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Banfalvi G. The Origin of RNA and the Formose-Ribose-RNA Pathway. Int J Mol Sci 2024; 25:6727. [PMID: 38928433 PMCID: PMC11203418 DOI: 10.3390/ijms25126727] [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: 05/10/2024] [Revised: 06/03/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Prebiotic pre-Darwinian reactions continued throughout biochemical or Darwinian evolution. Early chemical processes could have occurred on Earth between 4.5 and 3.6 billion years ago when cellular life was about to come into being. Pre-Darwinian evolution assumes the development of hereditary elements but does not regard them as self-organizing processes. The presence of biochemical self-organization after the pre-Darwinian evolution did not justify distinguishing between different types of evolution. From the many possible solutions, evolution selected from among those stable reactions that led to catalytic networks, and under gradually changing external conditions produced a reproducible, yet constantly evolving and adaptable, living system. Major abiotic factors included sunlight, precipitation, air, minerals, soil and the Earth's atmosphere, hydrosphere and lithosphere. Abiotic sources of chemicals contributed to the formation of prebiotic RNA, the development of genetic RNA, the RNA World and the initial life forms on Earth and the transition of genRNA to the DNA Empire, and eventually to the multitude of life forms today. The transition from the RNA World to the DNA Empire generated new processes such as oxygenic photosynthesis and the hierarchical arrangement of processes involved in the transfer of genetic information. The objective of this work is to unite earlier work dealing with the formose, the origin and synthesis of ribose and RNA reactions that were published as a series of independent reactions. These reactions are now regarded as the first metabolic pathway.
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Affiliation(s)
- Gaspar Banfalvi
- Department of Molecular Biotechnology and Microbiology, University of Debrecen, 4032 Debrecen, Hungary
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2
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Chen J, Chen W, Zhang J, Zhao H, Cui J, Wu J, Shi A. Dual effects of endogenous formaldehyde on the organism and drugs for its removal. J Appl Toxicol 2024; 44:798-817. [PMID: 37766419 DOI: 10.1002/jat.4546] [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: 07/31/2023] [Revised: 08/25/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023]
Abstract
Endogenous formaldehyde (FA) is produced in the human body via various mechanisms to preserve healthy energy metabolism and safeguard the organism. However, endogenous FA can have several negative effects on the body through epigenetic alterations, including cancer growth promotion; neuronal, hippocampal and endothelial damages; atherosclerosis acceleration; haemopoietic stem cell destruction and haemopoietic cell production reduction. Certain medications with antioxidant effects, such as glutathione, vitamin E, resveratrol, alpha lipoic acid and polyphenols, lessen the detrimental effects of endogenous FA by reducing oxidative stress, directly scavenging endogenous FA or promoting its degradation. This study offers fresh perspectives for managing illnesses associated with endogenous FA exposure.
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Affiliation(s)
- Jiaxin Chen
- Yunnan Key Laboratory of Integrated Traditional Chinese and Western Medicine for Chronic Disease in Prevention and Treatment, Yunnan University of Chinese Medicine, Kunming, China
- Key Laboratory of Microcosmic Syndrome Differentiation, Yunnan University of Chinese Medicine, Kunming, China
| | - Wenhui Chen
- Yunnan Key Laboratory of Integrated Traditional Chinese and Western Medicine for Chronic Disease in Prevention and Treatment, Yunnan University of Chinese Medicine, Kunming, China
- Key Laboratory of Microcosmic Syndrome Differentiation, Yunnan University of Chinese Medicine, Kunming, China
| | - Jinjia Zhang
- Yunnan Key Laboratory of Integrated Traditional Chinese and Western Medicine for Chronic Disease in Prevention and Treatment, Yunnan University of Chinese Medicine, Kunming, China
- Key Laboratory of Microcosmic Syndrome Differentiation, Yunnan University of Chinese Medicine, Kunming, China
| | - Huanhuan Zhao
- Yunnan Key Laboratory of Integrated Traditional Chinese and Western Medicine for Chronic Disease in Prevention and Treatment, Yunnan University of Chinese Medicine, Kunming, China
- Key Laboratory of Microcosmic Syndrome Differentiation, Yunnan University of Chinese Medicine, Kunming, China
| | - Ji Cui
- Yunnan Key Laboratory of Integrated Traditional Chinese and Western Medicine for Chronic Disease in Prevention and Treatment, Yunnan University of Chinese Medicine, Kunming, China
- Key Laboratory of Microcosmic Syndrome Differentiation, Yunnan University of Chinese Medicine, Kunming, China
| | - Junzi Wu
- Yunnan Key Laboratory of Integrated Traditional Chinese and Western Medicine for Chronic Disease in Prevention and Treatment, Yunnan University of Chinese Medicine, Kunming, China
- Key Laboratory of Microcosmic Syndrome Differentiation, Yunnan University of Chinese Medicine, Kunming, China
- Department of Basic Medical, Yunnan University of Chinese Medicine, Kunming, China
| | - Anhua Shi
- Yunnan Key Laboratory of Integrated Traditional Chinese and Western Medicine for Chronic Disease in Prevention and Treatment, Yunnan University of Chinese Medicine, Kunming, China
- Key Laboratory of Microcosmic Syndrome Differentiation, Yunnan University of Chinese Medicine, Kunming, China
- Department of Basic Medical, Yunnan University of Chinese Medicine, Kunming, China
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3
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Wang H, Zhang Y, Rong X, Wang B, Wang L, Wang C, Gao W, Ye X, Hou X, Liu W, Wu M, Cheng Y, Shu X, Shang J. A novel lysosome-targeted fluorescent probe for precise formaldehyde detection in water samples, living cells and breast cancer tumors. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 313:124105. [PMID: 38461560 DOI: 10.1016/j.saa.2024.124105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 03/12/2024]
Abstract
This study investigated the potential ability of the fluorescent probe Ly-CHO to detect formaldehyde (FA) in living cells and tumor-bearing mice. Ly-CHO exhibited great selectivity, excellent sensitivity, and rapid response to FA, making it a valuable tool for tracking FA concentration changes. The probe was also found to target lysosomes specifically. Furthermore, Ly-CHO showed an obvious fluorescence increase in endogenous CHO detection after adding tetrahydrogen folic acid (THFA). This study validated Ly-CHO's possibility for FA imaging in vivo, with potential applications in understanding formaldehyde-related diseases.
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Affiliation(s)
- Haiping Wang
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China; Cancer Institute, School of Medicine, Jianghan University, Wuhan, China
| | - Yibin Zhang
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China; College of Chemistry and Chemical Engineering, Yangtze Normal University, Chongqing, China.
| | - Xiaoqian Rong
- College of Chemistry and Chemical Engineering, Yangtze Normal University, Chongqing, China
| | - Boling Wang
- College of Chemistry and Chemical Engineering, Yangtze Normal University, Chongqing, China
| | - Li Wang
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China; Cancer Institute, School of Medicine, Jianghan University, Wuhan, China
| | - Chen Wang
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
| | - Wanxia Gao
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
| | - Xiansheng Ye
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China; Cancer Institute, School of Medicine, Jianghan University, Wuhan, China
| | - Xiaoying Hou
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China; Cancer Institute, School of Medicine, Jianghan University, Wuhan, China
| | - Wei Liu
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China
| | - Meihui Wu
- College of Chemistry and Chemical Engineering, Yangtze Normal University, Chongqing, China
| | - Yueting Cheng
- College of Chemistry and Chemical Engineering, Yangtze Normal University, Chongqing, China
| | - Xiji Shu
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China.
| | - Jinting Shang
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, China; Cancer Institute, School of Medicine, Jianghan University, Wuhan, China.
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4
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Todd ZR, Lozano GG, Kufner CL, Ranjan S, Catling DC, Sasselov DD. UV Transmission in Prebiotic Environments on Early Earth. ASTROBIOLOGY 2024; 24:559-569. [PMID: 38768432 DOI: 10.1089/ast.2023.0077] [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: 05/22/2024]
Abstract
Ultraviolet (UV) light is likely to have played important roles in surficial origins of life scenarios, potentially as a productive source of energy and molecular activation, as a selective means to remove unwanted side products, or as a destructive mechanism resulting in loss of molecules/biomolecules over time. The transmission of UV light through prebiotic waters depends upon the chemical constituents of such waters, but constraints on this transmission are limited. Here, we experimentally measure the molar decadic extinction coefficients for a number of small molecules used in various prebiotic synthetic schemes. We find that many small feedstock molecules absorb most at short (∼200 nm) wavelengths, with decreasing UV absorption at longer wavelengths. For comparison, we also measured the nucleobase adenine and found that adenine absorbs significantly more than the simpler molecules often invoked in prebiotic synthesis. Our results enable the calculation of UV photon penetration under varying chemical scenarios and allow further constraints on plausibility and self-consistency of such scenarios. While the precise path that prebiotic chemistry took remains elusive, improved understanding of the UV environment in prebiotically plausible waters can help constrain both the chemistry and the environmental conditions that may allow such chemistry to occur.
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Affiliation(s)
- Zoe R Todd
- Department of Earth and Space Sciences, University of Washington, Seattle, Washington, USA
- Department of Chemistry, Department of Astronomy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Gabriella G Lozano
- Center for Astrophysics, Harvard and Smithsonian, Cambridge, Massachusetts, USA
| | - Corinna L Kufner
- Center for Astrophysics, Harvard and Smithsonian, Cambridge, Massachusetts, USA
| | - Sukrit Ranjan
- Lunar & Planetary Laboratory/Department of Planetary Sciences, University of Arizona, Tucson, Arizona, USA
| | - David C Catling
- Department of Earth and Space Sciences, University of Washington, Seattle, Washington, USA
| | - Dimitar D Sasselov
- Center for Astrophysics, Harvard and Smithsonian, Cambridge, Massachusetts, USA
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5
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Ono C, Sunami S, Ishii Y, Kim HJ, Kakegawa T, Benner SA, Furukawa Y. Abiotic Ribose Synthesis Under Aqueous Environments with Various Chemical Conditions. ASTROBIOLOGY 2024; 24:489-497. [PMID: 38696654 DOI: 10.1089/ast.2023.0071] [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: 05/04/2024]
Abstract
Ribose is the defining sugar in ribonucleic acid (RNA), which is often proposed to have carried the genetic information and catalyzed the biological reactions of the first life on Earth. Thus, abiological processes that yield ribose under prebiotic conditions have been studied for decades. However, aqueous environments required for the formation of ribose from materials available in quantity under geologically reasonable models, where the ribose formed is not immediately destroyed, remain unclear. This is due in large part to the challenge of analysis of carbohydrates formed under a wide range of aqueous conditions. Thus, the formation of ribose on prebiotic Earth has sometimes been questioned. We investigated the quantitative effects of pH, temperature, cation, and the concentrations of formaldehyde and glycolaldehyde on the synthesis of diverse sugars, including ribose. The results suggest a range of conditions that produce ribose and that ribose could have formed in constrained aquifers on prebiotic Earth.
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Affiliation(s)
- Chinatsu Ono
- Department of Earth Science, Tohoku University, Aoba-ku, Sendai, Japan
| | - Sako Sunami
- Department of Earth Science, Tohoku University, Aoba-ku, Sendai, Japan
| | - Yuka Ishii
- Department of Earth Science, Tohoku University, Aoba-ku, Sendai, Japan
| | - Hyo-Joong Kim
- Foundation for Applied Molecular Evolution, Alachua, Florida, USA
- Firebird Biomolecular Sciences LLC, Alachua, Florida, USA
| | - Takeshi Kakegawa
- Department of Earth Science, Tohoku University, Aoba-ku, Sendai, Japan
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, Florida, USA
- Firebird Biomolecular Sciences LLC, Alachua, Florida, USA
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6
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Koyama S, Kamada A, Furukawa Y, Terada N, Nakamura Y, Yoshida T, Kuroda T, Vandaele AC. Atmospheric formaldehyde production on early Mars leading to a potential formation of bio-important molecules. Sci Rep 2024; 14:2397. [PMID: 38336798 PMCID: PMC10858170 DOI: 10.1038/s41598-024-52718-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Formaldehyde (H2CO) is a critical precursor for the abiotic formation of biomolecules, including amino acids and sugars, which are the building blocks of proteins and RNA. Geomorphological and geochemical evidence on Mars indicates a temperate environment compatible with the existence of surface liquid water during its early history at 3.8-3.6 billion years ago (Ga), which was maintained by the warming effect of reducing gases, such as H2. However, it remains uncertain whether such a temperate and weakly reducing surface environment on early Mars was suitable for producing H2CO. In this study, we investigated the atmospheric production of H2CO on early Mars using a 1-D photochemical model assuming a thick CO2-dominated atmosphere with H2 and CO. Our results show that a continuous supply of atmospheric H2CO can be used to form various organic compounds, including amino acids and sugars. This could be a possible origin for the organic matter observed on the Martian surface. Given the previously reported conversion rate from H2CO into ribose, the calculated H2CO deposition flux suggests a continuous supply of bio-important sugars on early Mars, particularly during the Noachian and early Hesperian periods.
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Affiliation(s)
- Shungo Koyama
- Graduate School of Science, Tohoku University, Sendai, Miyagi, 980-8578, Japan.
| | - Arihiro Kamada
- Graduate School of Science, Tohoku University, Sendai, Miyagi, 980-8578, Japan
| | - Yoshihiro Furukawa
- Graduate School of Science, Tohoku University, Sendai, Miyagi, 980-8578, Japan
| | - Naoki Terada
- Graduate School of Science, Tohoku University, Sendai, Miyagi, 980-8578, Japan
| | - Yuki Nakamura
- Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Tatsuya Yoshida
- Graduate School of Science, Tohoku University, Sendai, Miyagi, 980-8578, Japan
| | - Takeshi Kuroda
- Graduate School of Science, Tohoku University, Sendai, Miyagi, 980-8578, Japan
- Division for the Establishment of Frontier Sciences of Organization for Advanced Studies, Tohoku University, Sendai, Japan
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7
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Hirakawa Y, Kakegawa T, Furukawa Y. Hexose phosphorylation for a non-enzymatic glycolysis and pentose phosphate pathway on early Earth. Sci Rep 2024; 14:264. [PMID: 38168787 PMCID: PMC10762079 DOI: 10.1038/s41598-023-50743-8] [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: 09/08/2023] [Accepted: 12/24/2023] [Indexed: 01/05/2024] Open
Abstract
Glycolysis and pentose phosphate pathways play essential roles in cellular processes and are assumed to be among the most ancient metabolic pathways. Non-enzymatic metabolism-like reactions might have occurred on the prebiotic Earth and been inherited by the biological reactions. Previous research has identified a part of the non-enzymatic glycolysis and the non-enzymatic pentose phosphate pathway from glucose 6-phosphate and 6-phosphogluconate, which are intermediates of these reactions. However, how these phosphorylated molecules were formed on the prebiotic Earth remains unclear. Herein, we demonstrate the synthesis of glucose and gluconate from simple aldehydes in alkaline solutions and the formation of glucose 6-phosphate and 6-phosphogluconate with borate using thermal evaporation. These results imply that the initial stages of glycolysis-like and pentose phosphate pathway-like reactions were achieved in borate-rich evaporative environments on prebiotic Earth, suggesting that non-enzymatic metabolism provided biomolecules and their precursors on prebiotic Earth.
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Affiliation(s)
- Yuta Hirakawa
- Department of Earth Science, Tohoku University, 6-3, Aza-Aoba, Aramaki, Aoba-Ku, Sendai, 980-8578, Japan.
| | - Takeshi Kakegawa
- Department of Earth Science, Tohoku University, 6-3, Aza-Aoba, Aramaki, Aoba-Ku, Sendai, 980-8578, Japan
| | - Yoshihiro Furukawa
- Department of Earth Science, Tohoku University, 6-3, Aza-Aoba, Aramaki, Aoba-Ku, Sendai, 980-8578, Japan
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8
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Tran QP, Yi R, Fahrenbach AC. Towards a prebiotic chemoton - nucleotide precursor synthesis driven by the autocatalytic formose reaction. Chem Sci 2023; 14:9589-9599. [PMID: 37712016 PMCID: PMC10498504 DOI: 10.1039/d3sc03185c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/17/2023] [Indexed: 09/16/2023] Open
Abstract
The formose reaction is often cited as a prebiotic source of sugars and remains one of the most plausible forms of autocatalysis on the early Earth. Herein, we investigated how cyanamide and 2-aminooxazole, molecules proposed to be present on early Earth and precursors for nonenzymatic ribonucleotide synthesis, mediate the formose reaction using HPLC, LC-MS and 1H NMR spectroscopy. Cyanamide was shown to delay the exponential phase of the formose reaction by reacting with formose sugars to form 2-aminooxazole and 2-aminooxazolines thereby diverting some of these sugars from the autocatalytic cycle, which nonetheless remains intact. Masses for tetrose and pentose aminooxazolines, precursors for nucleotide synthesis including TNA and RNA, were also observed. The results of this work in the context of the chemoton model are further discussed. Additionally, we highlight other prebiotically plausible molecules that could have mediated the formose reaction and alternative prebiotic autocatalytic systems.
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Affiliation(s)
- Quoc Phuong Tran
- School of Chemistry, University of New South Wales Sydney NSW 2052 Australia
- Australian Centre for Astrobiology, University of New South Wales Sydney NSW 2052 Australia
| | - Ruiqin Yi
- Earth-Life Science Institute, Tokyo Institute of Technology Tokyo 152-8550 Japan
| | - Albert C Fahrenbach
- School of Chemistry, University of New South Wales Sydney NSW 2052 Australia
- Australian Centre for Astrobiology, University of New South Wales Sydney NSW 2052 Australia
- UNSW RNA Institute, University of New South Wales Sydney NSW 2052 Australia
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9
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Omran A. Plausibility of the Formose Reaction in Alkaline Hydrothermal Vent Environments. ORIGINS LIFE EVOL B 2023; 53:113-125. [PMID: 32749559 DOI: 10.1007/s11084-020-09599-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/27/2020] [Accepted: 06/22/2020] [Indexed: 01/09/2023]
Abstract
Prebiotic processes required a reliable source of free energy and complex chemical mixtures that may have included sugars. The formose reaction is a potential source of those sugars. At moderate to elevated temperature and pH ranges, these sugars rapidly decay. Here it is shown that CaCO3-based chemical gardens catalyze the formose reaction to produce glucose, ribose, and other monosaccharides. These thin inorganic membranes are explored as analogs of hydrothermal vent materials-a possible place for the origin of life-and similarly exposed to very steep pH gradients. Supported by simulations of a simple reaction-diffusion model, this study shows that such gradients allow for the dynamic accumulation of sugars in specific layers of the thin membrane, effectively protecting formose sugar yields. Therefore, the formose reaction may be a plausible prebiotic reaction in alkaline hydrothermal vent environments, possibly setting the stage for an RNA world.
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Affiliation(s)
- Arthur Omran
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306-4390, USA.
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10
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Zhang T, Wen M, Ding C, Zhang Y, Ma X, Wang Z, Lily M, Liu J, Wang R. Multiple evaluations of atmospheric behavior between Criegee intermediates and HCHO: Gas-phase and air-water interface reaction. J Environ Sci (China) 2023; 127:308-319. [PMID: 36522063 DOI: 10.1016/j.jes.2022.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/31/2022] [Accepted: 06/02/2022] [Indexed: 06/17/2023]
Abstract
Given the high abundance of water in the atmosphere, the reaction of Criegee intermediates (CIs) with (H2O)2 is considered to be the predominant removal pathway for CIs. However, recent experimental findings reported that the reactions of CIs with organic acids and carbonyls are faster than expected. At the same time, the interface behavior between CIs and carbonyls has not been reported so far. Here, the gas-phase and air-water interface behavior between Criegee intermediates and HCHO were explored by adopting high-level quantum chemical calculations and Born-Oppenheimer molecular dynamics (BOMD) simulations. Quantum chemical calculations evidence that the gas-phase reactions of CIs + HCHO are submerged energy or low energy barriers processes. The rate ratios speculate that the HCHO could be not only a significant tropospheric scavenger of CIs, but also an inhibitor in the oxidizing ability of CIs on SOx in dry and highly polluted areas with abundant HCHO concentration. The reactions of CH2OO with HCHO at the droplet's surface follow a loop structure mechanism to produce i) SOZ (), ii) BHMP (HOCH2OOCH2OH), and iii) HMHP (HOCH2OOH). Considering the harsh reaction conditions between CIs and HCHO at the interface (i.e., the two molecules must be sufficiently close to each other), the hydration of CIs is still their main atmospheric loss pathway. These results could help us get a better interpretation of the underlying CIs-aldehydes chemical processes in the global polluted urban atmospheres.
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Affiliation(s)
- Tianlei Zhang
- Institute of Theoretical and Computational Chemistry, Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong 723001, China.
| | - Mingjie Wen
- Institute of Theoretical and Computational Chemistry, Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong 723001, China
| | - Chao Ding
- Institute of Theoretical and Computational Chemistry, Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong 723001, China
| | - Yongqi Zhang
- Institute of Theoretical and Computational Chemistry, Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong 723001, China
| | - Xiaohui Ma
- School of Environmental Science and Engineering, Institute of Environmental Health and Pollution Control, Guangdong University of Technology, Guangzhou 510006, China.
| | - Zhuqing Wang
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Makroni Lily
- Environmental Research Institute, Shandong University, Qingdao 266237, China
| | - Junhai Liu
- Institute of Theoretical and Computational Chemistry, Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong 723001, China; Qinba Mountains of Bio-Resource Collaborative Innovation Center of Southern Shaanxi Province, Shaanxi University of Technology, Hanzhong 723001, China
| | - Rui Wang
- Institute of Theoretical and Computational Chemistry, Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi University of Technology, Hanzhong 723001, China
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11
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Prebiotic Synthesis of ATP: A Terrestrial Volcanism-Dependent Pathway. Life (Basel) 2023; 13:life13030731. [PMID: 36983886 PMCID: PMC10053121 DOI: 10.3390/life13030731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/27/2023] [Accepted: 03/06/2023] [Indexed: 03/12/2023] Open
Abstract
Adenosine triphosphate (ATP) is a multifunctional small molecule, necessary for all modern Earth life, which must be a component of the last universal common ancestor (LUCA). However, the relatively complex structure of ATP causes doubts about its accessibility on prebiotic Earth. In this paper, based on previous studies on the synthesis of ATP components, a plausible prebiotic pathway yielding this key molecule is constructed, which relies on terrestrial volcanism to provide the required materials and suitable conditions.
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12
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Benner SA. Rethinking nucleic acids from their origins to their applications. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220027. [PMID: 36633284 PMCID: PMC9835595 DOI: 10.1098/rstb.2022.0027] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/17/2022] [Indexed: 01/13/2023] Open
Abstract
Reviewed are three decades of synthetic biology research in our laboratory that has generated alternatives to standard DNA and RNA as possible informational systems to support Darwinian evolution, and therefore life, and to understand their natural history, on Earth and throughout the cosmos. From this, we have learned that: • the core structure of nucleic acids appears to be a natural outcome of non-biological chemical processes probably in constrained, intermittently irrigated, sub-aerial aquifers on the surfaces of rocky planets like Earth and/or Mars approximately 4.36 ± 0.05 billion years ago; • however, this core is not unique. Synthetic biology has generated many different molecular systems able to support the evolution of molecular information; • these alternatives to standard DNA and RNA support biotechnology, including DNA synthesis, human diagnostics, biomedical research and medicine; • in particular, they support laboratory in vitro evolution (LIVE) with performance to generate catalysts at least 104-105 fold better than standard DNA libraries, enhancing access to receptors and catalysts on demand. Coupling nanostructures to the products of LIVE with expanded DNA offers new approaches for disease therapy; and • nevertheless, a polyelectrolyte structure and size regular building blocks are required for any informational polymer to support Darwinian evolution. These features serve as universal and agnostic biosignatures, useful for seeking life throughout the Solar System. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.
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Affiliation(s)
- Steven A. Benner
- Foundation for Applied Molecular Evolution, 13709 Progress Boulevard no. 7, Alachua, FL 32615, USA
- Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard no. 17, Alachua, FL 32615, USA
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13
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Tian Z, Wang P, Huang K, Yu J, Zhang M, Liu Y, Zhao H, Zhu B, Huang X, Tong Z. Photobiomodulation for Alzheimer's disease: photoelectric coupling effect on attenuating Aβ neurotoxicity. Lasers Med Sci 2023; 38:39. [PMID: 36633696 PMCID: PMC9837011 DOI: 10.1007/s10103-022-03692-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/12/2022] [Indexed: 01/13/2023]
Abstract
Alzheimer's disease (AD) and dementia are the most worrying health problems faced by people globally today. Although the pathological features of AD consisting of amyloid-beta (Aβ) plaques in the extracellular space (ECS) and intracellular tau tangles are well established, the developed medicines targeting these two proteins have not obtained the expected clinical effects. Photobiomodulation (PBM) describes the therapeutic use of red light (RL) or near-infrared light (NIR) to serve as a noninvasive neuroprotective strategy for brain diseases. The present review discusses the mechanisms of the photoelectric coupling effect (light energy-induced special electronic transition-related alterations in protein structure) of PBM on reducing Aβ toxicity. On the one hand, RL or NIR can directly disassemble Aβ in vitro and in vivo. On the other hand, formaldehyde (FA)-inhibited catalase (CAT) and H2O2-inactived formaldehyde dehydrogenase (FDH) are formed a vicious circle in AD; however, light energy not only activates FDH to degrade excessive FA (which crosslinks Aβ monomer to form Aβ oligomers and senile plaques) but also sensitizes CAT to reduce hydrogen peroxide levels (H2O2, which can facilitate Aβ aggregation and enhance FA generation). In addition, it also activates mitochondrial cytochrome-c to produce ATP in the neurons. Clinical trials of phototherapeutics or oral coenzyme Q10 have shown positive effects in AD patients. Hence, a promising strategy combined PBM with nanopacked Q10 has been proposed to apply for treating AD.
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Affiliation(s)
- Zixi Tian
- Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of Aging, Oujiang Laboratory, School of Mental Health, Wenzhou Medical University, Wenzhou, 325035, China
| | - Panpan Wang
- Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of Aging, Oujiang Laboratory, School of Mental Health, Wenzhou Medical University, Wenzhou, 325035, China
- Department Neurology, Wenzhou Medical University Affiliated Hospital 3, Wenzhou, 325200, China
| | - Kai Huang
- Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of Aging, Oujiang Laboratory, School of Mental Health, Wenzhou Medical University, Wenzhou, 325035, China
| | - Jie Yu
- Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of Aging, Oujiang Laboratory, School of Mental Health, Wenzhou Medical University, Wenzhou, 325035, China
| | - Mange Zhang
- Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of Aging, Oujiang Laboratory, School of Mental Health, Wenzhou Medical University, Wenzhou, 325035, China
| | - Yanming Liu
- Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of Aging, Oujiang Laboratory, School of Mental Health, Wenzhou Medical University, Wenzhou, 325035, China
| | - Hang Zhao
- Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of Aging, Oujiang Laboratory, School of Mental Health, Wenzhou Medical University, Wenzhou, 325035, China
| | - Beilei Zhu
- Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of Aging, Oujiang Laboratory, School of Mental Health, Wenzhou Medical University, Wenzhou, 325035, China
| | - Xuerong Huang
- Department Neurology, Wenzhou Medical University Affiliated Hospital 3, Wenzhou, 325200, China.
| | - Zhiqian Tong
- Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of Aging, Oujiang Laboratory, School of Mental Health, Wenzhou Medical University, Wenzhou, 325035, China.
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14
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Cai T, Teng Z, Wen Y, Zhang H, Wang S, Fu X, Song L, Li M, Lv J, Zeng Q. Single-atom site catalysts for environmental remediation: Recent advances. JOURNAL OF HAZARDOUS MATERIALS 2022; 440:129772. [PMID: 35988491 DOI: 10.1016/j.jhazmat.2022.129772] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Single-atom site catalysts (SACs) can maximize the utilization of active metal species and provide an attractive way to regulate the activity and selectivity of catalytic reactions. The adjustable coordination configuration and atomic structure of SACs enable them to be an ideal candidate for revealing reaction mechanisms in various catalytic processes. The minimum use of metals and relatively tight anchoring of the metal atoms significantly reduce leaching and environmental risks. Additionally, the unique physicochemical properties of single atom sites endow SACs with superior activity in various catalytic processes for environmental remediation (ER). Generally, SACs are burgeoning and promising materials in the application of ER. However, a systematic and critical review on the mechanism and broad application of SACs-based ER is lacking. Herein, we review emerging studies applying SACs for different ERs, such as eliminating organic pollutants in water, removing volatile organic compounds, purifying automobile exhaust, and others (hydrodefluorination and disinfection). We have summarized the synthesis, characterization, reaction mechanism and structural-function relationship of SACs in ER. In addition, the perspectives and challenges of SACs for ER are also analyzed. We expect that this review can provide constructive inspiration for discoveries and applications of SACs in environmental catalysis in the future.
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Affiliation(s)
- Tao Cai
- School of Resources & Environment and Safety Engineering, University of South China, Hengyang, Hunan 421001, China
| | - Zhenzhen Teng
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Yanjun Wen
- School of Resources & Environment and Safety Engineering, University of South China, Hengyang, Hunan 421001, China
| | - Huayang Zhang
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Shaobin Wang
- School of Chemical Engineering and Advanced Materials, The University of Adelaide, Adelaide, SA 5005, Australia.
| | - Xijun Fu
- School of Resources & Environment and Safety Engineering, University of South China, Hengyang, Hunan 421001, China
| | - Lu Song
- School of Resources & Environment and Safety Engineering, University of South China, Hengyang, Hunan 421001, China
| | - Mi Li
- School of Resources & Environment and Safety Engineering, University of South China, Hengyang, Hunan 421001, China
| | - Junwen Lv
- School of Resources & Environment and Safety Engineering, University of South China, Hengyang, Hunan 421001, China
| | - Qingyi Zeng
- School of Resources & Environment and Safety Engineering, University of South China, Hengyang, Hunan 421001, China.
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15
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Borate-guided ribose phosphorylation for prebiotic nucleotide synthesis. Sci Rep 2022; 12:11828. [PMID: 35853897 PMCID: PMC9296462 DOI: 10.1038/s41598-022-15753-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/29/2022] [Indexed: 11/15/2022] Open
Abstract
Polymers of ribonucleotides (RNAs) are considered to store genetic information and promote biocatalytic reactions for the proto life on chemical evolution. Abiotic synthesis of ribonucleotide was successful in past experiments; nucleoside synthesis occurred first, followed by phosphorylation. These abiotic syntheses are far from biotic reactions and have difficulties as a prebiotic reaction in reacting chemicals in a specific order and purifying intermediates from other molecules in multi-steps of reactions. Another reaction, ribose phosphorylation followed by nucleobase synthesis or nucleobase addition, is close to the biotic reactions of nucleotide synthesis. However, the synthesis of ribose 5′-phosphate under prebiotically plausible conditions remains unclear. Here, we report a high-yield regioselective one-pot synthesis of ribose 5′-phosphate from an aqueous solution containing ribose, phosphate, urea, and borate by simple thermal evaporation. Of note, phosphorylation of ribose before the nucleoside formation differs from the traditional prebiotic nucleotide syntheses and is also consistent with biological nucleotide synthesis. Phosphorylation occurred to the greatest extent in ribose compared to other aldopentoses, only in the presence of borate. Borate is known to improve the stability of ribose preferentially. Geological evidence suggests the presence of borate-rich settings on the early Earth. Therefore, borate-rich evaporitic environments could have facilitated preferential synthesis of ribonucleotide coupled with enhanced stability of ribose on the early Earth.
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16
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Fustin JM. Methyl Metabolism and the Clock: An Ancient Story With New Perspectives. J Biol Rhythms 2022; 37:235-248. [PMID: 35382619 PMCID: PMC9160962 DOI: 10.1177/07487304221083507] [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] [Indexed: 11/16/2022]
Abstract
Methylation, that is, the transfer or synthesis of a –CH3 group onto a target molecule, is a pervasive biochemical modification found in organisms from bacteria to humans. In mammals, a complex metabolic pathway powered by the essential nutrients vitamin B9 and B12, methionine and choline, synthesizes S-adenosylmethionine, the methyl donor in the methylation of nucleic acids, proteins, fatty acids, and small molecules by over 200 substrate-specific methyltransferases described so far in humans. Methylations not only play a key role in scenarios for the origin and evolution of life, but they remain essential for the development and physiology of organisms alive today, and methylation deficiencies contribute to the etiology of many pathologies. The methylation of histones and DNA is important for circadian rhythms in many organisms, and global inhibition of methyl metabolism similarly affects biological rhythms in prokaryotes and eukaryotes. These observations, together with various pieces of evidence scattered in the literature on circadian gene expression and metabolism, indicate a close mutual interdependence between biological rhythms and methyl metabolism that may originate from prebiotic chemistry. This perspective first proposes an abiogenetic scenario for rhythmic methylations and then outlines mammalian methyl metabolism, before reanalyzing previously published data to draw a tentative map of its profound connections with the circadian clock.
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Affiliation(s)
- Jean-Michel Fustin
- Centre for Biological Timing, The University of Manchester, Manchester, UK
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17
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Depleted carbon isotope compositions observed at Gale crater, Mars. Proc Natl Acad Sci U S A 2022; 119:2115651119. [PMID: 35042808 PMCID: PMC8795525 DOI: 10.1073/pnas.2115651119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2021] [Indexed: 11/20/2022] Open
Abstract
Carbon isotopic analysis is among the most pervasive geochemical approaches because the fractionation of carbon isotopes produces a natural tracer of biological and chemical processes. Rover-based carbon isotopic analyses of sedimentary rocks on Mars have the potential to reveal modes of Martian carbon cycling. We report carbon isotopic values of the methane released during pyrolysis of samples obtained at Gale crater. The values show remarkable variation indicating different origins for the carbon evolved from different samples. Samples from multiple locations within Gale crater evolved methane with highly fractionated carbon isotopes. We suggest three routes by which highly fractionated carbon could be deposited on Mars, with each suggesting that Martian carbon cycling is quite distinct from that of the present Earth. Obtaining carbon isotopic information for organic carbon from Martian sediments has long been a goal of planetary science, as it has the potential to elucidate the origin of such carbon and aspects of Martian carbon cycling. Carbon isotopic values (δ13CVPDB) of the methane released during pyrolysis of 24 powder samples at Gale crater, Mars, show a high degree of variation (−137 ± 8‰ to +22 ± 10‰) when measured by the tunable laser spectrometer portion of the Sample Analysis at Mars instrument suite during evolved gas analysis. Included in these data are 10 measured δ13C values less than −70‰ found for six different sampling locations, all potentially associated with a possible paleosurface. There are multiple plausible explanations for the anomalously depleted 13C observed in evolved methane, but no single explanation can be accepted without further research. Three possible explanations are the photolysis of biological methane released from the subsurface, photoreduction of atmospheric CO2, and deposition of cosmic dust during passage through a galactic molecular cloud. All three of these scenarios are unconventional, unlike processes common on Earth.
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18
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Kou Y, Zhao H, Cui D, Han H, Tong Z. Formaldehyde toxicity in age-related neurological dementia. Ageing Res Rev 2022; 73:101512. [PMID: 34798299 DOI: 10.1016/j.arr.2021.101512] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/02/2021] [Accepted: 11/08/2021] [Indexed: 02/02/2023]
Abstract
The primordial small gaseous molecules, such as: NO, CO, H2S and formaldehyde (FA) are present in the brains. Whether FA as well as the other molecules participates in brain functions is unclear. Recently, its pathophysiological functions have been investigated. Notably, under physiological conditions, learning activity induces a transient generation of hippocampal FA, which promotes memory formation by enhancing N-methyl-D-aspartate (NMDA)-currents. However, ageing leads to FA accumulation in brain for the dysregulation of FA metabolism; and excessive FA directly impairs memory by inhibiting NMDA-receptor. Especially, in Alzheimer's disease (AD), amyloid-beta (Aβ) accelerates FA accumulation by inactivating alcohol dehydrogenase-5; in turn, FA promotes Aβ oligomerization, fibrillation and tau hyperphosphorylation. Hence, there is a vicious circle encompassing Aβ assembly and FA generation. Even worse, FA induces Aβ deposition in the extracellular space (ECS), which blocks the medicines (dissolved in the interstitial fluid) flowing into the damaged neurons in the deep cortex. However, phototherapy destroys Aβ deposits in the ECS and restores ISF flow. Coenzyme Q10, which scavenges FA, was shown to ameliorate Aβ-induced AD pathological phenotypes, thus suggesting a causative relation between FA toxicity and AD. These findings suggest that the combination of these two methods is a promising strategy for treating AD.
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19
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Rimmer PB, Thompson SJ, Xu J, Russell DA, Green NJ, Ritson DJ, Sutherland JD, Queloz DP. Timescales for Prebiotic Photochemistry Under Realistic Surface Ultraviolet Conditions. ASTROBIOLOGY 2021; 21:1099-1120. [PMID: 34152196 PMCID: PMC8570677 DOI: 10.1089/ast.2020.2335] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Ultraviolet (UV) light has long been invoked as a source of energy for prebiotic chemical synthesis, but experimental support does not involve sources of UV light that look like the young Sun. Here we experimentally investigate whether the UV flux available on the surface of early Earth, given a favorable atmosphere, can facilitate a variety of prebiotic chemical syntheses. We construct a solar simulator for the UV light of the faint young Sun on the surface of early Earth, called StarLab. We then attempt a series of reactions testing different aspects of a prebiotic chemical scenario involving hydrogen cyanide (HCN), sulfites, and sulfides under the UV light of StarLab, including hypophosphite oxidation by UV light and hydrogen sulfide, photoreduction of HCN with bisulfite, the photoanomerization of α-thiocytidine, the production of a chemical precursor of a potentially prebiotic activating agent (nitroprusside), the photoreduction of thioanhydrouridine and thioanhydroadenosine, and the oxidation of ethanol (EtOH) by photochemically generated hydroxyl radicals. We compare the output of StarLab to the light of the faint young Sun to constrain the timescales over which these reactions would occur on the surface of early Earth. We predict that hypophosphite oxidation, HCN reduction, and photoproduction of nitroprusside would all operate on the surface of early Earth in a matter of days to weeks. The photoanomerization of α-thiocytidine would take months to complete, and the production of oxidation products from hydroxyl radicals would take years. The photoreduction of thioanhydrouridine with hydrogen sulfide did not succeed even after a long period of irradiation, providing a lower limit on the timescale of several years. The photoreduction of thioanhydroadenosine with bisulfite produced 2'-deoxyriboadenosine (dA) on the timescale of days. This suggests the plausibility of the photoproduction of purine deoxyribonucleotides, such as the photoproduction of simple sugars, proceeds more efficiently in the presence of bisulfite.
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Affiliation(s)
- Paul B. Rimmer
- Department of Earth Sciences, University of Cambridge, Cambridge, United Kingdom
- Cavendish Laboratory, University of Cambridge, Cambridge, United Kingdom
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- Address correspondence to: Paul B. Rimmer, Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EQ, United Kingdom
| | | | - Jianfeng Xu
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | | | | | | | - Didier P. Queloz
- Cavendish Laboratory, University of Cambridge, Cambridge, United Kingdom
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20
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Abstract
A major goal of synthetic biology is to understand the transition between non-living matter and life. The bottom-up development of an artificial cell would provide a minimal system with which to study the border between chemistry and biology. So far, a fully synthetic cell has remained elusive, but chemists are progressing towards this goal by reconstructing cellular subsystems. Cell boundaries, likely in the form of lipid membranes, were necessary for the emergence of life. In addition to providing a protective barrier between cellular cargo and the external environment, lipid compartments maintain homeostasis with other subsystems to regulate cellular processes. In this Review, we examine different chemical approaches to making cell-mimetic compartments. Synthetic strategies to drive membrane formation and function, including bioorthogonal ligations, dissipative self-assembly and reconstitution of biochemical pathways, are discussed. Chemical strategies aim to recreate the interactions between lipid membranes, the external environment and internal biomolecules, and will clarify our understanding of life at the interface of chemistry and biology.
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21
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Ma C, Sun S, Lu H, Hao Z, Yang C, Wang B, Chen C, Song M. Remarkable MnO 2 structure-dependent H 2O promoting effect in HCHO oxidation at room temperature. JOURNAL OF HAZARDOUS MATERIALS 2021; 414:125542. [PMID: 33667806 DOI: 10.1016/j.jhazmat.2021.125542] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/10/2021] [Accepted: 02/24/2021] [Indexed: 06/12/2023]
Abstract
H2O is often critical in determining the activity and stability of metal oxide catalysts for HCHO oxidation; however, synthesis of metal oxide catalysts with super resistance to H2O remains a challenging. Herein, we synthesized Akhtenskite-type MnO2 catalyst with Mn-O-Mn stretching along MnO6 octahedra layers, which promotes the utilization of the associatively adsorbed H2O. The activity and stability of formaldehyde oxidation at room temperature enhanced in humid air. Diffuse-reflectance infrared Fourier transform (DRIRFT) spectroscopy was used to characterize the H2O adsorption and intermediate species. The associatively adsorbed H2O promotes the oxidation of formaldehyde to CO2 via the formic acid intermediate. The service life of MnO2 is prolonged due to formic acid generation. MnO2 gradually deactivates when formic acid accumulates and forms formate and hydrogen carbonate species. This study provides significant insights into the development of a high-efficiency MnO2 catalyst for formaldehyde oxidation in humid air, and the developed MnO2 catalyst is a promising candidate for application in practical formaldehyde elimination.
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Affiliation(s)
- Chunyan Ma
- Key Laboratory of Environmental Nanotechnology and Health Effects, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shumei Sun
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Hao Lu
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Zhengping Hao
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenggong Yang
- Key Laboratory of Environmental Nanotechnology and Health Effects, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bin Wang
- Beijing Research Institute of Chemical Industry, Sinopec Group, Beijing 100013, China
| | - Cheng Chen
- Key Laboratory of Environmental Nanotechnology and Health Effects, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Maoyong Song
- Key Laboratory of Environmental Nanotechnology and Health Effects, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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22
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Masuda S, Furukawa Y, Kobayashi T, Sekine T, Kakegawa T. Experimental Investigation of the Formation of Formaldehyde by Hadean and Noachian Impacts. ASTROBIOLOGY 2021; 21:413-420. [PMID: 33784199 DOI: 10.1089/ast.2020.2320] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Formaldehyde (FA) is an important precursor in the abiotic synthesis of major biomolecules including amino acids, sugars, and nucleobases. Thus, spontaneous formation of prebiotic FA must have been crucial for the chemical origin of life. The frequent impacts of meteorites and asteroids on Hadean Earth have been considered one of the abiotic synthetic processes of organic compounds. However, the impact-induced formation of FA from CO2 as the major atmospheric constituent has not been confirmed yet. This study investigated the formation of FA in impact-induced reactions among meteoritic minerals, bicarbonate, gaseous nitrogen, and water to simulate the abiotic process experimentally. Products were analyzed with ultra-high-performance liquid chromatography/tandem mass spectrometry and powder X-ray diffraction techniques. The results show the formation of FA and oxidation of metallic iron to siderite in the impact shock experiments. This indicates that this important prebiotic molecule was also synthesized by impacts of iron-bearing meteorites/asteroids on the Hadean oceans. The impact events might have generated spatially and temporally FA-enriched localized environments. Moreover, the impact-induced synthesis of FA may have also occurred on Noachian Mars given the presence of liquid water and a CO2-N2-rich atmosphere on the planet.
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Affiliation(s)
- Saeka Masuda
- Department of Earth Science, Tohoku University, Sendai, Japan
| | | | | | - Toshimori Sekine
- Center for High Pressure Science & Technology Advanced Research, Shanghai, China
- Graduate School of Engineering, Osaka University, Osaka, Japan
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23
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Kim HJ, Benner SA. Abiotic Synthesis of Nucleoside 5'-Triphosphates with Nickel Borate and Cyclic Trimetaphosphate (CTMP). ASTROBIOLOGY 2021; 21:298-306. [PMID: 33533695 DOI: 10.1089/ast.2020.2264] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
While nucleoside 5'-triphosphates are precursors for RNA in modern biology, the presumed difficulty of making these triphosphates on Hadean Earth has caused many prebiotic researchers to consider other activated species for the prebiotic synthesis of RNA. We report here that nickel(II), in the presence of borate, gives substantial amounts (2-3%) of nucleoside 5'-triphosphates upon evaporative heating in the presence of urea, salts, and cyclic trimetaphosphate (CTMP). Also recovered are nucleoside 5'-diphosphates and nucleoside 5'-monophosphates, both likely arising from 5'-triphosphate intermediates. The total level of 5'-phosphorylation is typically 30%. Borate enhances the regiospecificity of phosphorylation, with increased amounts of other phosphorylated species seen in its absence. Experimentally supported paths are already available to make nucleosides in environments likely to have been present on Hadean Earth soon after a midsized 1021 to 1023 kg impactor, which would also have delivered nickel to the Hadean surface. Further, sources of prebiotic CTMP continue to be proposed. Thus, these results fill in one of the few remaining steps needed to demystify the prebiotic synthesis of RNA and support a continuous model from atmospheric components to oligomeric RNA that is lacking only a mechanism to obtain homochirality in the product RNA.
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Affiliation(s)
- Hyo-Joong Kim
- Foundation for Applied Molecular Evolution and Firebird Biomolecular Sciences LLC, Alachua, Florida, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution and Firebird Biomolecular Sciences LLC, Alachua, Florida, USA
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24
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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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25
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Ferus M, Rimmer P, Cassone G, Knížek A, Civiš S, Šponer JE, Ivanek O, Šponer J, Saeidfirozeh H, Kubelík P, Dudžák R, Petera L, Juha L, Pastorek A, Křivková A, Krůs M. One-Pot Hydrogen Cyanide-Based Prebiotic Synthesis of Canonical Nucleobases and Glycine Initiated by High-Velocity Impacts on Early Earth. ASTROBIOLOGY 2020; 20:1476-1488. [PMID: 32955922 DOI: 10.1089/ast.2020.2231] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Chemical environments of young planets are assumed to be significantly influenced by impacts of bodies lingering after the dissolution of the protoplanetary disk. We explore the chemical consequences of impacts of these bodies under reducing planetary atmospheres dominated by carbon monoxide, methane, and molecular nitrogen. Impacts were simulated by using a terawatt high-power laser system. Our experimental results show that one-pot impact-plasma-initiated synthesis of all the RNA canonical nucleobases and the simplest amino acid glycine is possible in this type of atmosphere in the presence of montmorillonite. This one-pot synthesis begins with de novo formation of hydrogen cyanide (HCN) and proceeds through intermediates such as cyanoacetylene and urea.
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Affiliation(s)
- Martin Ferus
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Paul Rimmer
- Department of Earth Sciences, University of Cambridge, Cambridge, United Kingdom
- Cavendish Astrophysics, University of Cambridge, Cambridge, United Kingdom
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Giuseppe Cassone
- Institute for Physical-Chemical Processes, National Research Council, Messina, Italy
| | - Antonín Knížek
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Svatopluk Civiš
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Judit E Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Ondřej Ivanek
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Homa Saeidfirozeh
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Petr Kubelík
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague, Czech Republic
- Department of Radiation and Chemical Physics, Institute of Physics, Czech Academy of Sciences, Prague, Czech Republic
| | - Roman Dudžák
- Department of Radiation and Chemical Physics, Institute of Physics, Czech Academy of Sciences, Prague, Czech Republic
- Institute of Plasma Physics, Czech Academy of Sciences, Prague, Czech Republic
| | - Lukáš Petera
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Libor Juha
- Department of Radiation and Chemical Physics, Institute of Physics, Czech Academy of Sciences, Prague, Czech Republic
- Institute of Plasma Physics, Czech Academy of Sciences, Prague, Czech Republic
| | - Adam Pastorek
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Prague, Czech Republic
| | - Anna Křivková
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University in Prague, Prague, Czech Republic
| | - Miroslav Krůs
- Institute of Plasma Physics, Czech Academy of Sciences, Prague, Czech Republic
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26
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Pearce BKD, Ayers PW, Pudritz RE. CRAHCN-O: A Consistent Reduced Atmospheric Hybrid Chemical Network Oxygen Extension for Hydrogen Cyanide and Formaldehyde Chemistry in CO 2-, N 2-, H 2O-, CH 4-, and H 2-Dominated Atmospheres. J Phys Chem A 2020; 124:8594-8606. [PMID: 32961050 DOI: 10.1021/acs.jpca.0c06804] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hydrogen cyanide (HCN) and formaldehyde (H2CO) are key precursors to biomolecules such as nucleobases and amino acids in planetary atmospheres. However, many reactions which produce and destroy these species in atmospheres containing CO2 and H2O are still missing from the literature. We use a quantum chemistry approach to find these missing reactions and calculate their rate coefficients using canonical variational transition state theory and Rice-Ramsperger-Kassel-Marcus/master equation theory at the BHandHLYP/aug-cc-pVDZ level of theory. We calculate the rate coefficients for 126 total reactions and validate our calculations by comparing with experimental data in the 39% of available cases. Our calculated rate coefficients are most frequently within a factor of 2 of experimental values and generally always within an order of magnitude of these values. We discover 45 previously unknown reactions and identify 6 from this list that are most likely to dominate H2CO and HCN production and destruction in planetary atmospheres. We highlight 1O + CH3 → H2CO + H as a new key source and H2CO + 1O → HCO + OH as a new key sink, for H2CO in upper planetary atmospheres. In this effort, we develop an oxygen extension to our consistent reduced atmospheric hybrid chemical network (CRAHCN-O), building off our previously developed network for HCN production in N2-, CH4-, and H2-dominated atmospheres (CRAHCN). This extension can be used to simulate both HCN and H2CO production in atmospheres dominated by any of CO2, N2, H2O, CH4, and H2.
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Affiliation(s)
- Ben K D Pearce
- Origins Institute and Department of Physics and Astronomy, McMaster University, ABB 241, 1280 Main Street, Hamilton, Ontario L8S 4M1, Canada
| | - Paul W Ayers
- Origins Institute and Department of Chemistry and Chemical Biology, McMaster University, ABB 156, 1280 Main Street, Hamilton, Ontario L8S 4M1, Canada
| | - Ralph E Pudritz
- Origins Institute and Department of Physics and Astronomy, McMaster University, ABB 241, 1280 Main Street, Hamilton, Ontario L8S 4M1, Canada
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27
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Zhang ZJ, Chen ZF, Liu J. Path integral Liouville dynamics simulations of vibrational spectra of formaldehyde and hydrogen peroxide. CHINESE J CHEM PHYS 2020. [DOI: 10.1063/1674-0068/cjcp2006099] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Zhi-jun Zhang
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zi-fei Chen
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jian Liu
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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28
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Kovalenko SP. Physicochemical Processes That Probably Originated Life. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162020040093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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29
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Mohammadi E, Petera L, Saeidfirozeh H, Knížek A, Kubelík P, Dudžák R, Krůs M, Juha L, Civiš S, Coulon R, Malina O, Ugolotti J, Ranc V, Otyepka M, Šponer J, Ferus M, Šponer JE. Formic Acid, a Ubiquitous but Overlooked Component of the Early Earth Atmosphere. Chemistry 2020; 26:12075-12080. [PMID: 32293757 DOI: 10.1002/chem.202000323] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 04/11/2020] [Indexed: 01/19/2023]
Abstract
Terrestrial volcanism has been one of the dominant geological forces shaping our planet since its earliest existence. Its associated phenomena, like atmospheric lightning and hydrothermal activity, provide a rich energy reservoir for chemical syntheses. Based on our laboratory simulations, we propose that on the early Earth volcanic activity inevitably led to a remarkable production of formic acid through various independent reaction channels. Large-scale availability of atmospheric formic acid supports the idea of the high-temperature accumulation of formamide in this primordial environment.
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Affiliation(s)
- Elmira Mohammadi
- Regional Centre of Advanced Technologies and Materials, Palacký University Olomouc, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Lukáš Petera
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223, Prague 8, Czech Republic.,Faculty of Science, Charles University, Albertov 2030, 12843, Prague, Czech Republic
| | - Homa Saeidfirozeh
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223, Prague 8, Czech Republic
| | - Antonín Knížek
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223, Prague 8, Czech Republic.,Faculty of Science, Charles University, Albertov 2030, 12843, Prague, Czech Republic
| | - Petr Kubelík
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223, Prague 8, Czech Republic.,Institute of Physics, Czech Academy of Sciences, Na Slovance 1999/2, 18221, Prague 8, Czech Republic
| | - Roman Dudžák
- Institute of Physics, Czech Academy of Sciences, Na Slovance 1999/2, 18221, Prague 8, Czech Republic.,Institute of Plasma Physics, Czech Academy of Sciences, Za Slovankou 1782/3, 18200, Prague 8, Czech Republic
| | - Miroslav Krůs
- Institute of Plasma Physics, Czech Academy of Sciences, Za Slovankou 1782/3, 18200, Prague 8, Czech Republic
| | - Libor Juha
- Institute of Physics, Czech Academy of Sciences, Na Slovance 1999/2, 18221, Prague 8, Czech Republic.,Institute of Plasma Physics, Czech Academy of Sciences, Za Slovankou 1782/3, 18200, Prague 8, Czech Republic
| | - Svatopluk Civiš
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223, Prague 8, Czech Republic
| | - Rémi Coulon
- Regional Centre of Advanced Technologies and Materials, Palacký University Olomouc, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Ondřej Malina
- Regional Centre of Advanced Technologies and Materials, Palacký University Olomouc, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Juri Ugolotti
- Regional Centre of Advanced Technologies and Materials, Palacký University Olomouc, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Václav Ranc
- Regional Centre of Advanced Technologies and Materials, Palacký University Olomouc, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Palacký University Olomouc, Šlechtitelů 27, 78371, Olomouc, Czech Republic
| | - Jiří Šponer
- Regional Centre of Advanced Technologies and Materials, Palacký University Olomouc, Šlechtitelů 27, 78371, Olomouc, Czech Republic.,Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265, Brno, Czech Republic
| | - Martin Ferus
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223, Prague 8, Czech Republic
| | - Judit E Šponer
- Regional Centre of Advanced Technologies and Materials, Palacký University Olomouc, Šlechtitelů 27, 78371, Olomouc, Czech Republic.,Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265, Brno, Czech Republic
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30
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The Messy Alkaline Formose Reaction and Its Link to Metabolism. Life (Basel) 2020; 10:life10080125. [PMID: 32731352 PMCID: PMC7460143 DOI: 10.3390/life10080125] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/23/2020] [Accepted: 07/25/2020] [Indexed: 12/18/2022] Open
Abstract
Sugars are essential for the formation of genetic elements such as RNA and as an energy/food source. Thus, the formose reaction, which autocatalytically generates a multitude of sugars from formaldehyde, has been viewed as a potentially important prebiotic source of biomolecules at the origins of life. When analyzing our formose solutions we find that many of the chemical species are simple carboxylic acids, including α-hydroxy acids, associated with metabolism. In this work we posit that the study of the formose reaction, under alkaline conditions and moderate hydrothermal temperatures, should not be solely focused on sugars for genetic materials, but should focus on the origins of metabolism (via metabolic molecules) as well.
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31
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Benner SA, Bell EA, Biondi E, Brasser R, Carell T, Kim H, Mojzsis SJ, Omran A, Pasek MA, Trail D. When Did Life Likely Emerge on Earth in an RNA‐First Process? CHEMSYSTEMSCHEM 2020. [DOI: 10.1002/syst.201900035] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Steven A. Benner
- Foundation for Applied Molecular Evolution Alachua FL USA
- Firebird Biomolecular Sciences LLC Alachua FL USA
| | - Elizabeth A. Bell
- Department of Earth, Planetary, and Space SciencesUniversity of California Los Angeles USA
| | - Elisa Biondi
- Foundation for Applied Molecular Evolution Alachua FL USA
| | - Ramon Brasser
- Earth Life Science InstituteTokyo Institute of Technology Tokyo Japan
| | - Thomas Carell
- Fakultät für Chemie und PharmazieLudwig-Maximilians-Universität München Germany
| | | | - Stephen J. Mojzsis
- Department of Geological SciencesUniversity of Colorado Boulder CO USA
- Hungarian Academy of Sciences Budapest Hungary
| | - Arthur Omran
- School of GeosciencesUniversity of South Florida Tampa, FL USA
| | | | - Dustin Trail
- Department of Earth and Environmental SciencesUniversity of Rochester Rochester NY USA
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32
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Abstract
The chemistry of abiotic nucleotide synthesis of RNA and DNA in the context of their prebiotic origins on early earth is a continuing challenge. How did (or how can) the nucleotides form and assemble from the small molecule inventories and under conditions that prevailed on early earth 3.5-4 billion years ago? This review provides a background and up-to-date progress that will allow the reader to judge where the field stands currently and what remains to be achieved. We start with a brief primer on the biological synthesis of nucleotides, followed by an extensive focus on the prebiotic formation of the components of nucleotides-either via the synthesis of ribose and the canonical nucleobases and then joining them together or by building both the conjoined sugar and nucleobase, part-by-part-toward the ultimate goal of forming RNA and DNA by polymerization. The review will emphasize that there are-and will continue to be-many more questions than answers from the synthetic, mechanistic, and analytical perspectives. We wrap up the review with a cautionary note in this context about coming to conclusions as to whether the problem of chemistry of prebiotic nucleotide synthesis has been solved.
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Affiliation(s)
- Mahipal Yadav
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
| | - Ravi Kumar
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
| | - Ramanarayanan Krishnamurthy
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States.,NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332, United States
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33
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Liu J, Li X, Yang Y, Wang H, Kuang C, Zhu Y, Chen M, Hu J, Zeng L, Zhang Y. Sensitive Detection of Ambient Formaldehyde by Incoherent Broadband Cavity Enhanced Absorption Spectroscopy. Anal Chem 2020; 92:2697-2705. [DOI: 10.1021/acs.analchem.9b04821] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jingwei Liu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
- International Joint Laboratory for Regional Pollution Control, Ministry of Education, Beijing 100816, China
| | - Xin Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
- International Joint Laboratory for Regional Pollution Control, Ministry of Education, Beijing 100816, China
- Collaborative Innovation Centre of Atmospheric Environment and Equipment Technology, Nanjing University of Information Science & Technology, Nanjing 210044, China P. R
| | - Yiming Yang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
- International Joint Laboratory for Regional Pollution Control, Ministry of Education, Beijing 100816, China
| | - Haichao Wang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Cailing Kuang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Yuan Zhu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Mindong Chen
- Collaborative Innovation Centre of Atmospheric Environment and Equipment Technology, Nanjing University of Information Science & Technology, Nanjing 210044, China P. R
| | - Jianlin Hu
- Collaborative Innovation Centre of Atmospheric Environment and Equipment Technology, Nanjing University of Information Science & Technology, Nanjing 210044, China P. R
| | - Limin Zeng
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
- International Joint Laboratory for Regional Pollution Control, Ministry of Education, Beijing 100816, China
| | - Yuanhang Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
- International Joint Laboratory for Regional Pollution Control, Ministry of Education, Beijing 100816, China
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34
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Endogenous formaldehyde is a memory-related molecule in mice and humans. Commun Biol 2019; 2:446. [PMID: 31815201 PMCID: PMC6884489 DOI: 10.1038/s42003-019-0694-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 11/04/2019] [Indexed: 01/09/2023] Open
Abstract
Gaseous formaldehyde is an organic small molecule formed in the early stages of earth’s evolution. Although toxic in high concentrations, formaldehyde plays an important role in cellular metabolism and, unexpectedly, is found even in the healthy brain. However, its pathophysiological functions in the brain are unknown. Here, we report that under physiological conditions, spatial learning activity elicits rapid formaldehyde generation from mitochondrial sarcosine dehydrogenase (SARDH). We find that elevated formaldehyde levels facilitate spatial memory formation by enhancing N-methyl-D-aspartate (NMDA) currents via the C232 residue of the NMDA receptor, but that high formaldehyde concentrations gradually inactivate the receptor by cross-linking NR1 subunits to NR2B. We also report that in mice with aldehyde dehydrogenase-2 (ALDH2) knockout, formaldehyde accumulation due to hypofunctional ALDH2 impairs memory, consistent with observations of Alzheimerʼs disease patients. We also find that formaldehyde deficiency caused by mutation of the mitochondrial SARDH gene in children with sarcosinemia or in mice with Sardh deletion leads to cognitive deficits. Hence, we conclude that endogenous formaldehyde regulates learning and memory via the NMDA receptor. Ai et al. report that endogenous formaldehyde bidirectionally modulates cognition via the NMDA-R receptor, with both insufficiency and overabundance resulting in cognitive defects. The target site of formaldehyde enhancing NMDA-currents is cysteine C232 residue in amino terminal domain sequence of the NR2B subunit of NMDA-R and excessive formaldehyde suppresses NMDA-R activity by cross-linking NR1 to NR2B residues.
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35
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Kawai J, McLendon DC, Kim HJ, Benner S. Hydroxymethanesulfonate from Volcanic Sulfur Dioxide: A "Mineral" Reservoir for Formaldehyde and Other Simple Carbohydrates in Prebiotic Chemistry. ASTROBIOLOGY 2019; 19:506-516. [PMID: 30615473 PMCID: PMC6459274 DOI: 10.1089/ast.2017.1800] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 09/12/2018] [Indexed: 05/03/2023]
Abstract
While formaldehyde (HCHO) was likely generated in Earth's prebiotic atmosphere by ultraviolet light, electrical discharge, and/or volcano-created lightning, HCHO could not have accumulated in substantial amounts in prebiotic environments, including those needed for prebiotic processes that generate nucleosidic carbohydrates. HCHO at high concentrations in alkaline solutions self-reacts in the Cannizzaro reaction to give methanol and formate, neither having prebiotic value. Here, we explore the possibility that volcanic sulfur dioxide (SO2) might have generated a reservoir for Hadean HCHO by a reversible reaction with HCHO to give hydroxymethanesulfonate (HMS). We show that salts of HMS are stable as solids at 90°C and do not react with themselves in solution, even at high (>8 M) concentrations. This makes them effective stores of HCHO, since the reverse reaction slowly delivers HCHO back into an environment where it can participate in prebiotically useful reactions. Specifically, we show that in alkaline borate solutions, HCHO derived from HMS allows formation of borate-stabilized carbohydrates as effectively as free HCHO, without losing material to Cannizzaro products. Further, we show that SO2 can perform similar roles for glycolaldehyde and glyceraldehyde, two intrinsically unstable carbohydrates that are needed by various models as precursors for RNA building blocks. Zircons from the Hadean show that the Hadean mantle likely provided volcanic SO2 at rates at least as great as the rates of atmospheric HCHO generation, making the formation of Hadean HMS essentially unavoidable. Thus, hydroxymethylsulfonate adducts of formaldehyde, glycolaldehyde, and glyceraldehyde, including the less soluble barium, strontium, and calcium salts, are likely candidates for prebiotically useful organic minerals on early Earth.
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Affiliation(s)
- J. Kawai
- Foundation for Applied Molecular Evolution, Alachua, Florida, USA
- High Energy Accelerator Research Organization, Institute of Materials Structure Science, Tsukuba, Japan
| | - D. Chris McLendon
- Foundation for Applied Molecular Evolution, Alachua, Florida, USA
- Firebird Biomolecular Sciences LLC, Alachua, Florida, USA
| | - H.-J. Kim
- Firebird Biomolecular Sciences LLC, Alachua, Florida, USA
| | - S.A. Benner
- Foundation for Applied Molecular Evolution, Alachua, Florida, USA
- Firebird Biomolecular Sciences LLC, Alachua, Florida, USA
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36
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Gas-phase sugar formation using hydroxymethylene as the reactive formaldehyde isomer. Nat Chem 2018; 10:1141-1147. [DOI: 10.1038/s41557-018-0128-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Accepted: 07/26/2018] [Indexed: 11/08/2022]
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37
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Xu J, Ritson DJ, Ranjan S, Todd ZR, Sasselov DD, Sutherland JD. Photochemical reductive homologation of hydrogen cyanide using sulfite and ferrocyanide. Chem Commun (Camb) 2018; 54:5566-5569. [PMID: 29761807 PMCID: PMC5972737 DOI: 10.1039/c8cc01499j] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Photoredox cycling during UV irradiation of ferrocyanide ([FeII(CN)6]4-) in the presence of stoichiometric sulfite (SO32-) is shown to be an extremely effective way to drive the reductive homologation of hydrogen cyanide (HCN) to simple sugars and precursors of hydroxy acids and amino acids.
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Affiliation(s)
- Jianfeng Xu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK.
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38
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Gao J, Huang Z, Chen Y, Wan J, Gu X, Ma Z, Chen J, Tang X. Activating Inert Alkali-Metal Ions by Electron Transfer from Manganese Oxide for Formaldehyde Abatement. Chemistry 2017; 24:681-689. [DOI: 10.1002/chem.201704398] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Jiayi Gao
- Institute of Atmospheric Sciences; Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP ); Department of Environmental Science & Engineering; Fudan University; 200433 Shanghai P.R. China
| | - Zhiwei Huang
- Institute of Atmospheric Sciences; Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP ); Department of Environmental Science & Engineering; Fudan University; 200433 Shanghai P.R. China
| | - Yaxin Chen
- Institute of Atmospheric Sciences; Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP ); Department of Environmental Science & Engineering; Fudan University; 200433 Shanghai P.R. China
| | - Jing Wan
- Department of Applied Physics; Chongqing University; 400044 Chongqing P.R. China
| | - Xiao Gu
- Department of Applied Physics; Chongqing University; 400044 Chongqing P.R. China
| | - Zhen Ma
- Institute of Atmospheric Sciences; Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP ); Department of Environmental Science & Engineering; Fudan University; 200433 Shanghai P.R. China
| | - Jianmin Chen
- Institute of Atmospheric Sciences; Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP ); Department of Environmental Science & Engineering; Fudan University; 200433 Shanghai P.R. China
| | - Xingfu Tang
- Institute of Atmospheric Sciences; Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP ); Department of Environmental Science & Engineering; Fudan University; 200433 Shanghai P.R. China
- Jiangsu Collaborative Innovation Center of Atmospheric, Environment & Equipment Technology (CICAEET); Nanjing University of Information Science & Technology; 210044 Nanjing P.R. China
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39
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Toumi I, Yazidi O, Jaidane NE, Al Mogren MM, Francisco JS, Hochlaf M. Stereoisomers of hydroxymethanes: Probing structural and spectroscopic features upon substitution. J Chem Phys 2016; 145:244305. [PMID: 28049302 DOI: 10.1063/1.4972415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ab initio studies on CHx(OH)4-x (x = 0-3) polyols are carried out to derive their structural and spectroscopic features. Several stereoisomers (both equilibrium structures and transition states) are found. Some are predicted here for the first time. We determined hence their geometrical parameters, vibrational frequencies, electronic excitation energies for the singlet manifold, and IR spectra. While the IR spectra for all polyols present similar shapes, their UV spectra exhibit however distinct band origin that are specific to each polyol and more interestingly to each diasteroisomer. Stereoelectronic effects are also noticed and discussed. It is suggested that UV spectroscopy is an efficient probe to experimentally identify polyols in mixtures involving polyols.
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Affiliation(s)
- I Toumi
- Laboratoire de Spectroscopie Atomique, Moléculaire et Applications-LSAMA, Université de Tunis El Manar, Tunis, Tunisia
| | - O Yazidi
- Laboratoire de Spectroscopie Atomique, Moléculaire et Applications-LSAMA, Université de Tunis El Manar, Tunis, Tunisia
| | - N-E Jaidane
- Laboratoire de Spectroscopie Atomique, Moléculaire et Applications-LSAMA, Université de Tunis El Manar, Tunis, Tunisia
| | - M Mogren Al Mogren
- Chemistry Department, Faculty of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - J S Francisco
- Department of Chemistry and Department of Earth and Atmospheric Science, Purdue University, West Lafayette, Indiana 49707, USA
| | - M Hochlaf
- Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est, 5 Blvd. Descartes, 77454 Marne-la-Vallée, France
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40
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Domagal-Goldman SD, Wright KE, Adamala K, Arina de la Rubia L, Bond J, Dartnell LR, Goldman AD, Lynch K, Naud ME, Paulino-Lima IG, Singer K, Walther-Antonio M, Abrevaya XC, Anderson R, Arney G, Atri D, Azúa-Bustos A, Bowman JS, Brazelton WJ, Brennecka GA, Carns R, Chopra A, Colangelo-Lillis J, Crockett CJ, DeMarines J, Frank EA, Frantz C, de la Fuente E, Galante D, Glass J, Gleeson D, Glein CR, Goldblatt C, Horak R, Horodyskyj L, Kaçar B, Kereszturi A, Knowles E, Mayeur P, McGlynn S, Miguel Y, Montgomery M, Neish C, Noack L, Rugheimer S, Stüeken EE, Tamez-Hidalgo P, Imari Walker S, Wong T. The Astrobiology Primer v2.0. ASTROBIOLOGY 2016; 16:561-653. [PMID: 27532777 PMCID: PMC5008114 DOI: 10.1089/ast.2015.1460] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 06/06/2016] [Indexed: 05/09/2023]
Affiliation(s)
- Shawn D Domagal-Goldman
- 1 NASA Goddard Space Flight Center , Greenbelt, Maryland, USA
- 2 Virtual Planetary Laboratory , Seattle, Washington, USA
| | - Katherine E Wright
- 3 University of Colorado at Boulder , Colorado, USA
- 4 Present address: UK Space Agency, UK
| | - Katarzyna Adamala
- 5 Department of Genetics, Cell Biology and Development, University of Minnesota , Minneapolis, Minnesota, USA
| | | | - Jade Bond
- 7 Department of Physics, University of New South Wales , Sydney, Australia
| | | | | | - Kennda Lynch
- 10 Division of Biological Sciences, University of Montana , Missoula, Montana, USA
| | - Marie-Eve Naud
- 11 Institute for research on exoplanets (iREx) , Université de Montréal, Montréal, Canada
| | - Ivan G Paulino-Lima
- 12 Universities Space Research Association , Mountain View, California, USA
- 13 Blue Marble Space Institute of Science , Seattle, Washington, USA
| | - Kelsi Singer
- 14 Southwest Research Institute , Boulder, Colorado, USA
| | | | - Ximena C Abrevaya
- 16 Instituto de Astronomía y Física del Espacio (IAFE) , UBA-CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - Rika Anderson
- 17 Department of Biology, Carleton College , Northfield, Minnesota, USA
| | - Giada Arney
- 18 University of Washington Astronomy Department and Astrobiology Program , Seattle, Washington, USA
| | - Dimitra Atri
- 13 Blue Marble Space Institute of Science , Seattle, Washington, USA
| | | | - Jeff S Bowman
- 19 Lamont-Doherty Earth Observatory, Columbia University , Palisades, New York, USA
| | | | | | - Regina Carns
- 22 Polar Science Center, Applied Physics Laboratory, University of Washington , Seattle, Washington, USA
| | - Aditya Chopra
- 23 Planetary Science Institute, Research School of Earth Sciences, Research School of Astronomy and Astrophysics, The Australian National University , Canberra, Australia
| | - Jesse Colangelo-Lillis
- 24 Earth and Planetary Science, McGill University , and the McGill Space Institute, Montréal, Canada
| | | | - Julia DeMarines
- 13 Blue Marble Space Institute of Science , Seattle, Washington, USA
| | | | - Carie Frantz
- 27 Department of Geosciences, Weber State University , Ogden, Utah, USA
| | - Eduardo de la Fuente
- 28 IAM-Departamento de Fisica, CUCEI , Universidad de Guadalajara, Guadalajara, México
| | - Douglas Galante
- 29 Brazilian Synchrotron Light Laboratory , Campinas, Brazil
| | - Jennifer Glass
- 30 School of Earth and Atmospheric Sciences, Georgia Institute of Technology , Atlanta, Georgia , USA
| | | | | | - Colin Goldblatt
- 33 School of Earth and Ocean Sciences, University of Victoria , Victoria, Canada
| | - Rachel Horak
- 34 American Society for Microbiology , Washington, DC, USA
| | | | - Betül Kaçar
- 36 Harvard University , Organismic and Evolutionary Biology, Cambridge, Massachusetts, USA
| | - Akos Kereszturi
- 37 Research Centre for Astronomy and Earth Sciences , Hungarian Academy of Sciences, Budapest, Hungary
| | - Emily Knowles
- 38 Johnson & Wales University , Denver, Colorado, USA
| | - Paul Mayeur
- 39 Rensselaer Polytechnic Institute , Troy, New York, USA
| | - Shawn McGlynn
- 40 Earth Life Science Institute, Tokyo Institute of Technology , Tokyo, Japan
| | - Yamila Miguel
- 41 Laboratoire Lagrange, UMR 7293, Université Nice Sophia Antipolis , CNRS, Observatoire de la Côte d'Azur, Nice, France
| | | | - Catherine Neish
- 43 Department of Earth Sciences, The University of Western Ontario , London, Canada
| | - Lena Noack
- 44 Royal Observatory of Belgium , Brussels, Belgium
| | - Sarah Rugheimer
- 45 Department of Astronomy, Harvard University , Cambridge, Massachusetts, USA
- 46 University of St. Andrews , St. Andrews, UK
| | - Eva E Stüeken
- 47 University of Washington , Seattle, Washington, USA
- 48 University of California , Riverside, California, USA
| | | | - Sara Imari Walker
- 13 Blue Marble Space Institute of Science , Seattle, Washington, USA
- 50 School of Earth and Space Exploration and Beyond Center for Fundamental Concepts in Science, Arizona State University , Tempe, Arizona, USA
| | - Teresa Wong
- 51 Department of Earth and Planetary Sciences, Washington University in St. Louis , St. Louis, Missouri, USA
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41
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Civiš S, Szabla R, Szyja BM, Smykowski D, Ivanek O, Knížek A, Kubelík P, Šponer J, Ferus M, Šponer JE. TiO2-catalyzed synthesis of sugars from formaldehyde in extraterrestrial impacts on the early Earth. Sci Rep 2016; 6:23199. [PMID: 26979666 PMCID: PMC4793247 DOI: 10.1038/srep23199] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 02/24/2016] [Indexed: 01/05/2023] Open
Abstract
Recent synthetic efforts aimed at reconstructing the beginning of life on our planet point at the plausibility of scenarios fueled by extraterrestrial energy sources. In the current work we show that beyond nucleobases the sugar components of the first informational polymers can be synthesized in this way. We demonstrate that a laser-induced high-energy chemistry combined with TiO2 catalysis readily produces a mixture of pentoses, among them ribose, arabinose and xylose. This chemistry might be highly relevant to the Late Heavy Bombardment period of Earth’s history about 4–3.85 billion years ago. In addition, we present an in-depth theoretical analysis of the most challenging step of the reaction pathway, i.e., the TiO2-catalyzed dimerization of formaldehyde leading to glycolaldehyde.
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Affiliation(s)
- Svatopluk Civiš
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-182 23 Prague 8, Czech Republic
| | - Rafał Szabla
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic
| | - Bartłomiej M Szyja
- Inorganic Materials Chemistry, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands.,Division of Fuels Chemistry and Technology, Faculty of Chemistry, Wrocław University of Technology, Gdańska 7/9, 50-344 Wrocław, Poland
| | - Daniel Smykowski
- Faculty of Mechanical and Power Engineering, Wrocław University of Technology, Ul. Wybrzeże Wyspiańskiego 27, 50-370, Wrocław
| | - Ondřej Ivanek
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-182 23 Prague 8, Czech Republic
| | - Antonín Knížek
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-182 23 Prague 8, Czech Republic
| | - Petr Kubelík
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-182 23 Prague 8, Czech Republic.,Institute of Physics, Czech Academy of Sciences, Na Slovance 2, 182 21 Prague 8, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic.,CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, CZ-62500 Brno, Czech Republic
| | - Martin Ferus
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-182 23 Prague 8, Czech Republic
| | - Judit E Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, CZ-612 65 Brno, Czech Republic.,CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, CZ-62500 Brno, Czech Republic
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42
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Rapf RJ, Vaida V. Sunlight as an energetic driver in the synthesis of molecules necessary for life. Phys Chem Chem Phys 2016; 18:20067-84. [DOI: 10.1039/c6cp00980h] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
This review considers how photochemistry and sunlight-driven reactions can abiotically generate prebiotic molecules necessary for the evolution of life.
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Affiliation(s)
- Rebecca J. Rapf
- Department of Chemistry and Biochemistry
- CIRES
- University of Colorado at Boulder
- Boulder
- USA
| | - Veronica Vaida
- Department of Chemistry and Biochemistry
- CIRES
- University of Colorado at Boulder
- Boulder
- USA
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43
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Effects of Silicate, Phosphate, and Calcium on the Stability of Aldopentoses. ORIGINS LIFE EVOL B 2015; 46:189-202. [PMID: 26559965 DOI: 10.1007/s11084-015-9472-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/28/2015] [Indexed: 10/22/2022]
Abstract
Ribose is an important constituent of RNA: ribose connects RNA bases and forms a strand of sugar phosphates. Accumulation of ribose on prebiotic Earth was difficult because of its low stability. Improvement in the yield of ribose by the introduction of borate or silicate in a formose-like reaction has been proposed. The effects of borates have been further analyzed and confirmed in subsequent studies. Nonetheless, the effects of silicates and phosphates remain unclear. In the present study, we incubated aldopentoses in a highly alkaline aqueous solution at a moderate temperature to determine the effects of silicate or phosphate on the degradation rates of ribose and its isomeric aldopentoses. The formation of a complex of silicate (or phosphate) with ribose was also analyzed in experiments with (29)Si and (31)P nuclear magnetic resonance (NMR). We found that silicate or phosphate complexes of ribose were not detectable under our experimental conditions. The stability of ribose and lyxose improved after addition of 40-fold molar excess (relative to a pentose) of sodium silicate or sodium phosphate to the alkaline solution. The stability was not improved further when an 80-fold molar excess of sodium silicate or sodium phosphate was added. Calcium was removed from these solutions by precipitation of calcium salts. The drop in Ca(2+) concentration might have improved the stability of ribose and lyxose, which are susceptible to aldol addition. The improvement of ribose stability by the removal of Ca(2+) and by addition of silicate or phosphate was far smaller than the improvement by borate. Furthermore, all aldopentoses showed similar stability in silicate- and phosphate-containing solutions. These results clearly show that selective stabilization of ribose by borate cannot be replaced by the effects of silicate or phosphate; this finding points to the importance of borate in prebiotic RNA formation.
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44
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Li W, Wu XF. The Applications of (Para)formaldehyde in Metal-Catalyzed Organic Synthesis. Adv Synth Catal 2015. [DOI: 10.1002/adsc.201500753] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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45
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Harman CE, Schwieterman EW, Schottelkotte JC, Kasting JF. ABIOTIC O2LEVELS ON PLANETS AROUND F, G, K, AND M STARS: POSSIBLE FALSE POSITIVES FOR LIFE? ACTA ACUST UNITED AC 2015. [DOI: 10.1088/0004-637x/812/2/137] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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46
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Kumar M, Francisco JS. The Role of Catalysis in Alkanediol Decomposition: Implications for General Detection of Alkanediols and Their Formation in the Atmosphere. J Phys Chem A 2015; 119:9821-33. [DOI: 10.1021/acs.jpca.5b07642] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Manoj Kumar
- Department of Chemistry, University of Nebraska—Lincoln, 639 North 12th Street, Lincoln, Nebraska 68588, United States
| | - Joseph S. Francisco
- Department of Chemistry, University of Nebraska—Lincoln, 639 North 12th Street, Lincoln, Nebraska 68588, United States
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47
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Pavlov VA, Klabunovskii EI. The origin of homochirality in nature: a possible version. RUSSIAN CHEMICAL REVIEWS 2015. [DOI: 10.1070/rcr4444] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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48
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Hu P, Amghouz Z, Huang Z, Xu F, Chen Y, Tang X. Surface-confined atomic silver centers catalyzing formaldehyde oxidation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:2384-2390. [PMID: 25634796 DOI: 10.1021/es504570n] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Formaldehyde (HCHO) is a prior pollutant in both indoor and outdoor air, and catalytic oxidation proves the most promising technology for HCHO abatement. For this purpose, supported metal catalysts with single silver atoms confined at 4-fold O4-terminated surface hollow sites of a hollandite manganese oxide (HMO) as catalytic centers were synthesized and investigated in the complete oxidation of HCHO. Synchrotron X-ray diffraction patterns, X-ray absorption spectra, and electron diffraction tomography revealed that geometric structures and electronic states of the catalytic centers were tuned by the changes of HMO structures via controllable metal-support interactions. The catalytic tests demonstrated that the catalytically active centers with high electronic density of states and strong redox ability are favorable for enhancement of the catalytic efficiency in the HCHO oxidation. This work provides a strategy for designing efficient oxidation catalysts for controlling air pollution.
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Affiliation(s)
- Pingping Hu
- Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP3), Department of Environmental Science and Engineering, Fudan University , Shanghai 200433, China
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49
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Griffith EC, Shoemaker RK, Vaida V. Sunlight-initiated chemistry of aqueous pyruvic acid: building complexity in the origin of life. ORIGINS LIFE EVOL B 2013; 43:341-52. [PMID: 24362712 DOI: 10.1007/s11084-013-9349-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 09/20/2013] [Indexed: 10/25/2022]
Abstract
Coupling chemical reactions to an energy source is a necessary step in the origin of life. Here, we utilize UV photons provided by a simulated sun to activate aqueous pyruvic acid and subsequently prompt chemical reactions mimicking some of the functions of modern metabolism. Pyruvic acid is interesting in a prebiotic context due to its prevalence in modern metabolism and its abiotic availability on early Earth. Here, pyruvic acid (CH3COCOOH, a C3 molecule) photochemically reacts to produce more complex molecules containing four or more carbon atoms. Acetoin (CH3CHOHCOCH3), a C4 molecule and a modern bacterial metabolite, is produced in this chemistry as well as lactic acid (CH3CHOHCOOH), a molecule which, when coupled with other abiotic chemical reaction pathways, can provide a regeneration pathway for pyruvic acid. This chemistry is discussed in the context of plausible environments on early Earth such as near the ocean surface and atmospheric aerosol particles. These environments allow for combination and exchange of reactants and products of other reaction environments (such as shallow hydrothermal vents). The result could be a contribution to the steady increase in chemical complexity requisite in the origin of life.
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Affiliation(s)
- Elizabeth C Griffith
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Campus Box 215, Boulder, CO, 80309, USA
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50
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Hazra MK, Francisco JS, Sinha A. Gas Phase Hydrolysis of Formaldehyde To Form Methanediol: Impact of Formic Acid Catalysis. J Phys Chem A 2013; 117:11704-10. [DOI: 10.1021/jp4008043] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Montu K. Hazra
- Chemical Sciences
Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar,
Kolkata-700064, India
| | - Joseph S. Francisco
- Department
of Chemistry, Purdue University, West Lafayette,
Indiana 47907-2084,
United States
| | - Amitabha Sinha
- Department
of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California
92093-0314, United States
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