1
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Hyde AS, House CH. Prebiotic thiol-catalyzed thioamide bond formation. GEOCHEMICAL TRANSACTIONS 2024; 25:5. [PMID: 39098875 PMCID: PMC11299287 DOI: 10.1186/s12932-024-00088-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 06/20/2024] [Indexed: 08/06/2024]
Abstract
Thioamide bonds are important intermediates in prebiotic chemistry. In cyanosulfidic prebiotic chemistry, they serve as crucial intermediates in the pathways that lead to the formation of many important biomolecules (e.g., amino acids). They can also serve as purine and pyrimidine precursors, the two classes of heterocycle employed in genetic molecules. Despite their importance, the formation of thioamide bonds from nitriles under prebiotic conditions has required large excesses of sulfide or compounds with unknown prebiotic sources. Here, we describe the thiol-catalyzed formation of thioamide bonds from nitriles. We show that the formation of the simplest of these compounds, thioformamide, forms readily in spark-discharge experiments from hydrogen cyanide, sulfide, and a methanethiol catalyst, suggesting potential accumulation on early Earth. Lastly, we demonstrate that thioformamide has a Gibbs energy of hydrolysis ( Δ G r ∘ ) comparable to other energy-currencies on early Earth such as pyrophosphate and thioester bonds. Overall, our findings imply that thioamides might have been abundant on early Earth and served a variety of functions during chemical evolution.
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Affiliation(s)
- Andrew S Hyde
- Department of Geosciences and Earth and Environmental Systems Institute, The Pennsylvania State University, University Park, 16802, PA, USA.
| | - Christopher H House
- Department of Geosciences and Earth and Environmental Systems Institute, The Pennsylvania State University, University Park, 16802, PA, USA
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2
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Barat A, Powner MW. Spontaneous Peptide Ligation Mediated by Cysteamine. JACS AU 2024; 4:1752-1757. [PMID: 38818061 PMCID: PMC11134366 DOI: 10.1021/jacsau.4c00243] [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: 03/15/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 06/01/2024]
Abstract
The fundamental and universal nature of life's exploitation of peptides suggests they must have played a vital role during the onset of life, but their spontaneous chemoselective synthesis in water remains unknown. Aminonitriles (1) are widely accepted as prebiotic precursors of both amino acids and peptides, but they do not spontaneously polymerize in water to yield peptides. Here, we demonstrate that the simple prebiotically plausible aminothiol, cysteamine (5), participates in Strecker chemistry to furnish β-mercaptoethyl-α-aminonitriles (8) and β-mercaptoethyl-amino acids (16), which are predisposed to spontaneously form peptides in water. Intramolecular thiol catalyzed ligation is faster, higher-yielding, and more α-selective than previously reported prebiotic peptide ligation chemistries, enabling, for example, the highly regioselective α-ligation of Asp- and Glu-dinitriles in quantitative yields. Our findings suggest that cysteamine (5), the thiol bearing moiety of the universal thiol cofactor coenzyme A, may have played an important role in the selective chemical synthesis of prebiotic α-peptides.
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Affiliation(s)
- Abid Barat
- Department
of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | - Matthew W. Powner
- Department
of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, United Kingdom
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3
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Fairchild J, Islam S, Singh J, Bučar DK, Powner MW. Prebiotically plausible chemoselective pantetheine synthesis in water. Science 2024; 383:911-918. [PMID: 38386754 DOI: 10.1126/science.adk4432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/23/2024] [Indexed: 02/24/2024]
Abstract
Coenzyme A (CoA) is essential to all life on Earth, and its functional subunit, pantetheine, is important in many origin-of-life scenarios, but how pantetheine emerged on the early Earth remains a mystery. Earlier attempts to selectively synthesize pantetheine failed, leading to suggestions that "simpler" thiols must have preceded pantetheine at the origin of life. In this work, we report high-yielding and selective prebiotic syntheses of pantetheine in water. Chemoselective multicomponent aldol, iminolactone, and aminonitrile reactions delivered spontaneous differentiation of pantoic acid and proteinogenic amino acid syntheses, as well as the dihydroxyl, gem-dimethyl, and β-alanine-amide moieties of pantetheine in dilute water. Our results are consistent with a role for canonical pantetheine at the outset of life on Earth.
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Affiliation(s)
- Jasper Fairchild
- Department of Chemistry, University College London, London WC1H 0AJ, UK
| | - Saidul Islam
- Department of Chemistry, University College London, London WC1H 0AJ, UK
- Department of Chemistry and Centre for the Physical Science of Life, King's College London, London SE1 1DB, UK
| | - Jyoti Singh
- Department of Chemistry, University College London, London WC1H 0AJ, UK
| | | | - Matthew W Powner
- Department of Chemistry, University College London, London WC1H 0AJ, UK
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4
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Aleksandrova M, Rahmatova F, Russell DA, Bonfio C. Ring Opening of Glycerol Cyclic Phosphates Leads to a Diverse Array of Potentially Prebiotic Phospholipids. J Am Chem Soc 2023; 145:25614-25620. [PMID: 37971368 PMCID: PMC10690765 DOI: 10.1021/jacs.3c07319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023]
Abstract
Phospholipids are the primary constituents of cell membranes across all domains of life, but how and when phospholipids appeared on early Earth remains unknown. Pressingly, most prebiotic syntheses of complex phospholipids rely upon substrates not yet shown to have been available on early Earth. Here, we describe potentially prebiotic syntheses of a diverse array of complex phospholipids and their building blocks. First, we show that choline could have been produced on early Earth by stepwise N-methylation of ethanolamine. Second, taking a systems chemistry approach, we demonstrate that the intrinsically activated glycerol-2,3-cyclic phosphate undergoes ring opening with combinations of prebiotic amino alcohols to yield complex phospholipid headgroups. Importantly, this pathway selects for the formation of 2-amino alcohol-bearing phospholipid headgroups and enables the accumulation of their natural regioisomers. Finally, we show that the dry-state ring opening of cyclic lysophosphatidic acids leads to a range of self-assembling lysophospholipids. Our results provide new prebiotic routes to key intermediates on the way toward modern phospholipids and illuminate the potential origin and evolution of cell membranes.
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Affiliation(s)
- Maiia Aleksandrova
- Institut de Science et d’Ingénierie
Supramoléculaires (ISIS), CNRS UMR 7006, University of Strasbourg, 8 Allée Gaspard Monge, 67000 Strasbourg, France
| | - Fidan Rahmatova
- Institut de Science et d’Ingénierie
Supramoléculaires (ISIS), CNRS UMR 7006, University of Strasbourg, 8 Allée Gaspard Monge, 67000 Strasbourg, France
| | - David A. Russell
- Institut de Science et d’Ingénierie
Supramoléculaires (ISIS), CNRS UMR 7006, University of Strasbourg, 8 Allée Gaspard Monge, 67000 Strasbourg, France
| | - Claudia Bonfio
- Institut de Science et d’Ingénierie
Supramoléculaires (ISIS), CNRS UMR 7006, University of Strasbourg, 8 Allée Gaspard Monge, 67000 Strasbourg, France
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5
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Smith HH, Hyde AS, Simkus DN, Libby E, Maurer SE, Graham HV, Kempes CP, Sherwood Lollar B, Chou L, Ellington AD, Fricke GM, Girguis PR, Grefenstette NM, Pozarycki CI, House CH, Johnson SS. The Grayness of the Origin of Life. Life (Basel) 2021; 11:498. [PMID: 34072344 PMCID: PMC8226951 DOI: 10.3390/life11060498] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/22/2021] [Accepted: 05/26/2021] [Indexed: 12/05/2022] Open
Abstract
In the search for life beyond Earth, distinguishing the living from the non-living is paramount. However, this distinction is often elusive, as the origin of life is likely a stepwise evolutionary process, not a singular event. Regardless of the favored origin of life model, an inherent "grayness" blurs the theorized threshold defining life. Here, we explore the ambiguities between the biotic and the abiotic at the origin of life. The role of grayness extends into later transitions as well. By recognizing the limitations posed by grayness, life detection researchers will be better able to develop methods sensitive to prebiotic chemical systems and life with alternative biochemistries.
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Affiliation(s)
- Hillary H. Smith
- Department of Geosciences, The Pennsylvania State University, University Park, PA 16802, USA;
- Earth and Environmental Systems Institute, The Pennsylvania State University, University Park, PA 16802, USA
| | - Andrew S. Hyde
- Department of Geosciences, The Pennsylvania State University, University Park, PA 16802, USA;
- Earth and Environmental Systems Institute, The Pennsylvania State University, University Park, PA 16802, USA
| | - Danielle N. Simkus
- NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA; (D.N.S.); (H.V.G.); (L.C.); (C.I.P.)
- NASA Postdoctoral Program, USRA, Columbia, MD 20146, USA
- Department of Physics, Catholic University of America, Washington, DC 20064, USA
| | - Eric Libby
- Santa Fe Institute, Santa Fe, NM 87501, USA; (E.L.); (C.P.K.); (N.M.G.)
- Department of Mathematics and Mathematical Statistics, Umeå University, 90187 Umeå, Sweden
- Icelab, Umeå University, 90187 Umeå, Sweden
| | - Sarah E. Maurer
- Department of Chemistry and Biochemistry, Central Connecticut State University, New Britain, CT 06050, USA;
| | - Heather V. Graham
- NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA; (D.N.S.); (H.V.G.); (L.C.); (C.I.P.)
- Department of Physics, Catholic University of America, Washington, DC 20064, USA
| | | | | | - Luoth Chou
- NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA; (D.N.S.); (H.V.G.); (L.C.); (C.I.P.)
- NASA Postdoctoral Program, USRA, Columbia, MD 20146, USA
- Department of Biology, Georgetown University, Washington, DC 20057, USA
| | - Andrew D. Ellington
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX 78712, USA;
- Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - G. Matthew Fricke
- Department of Computer Science, University of New Mexico, Albuquerque, NM 87108, USA;
| | - Peter R. Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA;
| | - Natalie M. Grefenstette
- Santa Fe Institute, Santa Fe, NM 87501, USA; (E.L.); (C.P.K.); (N.M.G.)
- Blue Marble Space Institute of Science, Seattle, WA 98104, USA
| | - Chad I. Pozarycki
- NASA Goddard Space Flight Center, Greenbelt, MD 20771, USA; (D.N.S.); (H.V.G.); (L.C.); (C.I.P.)
- Department of Biology, Georgetown University, Washington, DC 20057, USA
| | - Christopher H. House
- Department of Geosciences, The Pennsylvania State University, University Park, PA 16802, USA;
- Earth and Environmental Systems Institute, The Pennsylvania State University, University Park, PA 16802, USA
| | - Sarah Stewart Johnson
- Department of Biology, Georgetown University, Washington, DC 20057, USA
- Science, Technology and International Affairs Program, Georgetown University, Washington, DC 20057, USA
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6
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Abstract
The evolution of coenzymes, or their impact on the origin of life, is fundamental for understanding our own existence. Having established reasonable hypotheses about the emergence of prebiotic chemical building blocks, which were probably created under palaeogeochemical conditions, and surmising that these smaller compounds must have become integrated to afford complex macromolecules such as RNA, the question of coenzyme origin and its relation to the evolution of functional biochemistry should gain new impetus. Many coenzymes have a simple chemical structure and are often nucleotide-derived, which suggests that they may have coexisted with the emergence of RNA and may have played a pivotal role in early metabolism. Based on current theories of prebiotic evolution, which attempt to explain the emergence of privileged organic building blocks, this Review discusses plausible hypotheses on the prebiotic formation of key elements within selected extant coenzymes. In combination with prebiotic RNA, coenzymes may have dramatically broadened early protometabolic networks and the catalytic scope of RNA during the evolution of life.
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Affiliation(s)
- Andreas Kirschning
- Institut für Organische Chemie und Biomolekulares Wirkstoffzentrum (BMWZ)Leibniz Universität HannoverSchneiderberg 1B30167HannoverGermany
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7
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The Role of Glycerol and Its Derivatives in the Biochemistry of Living Organisms, and Their Prebiotic Origin and Significance in the Evolution of Life. Catalysts 2021. [DOI: 10.3390/catal11010086] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The emergence and evolution of prebiotic biomolecules on the early Earth remain a question that is considered crucial to understanding the chemistry of the origin of life. Amongst prebiotic molecules, glycerol is significant due to its ubiquity in biochemistry. In this review, we discuss the significance of glycerol and its various derivatives in biochemistry, their plausible roles in the origin and evolution of early cell membranes, and significance in the biochemistry of extremophiles, followed by their prebiotic origin on the early Earth and associated catalytic processes that led to the origin of these compounds. We also discuss various scenarios for the prebiotic syntheses of glycerol and its derivates and evaluate these to determine their relevance to early Earth biochemistry and geochemistry, and recapitulate the utilization of various minerals (including clays), condensation agents, and solvents that could have led to the successful prebiotic genesis of these biomolecules. Furthermore, important prebiotic events such as meteoritic delivery and prebiotic synthesis reactions under astrophysical conditions are also discussed. Finally, we have also highlighted some novel features of glycerol, including glycerol nucleic acid (GNA), in the origin and evolution of the life.
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8
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Sivaram AK, Subashchandrabose SR, Logeshwaran P, Lockington R, Naidu R, Megharaj M. Metabolomics reveals defensive mechanisms adapted by maize on exposure to high molecular weight polycyclic aromatic hydrocarbons. CHEMOSPHERE 2019; 214:771-780. [PMID: 30296765 DOI: 10.1016/j.chemosphere.2018.09.170] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 09/22/2018] [Accepted: 09/29/2018] [Indexed: 05/28/2023]
Abstract
Polycyclic aromatic hydrocarbons are an important group of persistent organic pollutants. Using plants to remediate PAHs has been recognized as a cost-effective and environmentally friendly technique. However, the overall impact of PAHs on the regulation of plant metabolism has not yet been explored. In this study, we analyzed the alteration in the maize (Zea mays L.) metabolome on exposure to high molecular weight PAHs such as benzo[a]pyrene (BaP) and pyrene (PYR) in a hydroponic medium, individually and as a mixture (BaP + PYR) using GC-MS. The differences in the metabolites were analyzed using XCMS (an acronym for various forms (X) of chromatography-mass spectrometry), an online-based data analysis tool. A significant variation in metabolites was observed between treatment groups and the unspiked control group. The univariate, multivariate and pathway impact analysis showed there were more significant alterations in metabolic profiles between individual PAHs and the mixture of BaP and PYR. The marked changes in the metabolites of galactose metabolism and aminoacyl tRNA biosynthesis in PAHs treated maize leaves exhibit the adaptive defensive mechanisms for individual and PAHs mixture. Therefore, the metabolomics approach is essential for an understanding of the complex biochemical responses of plants to PAHs contaminants. This knowledge will shed new light in the field of phytoremediation, bio-monitoring, and environmental risk assessment.
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Affiliation(s)
- Anithadevi Kenday Sivaram
- Global Centre for Environmental Remediation, Faculty of Science, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia; Centre for Environmental Risk Assessment and Remediation (CERAR), University of South Australia, Mawson Lakes, SA, 5095, Australia; Cooperative Research Centre for Contamination Assessment and Remediation of the Environments, ATC Building, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
| | - Suresh Ramraj Subashchandrabose
- Global Centre for Environmental Remediation, Faculty of Science, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia; Centre for Environmental Risk Assessment and Remediation (CERAR), University of South Australia, Mawson Lakes, SA, 5095, Australia; Cooperative Research Centre for Contamination Assessment and Remediation of the Environments, ATC Building, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
| | - Panneerselvan Logeshwaran
- Global Centre for Environmental Remediation, Faculty of Science, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia; Centre for Environmental Risk Assessment and Remediation (CERAR), University of South Australia, Mawson Lakes, SA, 5095, Australia; Cooperative Research Centre for Contamination Assessment and Remediation of the Environments, ATC Building, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
| | - Robin Lockington
- Centre for Environmental Risk Assessment and Remediation (CERAR), University of South Australia, Mawson Lakes, SA, 5095, Australia; Cooperative Research Centre for Contamination Assessment and Remediation of the Environments, ATC Building, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
| | - Ravi Naidu
- Global Centre for Environmental Remediation, Faculty of Science, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia; Centre for Environmental Risk Assessment and Remediation (CERAR), University of South Australia, Mawson Lakes, SA, 5095, Australia; Cooperative Research Centre for Contamination Assessment and Remediation of the Environments, ATC Building, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
| | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation, Faculty of Science, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia; Centre for Environmental Risk Assessment and Remediation (CERAR), University of South Australia, Mawson Lakes, SA, 5095, Australia; Cooperative Research Centre for Contamination Assessment and Remediation of the Environments, ATC Building, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia.
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9
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Zhang X, Tian G, Gao J, Han M, Su R, Wang Y, Feng S. Prebiotic Synthesis of Glycine from Ethanolamine in Simulated Archean Alkaline Hydrothermal Vents. ORIGINS LIFE EVOL B 2017; 47:413-425. [PMID: 27663450 DOI: 10.1007/s11084-016-9520-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 09/05/2016] [Indexed: 12/18/2022]
Abstract
Submarine hydrothermal vents are generally considered as the likely habitats for the origin and evolution of early life on Earth. In recent years, a novel hydrothermal system in Archean subseafloor has been proposed. In this model, highly alkaline and high temperature hydrothermal fluids were generated in basalt-hosted hydrothermal vents, where H2 and CO2 could be abundantly provided. These extreme conditions could have played an irreplaceable role in the early evolution of life. Nevertheless, sufficient information has not yet been obtained for the abiotic synthesis of amino acids, which are indispensable components of life, at high temperature and alkaline condition. This study aims to propose a new method for the synthesis of glycine in simulated Archean submarine alkaline vent systems. We investigated the formation of glycine from ethanolamine under conditions of high temperature (80-160 °C) and highly alkaline solutions (pH = 9.70). Experiments were performed in an anaerobic environment under mild pressure (0.1-8.0 MPa) at the same time. The results suggested that the formation of glycine from ethanolamine occurred rapidly and efficiently in the presence of metal powders, and was favored by high temperatures and high pressures. The experiment provides a new pathway for prebiotic glycine formation and points out the phenomenal influence of high-temperature alkaline hydrothermal vents in origin of life in the early ocean.
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Affiliation(s)
- Xianlong Zhang
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun, 130012, People's Republic of China
| | - Ge Tian
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun, 130012, People's Republic of China
| | - Jing Gao
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun, 130012, People's Republic of China
| | - Mei Han
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun, 130012, People's Republic of China
| | - Rui Su
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun, 130012, People's Republic of China
| | - Yanxiang Wang
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun, 130012, People's Republic of China
| | - Shouhua Feng
- State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, College of Chemistry, Jilin University, Changchun, 130012, People's Republic of China.
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10
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Silicate-Promoted Phosphorylation of Glycerol in Non-Aqueous Solvents: A Prebiotically Plausible Route to Organophosphates. Life (Basel) 2017; 7:life7030029. [PMID: 28661422 PMCID: PMC5617954 DOI: 10.3390/life7030029] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 06/20/2017] [Accepted: 06/23/2017] [Indexed: 11/16/2022] Open
Abstract
Phosphorylation reactions of glycerol were studied using different inorganic phosphates such as sodium phosphate, trimetaphosphate (a condensed phosphate), and struvite. The reactions were carried out in two non-aqueous solvents: formamide and a eutectic solvent consisting of choline-chloride and glycerol in a ratio of 1:2.5. The glycerol reacted in formamide and in the eutectic solvent with phosphate to yield its phosphorylated derivatives in the presence of silicates such as quartz sand and kaolinite clay. The reactions were carried out by heating glycerol with a phosphate source at 85 °C for one week and were analyzed by 31P-nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS). The yield of the phosphorylated glycerol was improved by the presence of silicates, and reached 90% in some experiments. Our findings further support the proposal that non-aqueous solvents are advantageous for the prebiotic synthesis of biomolecules, and suggest that silicates may have aided in the formation of organophosphates on the prebiotic earth.
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11
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Immobilization of silver nanoparticle-decorated silica particles on polyamide thin film composite membranes for antibacterial properties. J Memb Sci 2016. [DOI: 10.1016/j.memsci.2015.09.060] [Citation(s) in RCA: 125] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Mirzahosseini A, Somlyay M, Noszál B. Species-Specific Thiol-Disulfide Equilibrium Constant: A Tool To Characterize Redox Transitions of Biological Importance. J Phys Chem B 2015; 119:10191-7. [PMID: 26172610 DOI: 10.1021/acs.jpcb.5b05708] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Microscopic redox equilibrium constants, a new species-specific type of physicochemical parameters, were introduced and determined to quantify thiol-disulfide equilibria of biological significance. The thiol-disulfide redox equilibria of glutathione with cysteamine, cysteine, and homocysteine were approached from both sides, and the equilibrium mixtures were analyzed by quantitative NMR methods to characterize the highly composite, co-dependent acid-base and redox equilibria. The directly obtained, pH-dependent, conditional constants were then decomposed by a new evaluation method, resulting in pH-independent, microscopic redox equilibrium constants for the first time. The 80 different, microscopic redox equilibrium constant values show close correlation with the respective thiolate basicities and provide sound means for the development of potent agents against oxidative stress.
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Affiliation(s)
- Arash Mirzahosseini
- Department of Pharmaceutical Chemistry, Semmelweis University, Budapest, 1085 Hungary.,Research Group of Drugs of Abuse and Doping Agents, Hungarian Academy of Sciences Budapest, 1051 Hungary
| | - Máté Somlyay
- Department of Pharmaceutical Chemistry, Semmelweis University, Budapest, 1085 Hungary.,Research Group of Drugs of Abuse and Doping Agents, Hungarian Academy of Sciences Budapest, 1051 Hungary
| | - Béla Noszál
- Department of Pharmaceutical Chemistry, Semmelweis University, Budapest, 1085 Hungary.,Research Group of Drugs of Abuse and Doping Agents, Hungarian Academy of Sciences Budapest, 1051 Hungary
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13
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Gull M, Zhou M, Fernández FM, Pasek MA. Prebiotic phosphate ester syntheses in a deep eutectic solvent. J Mol Evol 2013; 78:109-17. [PMID: 24368625 DOI: 10.1007/s00239-013-9605-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 12/03/2013] [Indexed: 11/25/2022]
Abstract
We report a route to synthesize a wide range of organophosphates of biological significance in a deep eutectic solvent (2:1 urea and choline chloride), utilizing various orthophosphate sources. Heating an organic alcohol in the solvent along with a soluble phosphorus source yields phosphorus esters of choline as well as that of the added organic in yields between 15 to 99 %. In addition, phosphite analogs of biological phosphates and peptides were also formed by the simple mixing of reagents and heating at 60-70 °C in the deep eutectic solvent. The presented dehydration reactions are relevant to prebiotic and green chemistry in alternative solvents.
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Affiliation(s)
- Maheen Gull
- School of Geosciences, University of South Florida, NES 107, 4202 East Fowler Ave, Tampa, FL, 33620, USA,
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14
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Warzecha Z, Ceranowicz D, Dembiński A, Ceranowicz P, Cieszkowski J, Kuwahara A, Kato I, Dembiński M, Konturek PC. Ghrelin accelerates the healing of cysteamine-induced duodenal ulcers in rats. Med Sci Monit 2012; 18:BR181-7. [PMID: 22534700 PMCID: PMC3560627 DOI: 10.12659/msm.882727] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background Previous studies have shown that administration of ghrelin exhibits protective and therapeutic effects in the gut. The aim of the present investigation was to examine the influence of ghrelin administration on the course of cysteamine-induced duodenal ulcers, as well as effects on mucosal production of oxygen free radicals and duodenal antioxidant defense. Material/Methods Duodenal ulcers were induced in male Wistar rats by cysteamine administered intragastrically at the dose of 200 mg/kg in 1 ml of saline, 3 times at 4-h intervals. Starting 24 h after the first dose of cysteamine, rats were treated intraperitoneally twice a day with saline or ghrelin given at the dose of 4, 8 or 16 nmol/kg/dose. Seven days after administration of the first dose of cysteamine, the study was terminated. Results Induction of ulcers by cysteamine was accompanied by a reduction in duodenal blood flow, mucosal DNA synthesis and mucosal activity of superoxide dismutase (SOD); whereas mucosal concentration of interleukin-1β and malonyldialdehyde (MDA – an index of lipid peroxidation) were increased. Treatment with ghrelin increased healing rate of duodenal ulcers and enhanced duodenal blood flow, mucosal DNA synthesis and mucosal activity of SOD, and reduced mucosal concentration of interleukin-1β and MDA. Conclusions Treatment with ghrelin increases the healing rate of duodenal ulcers and this effect is related, at least in part, to improvement of duodenal mucosal blood flow, mucosal cell proliferation and antioxidant defense, as well as being related to reduction in mucosal oxidative stress and inflammatory response.
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Affiliation(s)
- Zygmunt Warzecha
- Department of Physiology, Jagiellonian University Medical College, Cracow, Poland
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Khomenko T, Szabo S, Deng X, Ishikawa H, Anderson GJ, McLaren GD. Role of iron in the pathogenesis of cysteamine-induced duodenal ulceration in rats. Am J Physiol Gastrointest Liver Physiol 2009; 296:G1277-86. [PMID: 19342511 PMCID: PMC3834006 DOI: 10.1152/ajpgi.90257.2008] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Cysteamine induces perforating duodenal ulcers in rats within 24-48 h. This reducing aminothiol generates hydrogen peroxide in the presence of transition metals (e.g., ferric iron), producing oxidative stress, which may contribute to organ-specific tissue damage. Since most intestinal iron absorption takes place in the proximal duodenum, we hypothesized that cysteamine may disrupt regulation of mucosal iron transport, and iron may facilitate cysteamine-induced duodenal ulceration. We show here that cysteamine-induced ulceration was aggravated by pretreatment of rats with Fe(3+) or Fe(2+) compounds, which elevated iron concentration in the duodenal mucosa. In contrast, feeding rats an iron-deficient diet was associated with a 4.6-fold decrease in ulcer formation, accompanied by a 34% decrease (P < 0.05) in the duodenal mucosal iron concentration. Administration of deferoxamine inhibited ulceration by 65%. We also observed that the antiulcer effect of H2 receptor antagonist cimetidine included a 35% decrease in iron concentration in the duodenal mucosa. Cysteamine-induced duodenal ulcers were also decreased in iron-deficient Belgrade rats (P < 0.05). In normal rats, cysteamine administration increased the iron concentration in the proximal duodenal mucosa by 33% in the preulcerogenic stage but at the same time decreased serum iron (P < 0.05). Cysteamine also enhanced activation of mucosal iron regulatory protein 1 and increased the expression of divalent metal transporter 1 mRNA and protein. Transferrin receptor 1 protein expression was also increased, although mucosal ferroportin and ferritin remained almost unchanged. These results indicate an expansion of the intracellular labile iron pool in the duodenal mucosa, increasing its susceptibility to oxidative stress, and suggest a role for iron in the pathogenesis of organ-specific tissue injury such as duodenal ulcers.
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Affiliation(s)
- Tetyana Khomenko
- Diagnostic and Molecular Medicine and Medical Health Care Groups, Veterans Affairs Medical Center, Long Beach, California and Departments of Pathology, Pharmacology and Medicine, University of California, Irvine, California
| | - Sandor Szabo
- Diagnostic and Molecular Medicine and Medical Health Care Groups, Veterans Affairs Medical Center, Long Beach, California and Departments of Pathology, Pharmacology and Medicine, University of California, Irvine, California
| | - Xiaoming Deng
- Diagnostic and Molecular Medicine and Medical Health Care Groups, Veterans Affairs Medical Center, Long Beach, California and Departments of Pathology, Pharmacology and Medicine, University of California, Irvine, California
| | - Hideki Ishikawa
- Diagnostic and Molecular Medicine and Medical Health Care Groups, Veterans Affairs Medical Center, Long Beach, California and Departments of Pathology, Pharmacology and Medicine, University of California, Irvine, California
| | - Gregory J. Anderson
- Iron Metabolism Laboratory, Queensland Institute of Medical Research, Brisbane, Australia
| | - Gordon D. McLaren
- Diagnostic and Molecular Medicine and Medical Health Care Groups, Veterans Affairs Medical Center, Long Beach, California and Departments of Pathology, Pharmacology and Medicine, University of California, Irvine, California
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Ji HF, Kong DX, Shen L, Chen LL, Ma BG, Zhang HY. Distribution patterns of small-molecule ligands in the protein universe and implications for origin of life and drug discovery. Genome Biol 2008; 8:R176. [PMID: 17727706 PMCID: PMC2375006 DOI: 10.1186/gb-2007-8-8-r176] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2007] [Revised: 08/22/2007] [Accepted: 08/29/2007] [Indexed: 01/01/2023] Open
Abstract
Ligand-protein mapping was found to follow a power law and the preferential attachment principle, leading to the identification of the molecules, mostly nucleotide-containing compounds, that are likely to have evolved earliest. Background Extant life depends greatly on the binding of small molecules (such as ligands) with macromolecules (such as proteins), and one ligand can bind multiple proteins. However, little is known about the global patterns of ligand-protein mapping. Results By examining 2,186 well-defined small-molecule ligands and thousands of protein domains derived from a database of druggable binding sites, we show that a few ligands bind tens of protein domains or folds, whereas most ligands bind only one, which indicates that ligand-protein mapping follows a power law. Through assigning the protein-binding orders (early or late) for bio-ligands, we demonstrate that the preferential attachment principle still holds for the power-law relation between ligands and proteins. We also found that polar molecular surface area, H-bond acceptor counts, H-bond donor counts and partition coefficient are potential factors to discriminate ligands from ordinary molecules and to differentiate super ligands (shared by three or more folds) from others. Conclusion These findings have significant implications for evolution and drug discovery. First, the chronology of ligand-protein binding can be inferred by the power-law feature of ligand-protein mapping. Some nucleotide-containing ligands, such as ATP, ADP, GDP, NAD, FAD, dihydro-nicotinamide-adenine-dinucleotide phosphate (NDP), nicotinamide-adenine-dinucleotide phosphate (NAP), flavin mononucleotide (FMN) and AMP, are found to be the earliest cofactors bound to proteins, agreeing with the current understanding of evolutionary history. Second, the finding that about 30% of ligands are shared by two or more domains will help with drug discovery, such as in finding new functions from old drugs, developing promiscuous drugs and depending more on natural products.
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Affiliation(s)
- Hong-Fang Ji
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Center for Advanced Study, Shandong University of Technology, Zibo 255049, PR China
| | - De-Xin Kong
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Center for Advanced Study, Shandong University of Technology, Zibo 255049, PR China
| | - Liang Shen
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Center for Advanced Study, Shandong University of Technology, Zibo 255049, PR China
| | - Ling-Ling Chen
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Center for Advanced Study, Shandong University of Technology, Zibo 255049, PR China
| | - Bin-Guang Ma
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Center for Advanced Study, Shandong University of Technology, Zibo 255049, PR China
| | - Hong-Yu Zhang
- Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Center for Advanced Study, Shandong University of Technology, Zibo 255049, PR China
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Martin F, Penet MF, Malergue F, Lepidi H, Dessein A, Galland F, de Reggi M, Naquet P, Gharib B. Vanin-1(-/-) mice show decreased NSAID- and Schistosoma-induced intestinal inflammation associated with higher glutathione stores. J Clin Invest 2004; 113:591-7. [PMID: 14966568 PMCID: PMC338265 DOI: 10.1172/jci19557] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2003] [Accepted: 12/16/2003] [Indexed: 12/19/2022] Open
Abstract
Vanin-1 is a membrane-anchored pantetheinase highly expressed in the gut and liver. It hydrolyzes pantetheine to pantothenic acid (vitamin B5) and the low-molecular-weight thiol cysteamine. The latter is believed to be a key regulating factor of several essential metabolic pathways, acting through sulfhydryl-disulfide exchange reactions between sulfhydryl groups of the enzymes and the oxidized form, cystamine. Its physiological importance remains to be elucidated, however. To explore this point, we developed Vanin-1-deficient mice that lack free cysteamine. We examined the susceptibility of deficient mice to intestinal inflammation, either acute (NSAID administration) or chronic (Schistosoma infection). We found that Vanin-1(-/-) mice better controlled inflammatory reaction and intestinal injury in both experiments. This protection was associated with increased gamma-glutamylcysteine synthetase activity and increased stores of reduced glutathione, as well as reduced inflammatory cell activation in inflamed tissues. Oral administration of cystamine reversed all aspects of the deficient phenotype. These findings suggest that one cysteamine function is to upregulate inflammation. Consequently, the pantetheinase activity of Vanin-1 molecule could be a target for a new anti-inflammatory strategy.
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Affiliation(s)
- Florent Martin
- Centre d'Immunologie de Marseille-Luminy, Centre National de la Recherche Scientifique-Institut National de la Santé et de la Recherche Médicale, Universté de la Méditerranée, Marseille, France
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Huang F. Efficient incorporation of CoA, NAD and FAD into RNA by in vitro transcription. Nucleic Acids Res 2003; 31:e8. [PMID: 12560511 PMCID: PMC149220 DOI: 10.1093/nar/gng008] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Protein enzymes frequently recruit small molecule coenzymes to perform a variety of biochemical reactions. While the catalytic activities of RNA have been expanding rapidly, a similar strategy for RNA to utilize coenzymes and to increase its functional capabilities has yet to be demonstrated. A general in vitro transcription procedure has been developed to efficiently prepare RNA with coenzymes CoA, NAD and FAD covalently attached to the 5' end. These adenosine-containing coenzymes initiate transcription under the T7 class II promoter by T7 RNA polymerase. In addition to the three coenzymes, other adenosine-containing molecules may be incorporated into the first nucleotide position of RNA as well. This method provides easy access to CoA-, NAD- and FAD-RNA, which may find broad applications in generating coenzyme- utilizing ribozymes. In addition, both oxidized FAD and reduced NADH are highly fluorescent. NADH-RNA and FAD-RNA can therefore be used as probes for DNA/RNA detection and for structural investigation of RNA function by fluorescence spectroscopy.
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Affiliation(s)
- Faqing Huang
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, MS 39406-5043, USA.
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Waddell TG, Eilders LL, Patel BP, Sims M. Prebiotic methylation and the evolution of methyl transfer reactions in living cells. ORIGINS LIFE EVOL B 2000; 30:539-48. [PMID: 11196574 DOI: 10.1023/a:1026523222285] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
An hypothesis is presented for the prebiotic origin of methyl groups and the evolution of methyl transfer reactions in living cells. This hypothesis, described in terms of prebiotic and early biotic chemical evolution, is based on experimental observations in our lab and in those of others, and on the mechanisms of enzymatic methyl transfer reactions that occur in living cells. Of particular interest is our demonstration of the reductive methylation of ethanolamine and glycine in aqueous solution by excess formaldehyde. These reactions, involving prebiotic compounds and conditions, are mechanistically analogous to the de novo origin of methyl groups in modern cells by reduction of methylene tetrahydrofolate. Furthermore, modern cellular methyl transfers from S-adenosylmethionine to amine nitrogen may involve formaldehyde as an intermediate and subsequent reductive methylation, analogous to the prebiotic chemistry observed herein.
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Affiliation(s)
- T G Waddell
- Department of Chemistry, University of Tennessee at Chattanooga, Chattanooga, Tennessee 37403, USA
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Abstract
The first systems of molecules having the properties of the living state presumably self-assembled from a mixture of organic compounds available on the prebiotic Earth. To carry out the polymer synthesis characteristic of all forms of life, such systems would require one or more sources of energy to activate monomers to be incorporated into polymers. Possible sources of energy for this process include heat, light energy, chemical energy, and ionic potentials across membranes. These energy sources are explored here, with a particular focus on mechanisms by which self-assembled molecular aggregates could capture the energy and use it to form chemical bonds in polymers. Based on available evidence, a reasonable conjecture is that membranous vesicles were present on the prebiotic Earth and that systems of replicating and catalytic macromolecules could become encapsulated in the vesicles. In the laboratory, this can be modeled by encapsulated polymerases prepared as liposomes. By an appropriate choice of lipids, the permeability properties of the liposomes can be adjusted so that ionic substrates permeate at a sufficient rate to provide a source of monomers for the enzymes, with the result that nucleic acids accumulate in the vesicles. Despite this progress, there is still no clear mechanism by which the free energy of light, ion gradients, or redox potential can be coupled to polymer bond formation in a protocellular structure.
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Affiliation(s)
- D W Deamer
- Department of Chemistry and Biochemistry, University of California, Santa Cruz 95064, USA.
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