatory Response of Rat Skeletal Muscle. Front Physiol 2018; 9:1351. [PMID: 30323766 PMCID: PMC6172318 DOI: 10.3389/fphys.2018.01351] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 09/06/2018] [Indexed: 12/21/2022] Open
Abstract
Background: We have previously shown an accelerated recovery from muscle fatigue in men challenged by prolonged exercise after oral deep ocean minerals (DOM) supplementation. Here, we hypothesized a decrease in eccentric exercise-induced muscle inflammation in rats regularly consuming DOM-containing drinks (hardness 600 mg/L and fructose 11%). Methods: Forty-seven male Sprague Dawley rats were randomized into 4 groups: Control (C, N = 12), Fructose (F, N = 12), Fructose+Exercise (FE, N = 12), and Fructose+Exercise+DOM (FED, N = 11). Since fructose is a commonly used ingredient in beverages, 11% of fructose was added as a vehicle of the study. Soleus muscles of rats were analyzed 24 h after an acute bout of downhill running following 9 weeks of DOM supplementation. Results: Leukocyte infiltration and TNF-α mRNA of muscle in the FE group were 5 times and 4 times greater the F group, respectively, (P < 0.05). Both markers in the FED group were significantly lower than those in the FE group (P < 0.05). IL-10 mRNA of muscle in the F group was >eight fold greater than the C group (P < 0.05). The reduced glutathione (GSH) of muscle in the F group was 34% lower than that in the C group (P < 0.05). However, GSH levels were similar for the C and FED groups. Conclusion: Prolonged fructose supplementation modulates inflammatory balance of rat skeletal muscle. The results of the study suggest that DOM can minimize eccentric exercise-induced inflammatory cytokine responses in rat skeletal muscle.
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Affiliation(s)
- Suchada Saovieng
- Laboratory of Exercise Biochemistry, University of Taipei, Taipei, Taiwan
| | - Jinfu Wu
- Laboratory of Exercise Biochemistry, University of Taipei, Taipei, Taiwan
| | - Chih-Yang Huang
- Graduate Institute of Basic Medical Science, China Medical University, Taichung, Taiwan
| | - Chung-Lan Kao
- Department of Healthcare Administration, Asia University, Taichung, Taiwan
| | - Matthew F Higgins
- Department of Life Sciences, University of Derby, Derby, United Kingdom
| | | | - Chia-Hua Kuo
- Laboratory of Exercise Biochemistry, University of Taipei, Taipei, Taiwan.,Graduate Institute of Basic Medical Science, China Medical University, Taichung, Taiwan
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