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Mrnjavac N, Degli Esposti M, Mizrahi I, Martin WF, Allen JF. Three enzymes governed the rise of O 2 on Earth. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1865:149495. [PMID: 39004113 DOI: 10.1016/j.bbabio.2024.149495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/30/2024] [Accepted: 07/02/2024] [Indexed: 07/16/2024]
Abstract
Current views of O2 accumulation in Earth history depict three phases: The onset of O2 production by ∼2.4 billion years ago; 2 billion years of stasis at ∼1 % of modern atmospheric levels; and a rising phase, starting about 500 million years ago, in which oxygen eventually reached modern values. Purely geochemical mechanisms have been proposed to account for this tripartite time course of Earth oxygenation. In particular the second phase, the long period of stasis between the advent of O2 and the late rise to modern levels, has posed a puzzle. Proposed solutions involve Earth processes (geochemical, ecosystem, day length). Here we suggest that Earth oxygenation was not determined by geochemical processes. Rather it resulted from emergent biological innovations associated with photosynthesis and the activity of only three enzymes: 1) The oxygen evolving complex of cyanobacteria that makes O2; 2) Nitrogenase, with its inhibition by O2 causing two billion years of oxygen level stasis; 3) Cellulose synthase of land plants, which caused mass deposition and burial of carbon, thus removing an oxygen sink and therefore increasing atmospheric O2. These three enzymes are endogenously produced by, and contained within, cells that have the capacity for exponential growth. The catalytic properties of these three enzymes paved the path of Earth's atmospheric oxygenation, requiring no help from Earth other than the provision of water, CO2, salts, colonizable habitats, and sunlight.
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Affiliation(s)
- Natalia Mrnjavac
- Department of Biology, Institute for Molecular Evolution, Heinrich Heine University of Duesseldorf, Duesseldorf, Germany
| | | | - Itzhak Mizrahi
- Department of Life Sciences, Ben-Gurion University of the Negev and the National Institute for Biotechnology in the Negev, Marcus Family Campus, Be'er-Sheva, Israel
| | - William F Martin
- Department of Biology, Institute for Molecular Evolution, Heinrich Heine University of Duesseldorf, Duesseldorf, Germany
| | - John F Allen
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London, UK.
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2
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Pan Y, Rao Z, Yu W, Chen B, Chu C. Water Vapor Condensation Triggers Simultaneous Oxidation and Hydrolysis of Organic Pollutants on Iron Mineral Surfaces. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:12147-12154. [PMID: 38934559 DOI: 10.1021/acs.est.4c03195] [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: 06/28/2024]
Abstract
Increasing worldwide contamination with organic chemical compounds is a paramount environmental challenge facing humanity. Once they enter nature, pollutants undergo transformative processes that critically shape their environmental impacts and associated risks. This research unveils previously overlooked yet widespread pathways for the transformations of organic pollutants triggered by water vapor condensation, leading to spontaneous oxidation and hydrolysis of organic pollutants. These transformations exhibit variability through either sequential or parallel hydrolysis and oxidation, contingent upon the functional groups within the organic pollutants. For instance, acetylsalicylic acid on the goethite surface underwent sequential hydrolysis and oxidation that first hydrolyzed to salicylic acid followed by hydroxylation oxidation of the benzene moiety driven by the hydroxyl radical (•OH). In contrast, chloramphenicol underwent parallel oxidation and hydrolysis, forming hydroxylated chloramphenicol and 2-amino-1-(4-nitrophenyl)-1,3-propanediol, respectively. The spontaneous oxidation and hydrolysis occurred consistently on three naturally abundant iron minerals with the key factors being •OH production capacity and surface binding strength. Given the widespread presence of iron minerals on Earth's surface, these spontaneous transformation paths could play a role in the fate and risks of organic pollutants of health concerns.
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Affiliation(s)
- Yishuai Pan
- Faculty of Agriculture, Life, and Environmental Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zepeng Rao
- Faculty of Agriculture, Life, and Environmental Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wanchao Yu
- Faculty of Agriculture, Life, and Environmental Sciences, Zhejiang University, Hangzhou 310058, China
| | - Baoliang Chen
- Faculty of Agriculture, Life, and Environmental Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chiheng Chu
- Faculty of Agriculture, Life, and Environmental Sciences, Zhejiang University, Hangzhou 310058, China
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3
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Mrnjavac N, Nagies FSP, Wimmer JLE, Kapust N, Knopp MR, Trost K, Modjewski L, Bremer N, Mentel M, Esposti MD, Mizrahi I, Allen JF, Martin WF. The radical impact of oxygen on prokaryotic evolution-enzyme inhibition first, uninhibited essential biosyntheses second, aerobic respiration third. FEBS Lett 2024; 598:1692-1714. [PMID: 38750628 PMCID: PMC7616280 DOI: 10.1002/1873-3468.14906] [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: 02/13/2024] [Revised: 04/12/2024] [Accepted: 04/19/2024] [Indexed: 07/15/2024]
Abstract
Molecular oxygen is a stable diradical. All O2-dependent enzymes employ a radical mechanism. Generated by cyanobacteria, O2 started accumulating on Earth 2.4 billion years ago. Its evolutionary impact is traditionally sought in respiration and energy yield. We mapped 365 O2-dependent enzymatic reactions of prokaryotes to phylogenies for the corresponding 792 protein families. The main physiological adaptations imparted by O2-dependent enzymes were not energy conservation, but novel organic substrate oxidations and O2-dependent, hence O2-tolerant, alternative pathways for O2-inhibited reactions. Oxygen-dependent enzymes evolved in ancestrally anaerobic pathways for essential cofactor biosynthesis including NAD+, pyridoxal, thiamine, ubiquinone, cobalamin, heme, and chlorophyll. These innovations allowed prokaryotes to synthesize essential cofactors in O2-containing environments, a prerequisite for the later emergence of aerobic respiratory chains.
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Affiliation(s)
- Natalia Mrnjavac
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Falk S P Nagies
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Jessica L E Wimmer
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Nils Kapust
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Michael R Knopp
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Katharina Trost
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Luca Modjewski
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Nico Bremer
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
| | - Marek Mentel
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | | | - Itzhak Mizrahi
- Department of Life Sciences, Ben-Gurion University of the Negev and The National Institute for Biotechnology in the Negev, Be'er-Sheva, Israel
| | - John F Allen
- Research Department of Genetics, Evolution and Environment, University College London, UK
| | - William F Martin
- Institute of Molecular Evolution, Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Germany
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Ye J, Hu A, Gao C, Li F, Li L, Guo Y, Ren G, Li B, Rensing C, Nealson KH, Zhou S, Xiong Y. Abiotic Methane Production Driven by Ubiquitous Non-Fenton-Type Reactive Oxygen Species. Angew Chem Int Ed Engl 2024; 63:e202403884. [PMID: 38489233 DOI: 10.1002/anie.202403884] [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: 02/24/2024] [Revised: 03/15/2024] [Accepted: 03/15/2024] [Indexed: 03/17/2024]
Abstract
Abiotic CH4 production driven by Fenton-type reactive oxygen species (ROS) has been confirmed to be an indispensable component of the atmospheric CH4 budget. While the chemical reactions independent of Fenton chemistry to ROS are ubiquitous in nature, it remains unknown whether the produced ROS can drive abiotic CH4 production. Here, we first demonstrated the abiotic CH4 production at the soil-water interface under illumination. Leveraging this finding, polymeric carbon nitrides (CNx) as a typical analogue of natural geobattery material and dimethyl sulfoxide (DMSO) as a natural methyl donor were used to unravel the underlying mechanisms. We revealed that the ROS, photocatalytically produced by CNx, can oxidize DMSO into CH4 with a high selectivity of 91.5 %. Such an abiotic CH4 production process was further expanded to various non-Fenton-type reaction systems, such as electrocatalysis, pyrocatalysis and sonocatalysis. This work provides insights into the geochemical cycle of abiotic CH4, and offers a new route to CH4 production via integrated energy development.
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Affiliation(s)
- Jie Ye
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Andong Hu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chao Gao
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, 230026, China
| | - Fengqi Li
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lei Li
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yulin Guo
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Guoping Ren
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Bing Li
- Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Kenneth H Nealson
- Department of Earth Science, University of Southern California, Los Angeles, California, 90089, United States
| | - Shungui Zhou
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yujie Xiong
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, 230026, China
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Bellomo C, Lagostina V, Pavan C, Paganini MC, Turci F. Reaction with Water Vapor Defines Surface Reconstruction and Membranolytic Activity of Quartz Milled in Different Molecular Environments. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2308369. [PMID: 38102095 DOI: 10.1002/smll.202308369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/20/2023] [Indexed: 12/17/2023]
Abstract
Industrial processing of quartz (SiO2) and quartz-containing materials produces toxic dust. Fracturing quartz crystals opens the Si‒O bond and produces highly reactive surface species which mainly react with molecules like water and oxygen. This surface-reconstruction process forms silanol (Si‒OH) on the quartz surface, which can damage biological membranes under specific configurations. To comprehend the impact of the quartz surface restructuring on membranolytic activity, the formation and reactivity of quartz radicals produced in four distinct molecular environments with electron paramagnetic resonance (EPR) spectroscopy are evaluated and their membranolytic activity is measured through in vitro hemolysis test. The four molecular environments are formulated with and without molecular water vapor and oxygen (±H2O/±O2). The absence of water favored the formation of surface radical species. In water-rich environments, diamagnetic species prevailed due to radical recombination. Quartz milled in -H2O/±O2 acquired membranolytic activity when exposed to water vapor, unlike quartz milled in +H2O/±O2. After being stabilized by reaction with water vapor, the membranolytic activity of quartz is maintained over time. It is demonstrated that the type and the reactivity of radical sites on quartz are modulated by the outer molecular environment, ultimately determining the biological activity of milled quartz dust.
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Affiliation(s)
- Chiara Bellomo
- Department of Chemistry, Università degli Studi di Torino, Torino, 10125, Italy
- "G. Scansetti" Interdepartmental Center for Studies on Asbestos, Other Toxic Particulates, Università degli Studi di Torino, Torino, 10125, Italy
| | - Valeria Lagostina
- Department of Chemistry, Università degli Studi di Torino, Torino, 10125, Italy
| | - Cristina Pavan
- Department of Chemistry, Università degli Studi di Torino, Torino, 10125, Italy
- "G. Scansetti" Interdepartmental Center for Studies on Asbestos, Other Toxic Particulates, Università degli Studi di Torino, Torino, 10125, Italy
- Louvain Center for Toxicology, Applied Pharmacology, Université catholique de Louvain, Brussels, 1200, Belgium
| | - Maria Cristina Paganini
- Department of Chemistry, Università degli Studi di Torino, Torino, 10125, Italy
- NIS interdepartmental Center for Nanomaterials for Industry and Sustainability, Università degli Studi di Torino, Torino, 10125, Italy
| | - Francesco Turci
- Department of Chemistry, Università degli Studi di Torino, Torino, 10125, Italy
- "G. Scansetti" Interdepartmental Center for Studies on Asbestos, Other Toxic Particulates, Università degli Studi di Torino, Torino, 10125, Italy
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6
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Koppenol WH, Sies H. Was H 2O 2 generated before oxygenic photosynthesis? Redox Biol 2024; 71:103110. [PMID: 38492556 PMCID: PMC10957399 DOI: 10.1016/j.redox.2024.103110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 02/29/2024] [Accepted: 02/29/2024] [Indexed: 03/18/2024] Open
Abstract
We obviously agree with Wu et al. that H2O2 might accumulate in the Archean land waters devoid of Fe2+. We do disagree on the topic of the half-life of H2O2, as the work cited in support for a longer half-live is not relevant to the conditions in the Archean ocean. While the existence of radicals in quartz is not in doubt, we do question the hypothesis that these radicals oxidize water to HO• and H2O2.
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Affiliation(s)
- Willem H Koppenol
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology, Zürich, Switzerland.
| | - Helmut Sies
- Institute for Biochemistry and Molecular Biology I, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany; Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
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7
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Wu X, Zhu J, He H, Konhauser KO, Li Y. Comments on "was hydrogen peroxide present before the arrival of oxygenic photosynthesis? The important role of iron(II) in the archean ocean". Redox Biol 2024; 71:103111. [PMID: 38521703 PMCID: PMC11313173 DOI: 10.1016/j.redox.2024.103111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 02/29/2024] [Indexed: 03/25/2024] Open
Abstract
Recent research has hypothesized that hydrogen peroxide (H2O2) may have emerged from abiotic geochemical processes during the Archean eon (4.0-2.5 Ga), stimulating the evolution of an enzymatic antioxidant system in early life. This eventually led to the evolution of cyanobacteria, and in turn, the accumulation of oxygen on Earth. In the latest issue of Redox Biology, Koppenol and Sies (vol. 29, no. 103012, 2024) argued against this hypothesis and suggested instead that early organisms would not have been exposed to H2O2 due to its short half-life in the ferruginous oceans of the Archean. We find these arguments to be factually incomplete because they do not consider that freshwater or some coastal marine environments during the Archean could indeed have led to H2O2 generation and accumulation. In these environments, abiotic oxidants could have interacted with early life, thus steering its evolutionary course.
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Affiliation(s)
- Xiao Wu
- CAS Key Laboratory of Mineralogy and Metallogeny/Guangdong Provincial Key Laboratory of Mineral Physics and Materials, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences (CAS), Guangzhou, 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou, 510640, China
| | - Jianxi Zhu
- CAS Key Laboratory of Mineralogy and Metallogeny/Guangdong Provincial Key Laboratory of Mineral Physics and Materials, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences (CAS), Guangzhou, 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou, 510640, China.
| | - Hongping He
- CAS Key Laboratory of Mineralogy and Metallogeny/Guangdong Provincial Key Laboratory of Mineral Physics and Materials, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences (CAS), Guangzhou, 510640, China; CAS Center for Excellence in Deep Earth Science, Guangzhou, 510640, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kurt O Konhauser
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta, T6G 2E3, Canada
| | - Yiliang Li
- Department of Earth Sciences, The University of Hong Kong, Hong Kong, 999077, China.
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8
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Huang XL, Harmer JR, Schenk G, Southam G. Inorganic Fe-O and Fe-S oxidoreductases: paradigms for prebiotic chemistry and the evolution of enzymatic activity in biology. Front Chem 2024; 12:1349020. [PMID: 38389729 PMCID: PMC10881703 DOI: 10.3389/fchem.2024.1349020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/23/2024] [Indexed: 02/24/2024] Open
Abstract
Oxidoreductases play crucial roles in electron transfer during biological redox reactions. These reactions are not exclusive to protein-based biocatalysts; nano-size (<100 nm), fine-grained inorganic colloids, such as iron oxides and sulfides, also participate. These nanocolloids exhibit intrinsic redox activity and possess direct electron transfer capacities comparable to their biological counterparts. The unique metal ion architecture of these nanocolloids, including electron configurations, coordination environment, electron conductivity, and the ability to promote spontaneous electron hopping, contributes to their transfer capabilities. Nano-size inorganic colloids are believed to be among the earliest 'oxidoreductases' to have 'evolved' on early Earth, playing critical roles in biological systems. Representing a distinct type of biocatalysts alongside metalloproteins, these nanoparticles offer an early alternative to protein-based oxidoreductase activity. While the roles of inorganic nano-sized catalysts in current Earth ecosystems are intuitively significant, they remain poorly understood and underestimated. Their contribution to chemical reactions and biogeochemical cycles likely helped shape and maintain the balance of our planet's ecosystems. However, their potential applications in biomedical, agricultural, and environmental protection sectors have not been fully explored or exploited. This review examines the structure, properties, and mechanisms of such catalysts from a material's evolutionary standpoint, aiming to raise awareness of their potential to provide innovative solutions to some of Earth's sustainability challenges.
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Affiliation(s)
- Xiao-Lan Huang
- NYS Center for Clean Water Technology, School of Marine and Atmospheric Sciences, Stony Brook, NY, United States
| | - Jeffrey R Harmer
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Gerhard Schenk
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Sustainable Minerals Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Gordon Southam
- Sustainable Minerals Institute, The University of Queensland, Brisbane, QLD, Australia
- School of the Environment, The University of Queensland, Brisbane, QLD, Australia
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9
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Koppenol WH, Sies H. Was hydrogen peroxide present before the arrival of oxygenic photosynthesis? The important role of iron(II) in the Archean ocean. Redox Biol 2024; 69:103012. [PMID: 38183797 PMCID: PMC10808959 DOI: 10.1016/j.redox.2023.103012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/18/2023] [Accepted: 12/22/2023] [Indexed: 01/08/2024] Open
Abstract
We address the chemical/biological history of H2O2 back at the times of the Archean eon (2.5-3.9 billion years ago (Gya)). During the Archean eon the pO2 was million-fold lower than the present pO2, starting to increase gradually from 2.3 until 0.6 Gya, when it reached ca. 0.2 bar. The observation that some anaerobic organisms can defend themselves against O2 has led to the view that early organisms could do the same before oxygenic photosynthesis had developed at about 3 Gya. This would require the anaerobic generation of H2O2, and here we examine the various mechanisms which were suggested in the literature for this. Given the concentration of Fe2+ at 20-200 μM in the Archean ocean, the estimated half-life of H2O2 is ca. 0.7 s. The oceanic H2O2 concentration was practically zero. We conclude that early organisms were not exposed to H2O2 before the arrival of oxygenic photosynthesis.
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Affiliation(s)
- Willem H Koppenol
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology, Zürich, Switzerland.
| | - Helmut Sies
- Institute for Biochemistry and Molecular Biology I, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany; Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany
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10
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Siebieszuk A, Sejbuk M, Witkowska AM. Studying the Human Microbiota: Advances in Understanding the Fundamentals, Origin, and Evolution of Biological Timekeeping. Int J Mol Sci 2023; 24:16169. [PMID: 38003359 PMCID: PMC10671191 DOI: 10.3390/ijms242216169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
The recently observed circadian oscillations of the intestinal microbiota underscore the profound nature of the human-microbiome relationship and its importance for health. Together with the discovery of circadian clocks in non-photosynthetic gut bacteria and circadian rhythms in anucleated cells, these findings have indicated the possibility that virtually all microorganisms may possess functional biological clocks. However, they have also raised many essential questions concerning the fundamentals of biological timekeeping, its evolution, and its origin. This narrative review provides a comprehensive overview of the recent literature in molecular chronobiology, aiming to bring together the latest evidence on the structure and mechanisms driving microbial biological clocks while pointing to potential applications of this knowledge in medicine. Moreover, it discusses the latest hypotheses regarding the evolution of timing mechanisms and describes the functions of peroxiredoxins in cells and their contribution to the cellular clockwork. The diversity of biological clocks among various human-associated microorganisms and the role of transcriptional and post-translational timekeeping mechanisms are also addressed. Finally, recent evidence on metabolic oscillators and host-microbiome communication is presented.
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Affiliation(s)
- Adam Siebieszuk
- Department of Physiology, Faculty of Medicine, Medical University of Bialystok, Mickiewicza 2C, 15-222 Białystok, Poland;
| | - Monika Sejbuk
- Department of Food Biotechnology, Faculty of Health Sciences, Medical University of Bialystok, Szpitalna 37, 15-295 Białystok, Poland;
| | - Anna Maria Witkowska
- Department of Food Biotechnology, Faculty of Health Sciences, Medical University of Bialystok, Szpitalna 37, 15-295 Białystok, Poland;
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11
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Gull M, Feng T, Smith B, Calcul L, Pasek MA. Prebiotic Syntheses of Organophosphorus Compounds from Reduced Source of Phosphorus in Non-Aqueous Solvents. Life (Basel) 2023; 13:2134. [PMID: 38004274 PMCID: PMC10672063 DOI: 10.3390/life13112134] [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: 09/29/2023] [Revised: 10/23/2023] [Accepted: 10/28/2023] [Indexed: 11/26/2023] Open
Abstract
Reduced-oxidation-state phosphorus (reduced P, hereafter) compounds were likely available on the early Earth via meteorites or through various geologic processes. Due to their reactivity and high solubility, these compounds could have played a significant role in the origin of various organophosphorus compounds of biochemical significance. In the present work, we study the reactions between reduced P compounds and their oxidation products, with the three nucleosides (uridine, adenosine, and cytidine), with organic alcohols (glycerol and ethanolamine), and with the tertiary ammonium organic compound, choline chloride. These reactions were studied in the non-aqueous solvent formamide and in a semi-aqueous solvent comprised of urea: ammonium formate: water (UAFW, hereafter) at temperatures of 55-68 °C. The inorganic P compounds generated through Fenton chemistry readily dissolve in the non-aqueous and semi-aqueous solvents and react with organics to form organophosphites and organophosphates, including those which are identified as phosphate diesters. This dual approach (1) use of non-aqueous and semi-aqueous solvents and (2) use of a reactive inorganic P source to promote phosphorylation and phosphonylation reactions of organics readily promoted anhydrous chemistry and condensation reactions, without requiring any additive, catalyst, or other promoting agent under mild heating conditions. We also present a comparative study of the release of P from various prebiotically relevant phosphate minerals and phosphite salts (e.g., vivianite, apatite, and phosphites of iron and calcium) into formamide and UAFW. These results have direct implications for the origin of biological P compounds from non-aqueous solvents of prebiotic provenance.
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Affiliation(s)
- Maheen Gull
- School of Geosciences, University of South Florida, 4202 E. Fowler Ave. NES 204, Tampa, FL 33584, USA; (T.F.); (M.A.P.)
| | - Tian Feng
- School of Geosciences, University of South Florida, 4202 E. Fowler Ave. NES 204, Tampa, FL 33584, USA; (T.F.); (M.A.P.)
| | - Benjamin Smith
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave. CHE 205, Tampa, FL 33620, USA; (L.C.); (B.S.)
| | - Laurent Calcul
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave. CHE 205, Tampa, FL 33620, USA; (L.C.); (B.S.)
| | - Matthew A. Pasek
- School of Geosciences, University of South Florida, 4202 E. Fowler Ave. NES 204, Tampa, FL 33584, USA; (T.F.); (M.A.P.)
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12
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Kharabian-Masouleh A, Furtado A, Alsubaie B, Al-Dossary O, Wu A, Al-Mssalem I, Henry R. Loss of plastid ndh genes in an autotrophic desert plant. Comput Struct Biotechnol J 2023; 21:5016-5027. [PMID: 37867970 PMCID: PMC10589726 DOI: 10.1016/j.csbj.2023.10.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 10/24/2023] Open
Abstract
Plant plastid genomes are highly conserved with most flowering plants having the same complement of essential plastid genes. Here, we report the loss of five of the eleven NADH dehydrogenase subunit genes (ndh) in the plastid of a desert plant jojoba (Simmondsia chinensis). The plastid genome of jojoba was 156,496 bp with one large single copy region (LSC), a very small single copy region (SSC) and two expanded inverted repeats (IRA + IRB). The NADH dehydrogenase (NDH) complex is comprised of several protein subunits, encoded by the ndh genes of the plastome and the nucleus. The ndh genes are critical to the proper functioning of the photosynthetic electron transport chain and protection of plants from oxidative stress. Most plants are known to contain all eleven ndh genes. Plants with missing or defective ndh genes are often heterotrophs either due to their complete or holo- or myco- parasitic nature. Plants with a defective NDH complex, caused by the deletion/pseudogenisation of some or all the ndh genes, survive in milder climates suggesting the likely extinction of plant lineages lacking these genes under harsh climates. Interestingly, some autotrophic plants do exist without ndh gene/s and can cope with high or low light. This implies that these plants are protected from oxidative stress by mechanisms excluding ndh genes. Jojoba has evolved mechanisms to cope with a non-functioning NDH complex and survives in extreme desert conditions with abundant sunlight and limited water.
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Affiliation(s)
- Ardashir Kharabian-Masouleh
- Queensland Alliance for Innovation in Food and Agriculture (QAAFI), The University of Queensland, Carmody Rd, St Lucia, QLD 4072, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Carmody Rd, St Lucia, QLD 4072, Australia
| | - Agnelo Furtado
- Queensland Alliance for Innovation in Food and Agriculture (QAAFI), The University of Queensland, Carmody Rd, St Lucia, QLD 4072, Australia
| | - Bader Alsubaie
- Queensland Alliance for Innovation in Food and Agriculture (QAAFI), The University of Queensland, Carmody Rd, St Lucia, QLD 4072, Australia
- College of Agriculture and Food Sciences, King Faisal University (KFU), Al Hofuf, 36362 Saudi Arabia
| | - Othman Al-Dossary
- Queensland Alliance for Innovation in Food and Agriculture (QAAFI), The University of Queensland, Carmody Rd, St Lucia, QLD 4072, Australia
- College of Agriculture and Food Sciences, King Faisal University (KFU), Al Hofuf, 36362 Saudi Arabia
| | - Alex Wu
- Queensland Alliance for Innovation in Food and Agriculture (QAAFI), The University of Queensland, Carmody Rd, St Lucia, QLD 4072, Australia
| | - Ibrahim Al-Mssalem
- College of Agriculture and Food Sciences, King Faisal University (KFU), Al Hofuf, 36362 Saudi Arabia
| | - Robert Henry
- Queensland Alliance for Innovation in Food and Agriculture (QAAFI), The University of Queensland, Carmody Rd, St Lucia, QLD 4072, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Carmody Rd, St Lucia, QLD 4072, Australia
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13
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Liao Q, Sun Q, Xu H, Wang Y, Xu Y, Li Z, Hu J, Wang D, Li H, Xi K. Regulating Relative Nitrogen Locations of Diazine Functionalized Covalent Organic Frameworks for Overall H 2 O 2 Photosynthesis. Angew Chem Int Ed Engl 2023; 62:e202310556. [PMID: 37632257 DOI: 10.1002/anie.202310556] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/20/2023] [Accepted: 08/24/2023] [Indexed: 08/27/2023]
Abstract
Nitrogen-heterocycle-based covalent organic frameworks (COFs) are considered promising candidates for the overall photosynthesis of hydrogen peroxide (H2 O2 ). However, the effects of the relative nitrogen locations remain obscured and photocatalytic performances of COFs need to be further improved. Herein, a collection of COFs functionalized by various diazines including pyridazine, pyrimidine, and pyrazine have been judiciously designed and synthesized for photogeneration of H2 O2 without sacrificial agents. Compared with pyrimidine and pyrazine, pyridazine embedded in TpDz tends to stabilize endoperoxide intermediate species, leading toward the more efficient direct 2e- oxygen reduction reaction (ORR) pathway. Benefiting from the effective electron-hole separation, low charge transfer resistance, and high-efficiency ORR pathway, an excellent production rate of 7327 μmol g-1 h-1 and a solar-to-chemical conversion (SCC) value of 0.62 % has been achieved by TpDz, which ranks one of the best COF-based photocatalysts. This work might shed fresh light on the rational design of functional COFs targeting photocatalysts in H2 O2 production.
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Affiliation(s)
- Qiaobo Liao
- School of Materials and Chemistry, University of Shanghai for Science and Technology, Shanghai, 200093, P. R. China
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Qiannan Sun
- School of Materials and Chemistry, University of Shanghai for Science and Technology, Shanghai, 200093, P. R. China
| | - Haocheng Xu
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Yandong Wang
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Yang Xu
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
| | - Ziyu Li
- School of Materials and Chemistry, University of Shanghai for Science and Technology, Shanghai, 200093, P. R. China
| | - Jinwu Hu
- School of Materials and Chemistry, University of Shanghai for Science and Technology, Shanghai, 200093, P. R. China
| | - Ding Wang
- School of Materials and Chemistry, University of Shanghai for Science and Technology, Shanghai, 200093, P. R. China
| | - Huijun Li
- School of Materials and Chemistry, University of Shanghai for Science and Technology, Shanghai, 200093, P. R. China
| | - Kai Xi
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, P. R. China
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14
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Yi R, Mojica M, Fahrenbach AC, James Cleaves H, Krishnamurthy R, Liotta CL. Carbonyl Migration in Uronates Affords a Potential Prebiotic Pathway for Pentose Production. JACS AU 2023; 3:2522-2535. [PMID: 37772180 PMCID: PMC10523364 DOI: 10.1021/jacsau.3c00299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/15/2023] [Accepted: 08/15/2023] [Indexed: 09/30/2023]
Abstract
Carbohydrate biosynthesis is fundamental to modern terrestrial biochemistry, but how this collection of metabolic pathways originated remains an open question. Prebiotic sugar synthesis has focused primarily on the formose reaction and Kiliani-Fischer homologation; however, how they can transition to extant biochemical pathways has not been studied. Herein, a nonenzymatic pathway for pentose production with similar chemical transformations as those of the pentose phosphate pathway is demonstrated. Starting from a C6 aldonate, namely, gluconate, nonselective chemical oxidation yields a mixture of 2-oxo-, 4-oxo-, 5-oxo-, and 6-oxo-uronate regioisomers. Regardless at which carbinol the oxidation takes place, carbonyl migration enables β-decarboxylation to yield pentoses. In comparison, the pentose phosphate pathway selectively oxidizes 6-phosphogluconate to afford the 3-oxo-uronate derivative, which undergoes facile subsequent β-decarboxylation and carbonyl migration to afford ribose 5-phosphate. The similarities between these two pathways and the potential implications for prebiotic chemistry and protometabolism are discussed.
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Affiliation(s)
- Ruiqin Yi
- Earth-Life
Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Mike Mojica
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
| | - Albert C. Fahrenbach
- School
of Chemistry, Australian Centre for Astrobiology and the UNSW RNA
Institute, University of New South Wales, Sydney, NSW 2052, Australia
| | - H. James Cleaves
- Blue
Marble Space Institute of Science, Seattle, Washington 98154, United States
| | | | - Charles L. Liotta
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332, United States
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15
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Farr O, Gaudu N, Danger G, Russell MJ, Ferry D, Nitschke W, Duval S. Methanol on the rocks: green rust transformation promotes the oxidation of methane. J R Soc Interface 2023; 20:20230386. [PMID: 37727071 PMCID: PMC10509593 DOI: 10.1098/rsif.2023.0386] [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: 07/07/2023] [Accepted: 08/30/2023] [Indexed: 09/21/2023] Open
Abstract
Shared coordination geometries between metal ions within reactive minerals and enzymatic metal cofactors hints at mechanistic and possibly evolutionary homology between particular abiotic chemical mineralogies and biological metabolism. The octahedral coordination of reactive Fe2+/3+ minerals such as green rusts, endemic to anoxic sediments and the early Earth's oceans, mirrors the di-iron reaction centre of soluble methane monooxygenase (sMMO), responsible for methane oxidation in methanotrophy. We show that methane oxidation occurs in tandem with the oxidation of green rust to lepidocrocite and magnetite, mimicking radical-mediated methane oxidation found in sMMO to yield not only methanol but also halogenated hydrocarbons in the presence of seawater. This naturally occurring geochemical pathway for CH4 oxidation elucidates a previously unidentified carbon cycling mechanism in modern and ancient environments and reveals clues into mineral-mediated reactions in the synthesis of organic compounds necessary for the emergence of life.
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Affiliation(s)
- Orion Farr
- CNRS, CINaM, Aix-Marseille Univ, 13009 Marseille, France
- CNRS, BIP (UMR 7281), Aix Marseille Univ, Marseille, France
| | - Nil Gaudu
- CNRS, BIP (UMR 7281), Aix Marseille Univ, Marseille, France
| | | | | | - Daniel Ferry
- CNRS, CINaM, Aix-Marseille Univ, 13009 Marseille, France
| | | | - Simon Duval
- CNRS, BIP (UMR 7281), Aix Marseille Univ, Marseille, France
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16
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Xia Y, Li J, Zhang Y, Yin Y, Chen B, Liang Y, Jiang G, Zare RN. Contact between water vapor and silicate surface causes abiotic formation of reactive oxygen species in an anoxic atmosphere. Proc Natl Acad Sci U S A 2023; 120:e2302014120. [PMID: 37459548 PMCID: PMC10372544 DOI: 10.1073/pnas.2302014120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 06/10/2023] [Indexed: 07/29/2023] Open
Abstract
Spontaneous generation of reactive oxygen species (ROS) in aqueous microdroplets or at a water vapor-silicate interface is a new source of redox chemistry. However, such generation occurs with difficulty in liquid water having a large ionic strength. We report that ROS is spontaneously produced when water vapor contacts hydrogen-bonded hydroxyl groups on a silicate surface. The evolution of hydrogen-bonded species such as hydroxyl groups was investigated by using two-dimensional, time-resolved FT-IR spectroscopy. The participation of water vapor in ROS generation is confirmed by investigating the reaction of D2O vapor and hydroxyl groups on a silicate surface. We propose a reaction pathway for ROS generation based on the change of the hydrogen-bonding network and corresponding electron transfer onto the silicate surface in the water vapor-solid contact process. Our observations suggest that ROS production from water vapor-silicate contact electrification could have contributed to oxidation during the Archean Eon before the Great Oxidation Event.
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Affiliation(s)
- Yu Xia
- State Key Laboratory of Precision Blasting, Jianghan University, Wuhan430056, China
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan430056, China
- Department of Chemistry, Stanford University, Stanford, CA94305
| | - Juan Li
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan430056, China
- School of Physics and Technology, Wuhan University, Wuhan430072, China
| | - Yuanzheng Zhang
- School of Physics and Technology, Wuhan University, Wuhan430072, China
| | - Yongguang Yin
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing10085, China
| | - Bolei Chen
- State Key Laboratory of Precision Blasting, Jianghan University, Wuhan430056, China
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan430056, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing10085, China
| | - Yong Liang
- State Key Laboratory of Precision Blasting, Jianghan University, Wuhan430056, China
- Hubei Key Laboratory of Environmental and Health Effects of Persistent Toxic Substances, Jianghan University, Wuhan430056, China
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing10085, China
| | - Richard N. Zare
- Department of Chemistry, Stanford University, Stanford, CA94305
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17
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Vignane T, Filipovic MR. Emerging Chemical Biology of Protein Persulfidation. Antioxid Redox Signal 2023; 39:19-39. [PMID: 37288744 PMCID: PMC10433728 DOI: 10.1089/ars.2023.0352] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 05/30/2023] [Indexed: 06/09/2023]
Abstract
Significance: Protein persulfidation (the formation of RSSH), an evolutionarily conserved oxidative posttranslational modification in which thiol groups in cysteine residues are converted into persulfides, has emerged as one of the main mechanisms through which hydrogen sulfide (H2S) conveys its signaling. Recent Advances: New methodological advances in persulfide labeling started unraveling the chemical biology of this modification and its role in (patho)physiology. Some of the key metabolic enzymes are regulated by persulfidation. RSSH levels are important for the cellular defense against oxidative injury, and they decrease with aging, leaving proteins vulnerable to oxidative damage. Persulfidation is dysregulated in many diseases. Critical Issues: A relatively new field of signaling by protein persulfidation still has many unanswered questions: the mechanism(s) of persulfide formation and transpersulfidation and the identification of "protein persulfidases," the improvement of methods to monitor RSSH changes and identify protein targets, and understanding the mechanisms through which this modification controls important (patho)physiological functions. Future Directions: Deep mechanistic studies using more selective and sensitive RSSH labeling techniques will provide high-resolution structural, functional, quantitative, and spatiotemporal information on RSSH dynamics and help with better understanding how H2S-derived protein persulfidation affects protein structure and function in health and disease. This knowledge could pave the way for targeted drug design for a wide variety of pathologies. Antioxid. Redox Signal. 39, 19-39.
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Affiliation(s)
- Thibaut Vignane
- Leibniz Institute for Analytical Sciences, ISAS e.V., Dortmund, Germany
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18
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Yang H, Lu L, Chen Y, Ye J. Transcriptomic Analysis Reveals the Response of the Bacterium Priestia Aryabhattai SK1-7 to Interactions and Dissolution with Potassium Feldspar. Appl Environ Microbiol 2023; 89:e0203422. [PMID: 37154709 DOI: 10.1128/aem.02034-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
Potassium feldspar (K2O·Al2O3·6SiO2) is considered to be the most important source of potash fertilizer. The use of microorganisms to dissolve potassium feldspar is a low-cost and environmentally friendly method. Priestia aryabhattai SK1-7 is a strain with a strong ability to dissolve potassium feldspar; it showed a faster pH drop and produced more acid in the medium with potassium feldspar as the insoluble potassium source than in the medium with K2HPO4 as the soluble potassium source. We speculated whether the cause of acid production was related to one or more stresses, such as mineral-induced generation of reactive oxygen species (ROS), the presence of aluminum in potassium feldspar, and cell membrane damage due to friction between SK1-7 and potassium feldspar, and analyzed it by transcriptome. The results revealed that the expression of the genes related to pyruvate metabolism, the two-component system, DNA repair, and oxidative stress pathways in strain SK1-7 was significantly upregulated in potassium feldspar medium. The subsequent validation experiments revealed that ROS were the stress faced by strain SK1-7 when interacting with potassium feldspar and led to a decrease in the total fatty acid content of SK1-7. In the face of ROS stress, strain SK1-7 upregulated the expression of the maeA-1 gene, allowing malic enzyme (ME2) to produce more pyruvate to be secreted outside the cell using malate as a substrate. Pyruvate is both a scavenger of external ROS and a gas pedal of dissolved potassium feldspar. IMPORTANCE Mineral-microbe interactions play important roles in the biogeochemical cycling of elements. Manipulating mineral-microbe interactions and optimizing the consequences of such interactions can be used to benefit society. It is necessary to explore the black hole of the mechanism of interaction between the two. In this study, it is revealed that P. aryabhattai SK1-7 faces mineral-induced ROS stress by upregulating a series of antioxidant genes as a passive defense, while overexpression of malic enzyme (ME2) secretes pyruvate to scavenge ROS as well as to increase feldspar dissolution, releasing K, Al, and Si into the medium. Our research provides a theoretical basis for improving the ability of microorganisms to weather minerals through genetic manipulation in the future.
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Affiliation(s)
- Hui Yang
- College of Forestry and Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Lanxiang Lu
- College of Forestry and Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Yifan Chen
- College of Forestry and Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Jianren Ye
- College of Forestry and Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, Jiangsu, China
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19
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Chang JN, Li Q, Shi JW, Zhang M, Zhang L, Li S, Chen Y, Li SL, Lan YQ. Oxidation-Reduction Molecular Junction Covalent Organic Frameworks for Full Reaction Photosynthesis of H 2 O 2. Angew Chem Int Ed Engl 2023; 62:e202218868. [PMID: 36581593 DOI: 10.1002/anie.202218868] [Citation(s) in RCA: 46] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 12/31/2022]
Abstract
The full reaction photosynthesis of H2 O2 that can combine water-oxidation and oxygen-reduction without sacrificial agents is highly demanded to maximize the light-utilization and overcome the complex reaction-process of anthraquinone-oxidation. Here, a kind of oxidation-reduction molecular junction covalent-organic-framework (TTF-BT-COF) has been synthesized through the covalent-coupling of tetrathiafulvalene (photo-oxidation site) and benzothiazole (photo-reduction site), which presents visible-light-adsorption region, effective electron-hole separation-efficiency and photo-redox sites that enables full reaction generation of H2 O2 . Specifically, a record-high yield (TTF-BT-COF, ≈276 000 μM h-1 g-1 ) for H2 O2 photosynthesis without sacrificial agents has been achieved among porous crystalline photocatalysts. This is the first work that can design oxidation-reduction molecular junction COFs for full reaction photosynthesis of H2 O2 , which might extend the scope of COFs in H2 O2 production.
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Affiliation(s)
- Jia-Nan Chang
- Jiangsu Collaborative Innovation Centre of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China
| | - Qi Li
- Jiangsu Collaborative Innovation Centre of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China
| | - Jing-Wen Shi
- Jiangsu Collaborative Innovation Centre of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China
| | - Mi Zhang
- School of Chemistry, South China Normal University, Guangzhou, 510006, P. R. China
| | - Lei Zhang
- School of Chemistry, South China Normal University, Guangzhou, 510006, P. R. China
| | - Shan Li
- Jiangsu Collaborative Innovation Centre of Biomedical Functional Materials, Jiangsu Key Laboratory of New Power Batteries, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, P. R. China
| | - Yifa Chen
- School of Chemistry, South China Normal University, Guangzhou, 510006, P. R. China
| | - Shun-Li Li
- School of Chemistry, South China Normal University, Guangzhou, 510006, P. R. China
| | - Ya-Qian Lan
- School of Chemistry, South China Normal University, Guangzhou, 510006, P. R. China
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20
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Organophosphorus Compound Formation Through the Oxidation of Reduced Oxidation State Phosphorus Compounds on the Hadean Earth. J Mol Evol 2023; 91:60-75. [PMID: 36576533 DOI: 10.1007/s00239-022-10086-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/16/2022] [Indexed: 12/29/2022]
Abstract
Reduced oxidation state phosphorus compounds may have been brought to the early Earth via meteorites or could have formed through geologic processes. These compounds could have played a role in the origin of biological phosphorus (P, hereafter) compounds. Reduced oxidation state P compounds are generally more soluble in water and are more reactive than orthophosphate and its associated minerals. However, to date no facile routes to generate C-O-P type compounds using reduced oxidation state P compounds have been reported under prebiotic conditions. In this study, we investigate the reactions between reduced oxidation state P compounds-and their oxidized products generated via Fenton reactions-with the nucleosides uridine and adenosine. The inorganic P compounds generated via Fenton chemistry readily react with nucleosides to produce organophosphites and organophosphates, including phosphate diesters via one-pot syntheses. The reactions were facilitated by NH4+ ions and urea as a condensation agent. We also present the results of the plausible stability of the organic compounds such as adenosine in an environment containing an abundance of H2O2. Such results have direct implications on finding organic compounds in Martian environments and other rocky planets (including early Earth) that were richer in H2O2 than O2. Finally, we also suggest a route for the sink of these inorganic P compounds, as a part of a plausible natural P cycle and show the possible formation of secondary phosphate minerals such as struvite and brushite on the early Earth.
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21
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Pavan C, Escolano-Casado G, Bellomo C, Cananà S, Tomatis M, Leinardi R, Mino L, Turci F. Nearly free silanols drive the interaction of crystalline silica polymorphs with membranes: Implications for mineral toxicity. Front Chem 2023; 10:1092221. [PMID: 36726450 PMCID: PMC9884702 DOI: 10.3389/fchem.2022.1092221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/30/2022] [Indexed: 01/18/2023] Open
Abstract
Crystalline silica (CS) is a well-known hazardous material that causes severe diseases including silicosis, lung cancer, and autoimmune diseases. However, the hazard associated to crystalline silica is extremely variable and depends on some specific characteristics, including crystal structure and surface chemistry. The crystalline silica polymorphs share the SiO2 stoichiometry and differentiate for crystal structure. The different crystal lattices in turn expose differently ordered hydroxyl groups at the crystal surface, i.e., the silanols. The nearly free silanols (NFS), a specific population of weakly interacting silanols, have been recently advanced as the key surface feature that governs recognition mechanisms between quartz and cell membrane, initiating toxicity. We showed here that the nearly free silanols occur on the other crystalline silica polymorphs and take part in the molecular interactions with biomembranes. A set of crystalline silica polymorphs, including quartz, cristobalite, tridymite, coesite, and stishovite, was physico-chemically characterized and the membranolytic activity was assessed using red blood cells as model membranes. Infrared spectroscopy in highly controlled conditions was used to profile the surface silanol topochemistry and the occurrence of surface nearly free silanols on crystalline silica polymorphs. All crystalline silica polymorphs, but stishovite were membranolytic. Notably, pristine stishovite did not exhibited surface nearly free silanols. The topochemistry of surface silanols was modulated by thermal treatments, and we showed that the occurrence of nearly free silanols paralleled the membranolytic activity for the crystalline silica polymorphs. These results provide a comprehensive understanding of the structure-activity relationship between nearly free silanols and membranolytic activity of crystalline silica polymorphs, offering a possible clue for interpreting the molecular mechanisms associated with silica hazard and bio-minero-chemical interfacial phenomena, including prebiotic chemistry.
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Affiliation(s)
- Cristina Pavan
- Department of Chemistry, University of Turin, Turin, Italy,“G. Scansetti” Interdepartmental Centre for Studies on Asbestos and Other Toxic Particulates, University of Turin, Turin, Italy,Louvain Centre for Toxicology and Applied Pharmacology, Institute of Experimental and Clinical Research, Université catholique de Louvain, Brussels, Belgium
| | - Guillermo Escolano-Casado
- Department of Chemistry, University of Turin, Turin, Italy,Nanostructured Interfaces and Surfaces Interdepartmental Centre, University of Turin, Turin, Italy
| | - Chiara Bellomo
- Department of Chemistry, University of Turin, Turin, Italy,“G. Scansetti” Interdepartmental Centre for Studies on Asbestos and Other Toxic Particulates, University of Turin, Turin, Italy
| | - Stefania Cananà
- Department of Chemistry, University of Turin, Turin, Italy,“G. Scansetti” Interdepartmental Centre for Studies on Asbestos and Other Toxic Particulates, University of Turin, Turin, Italy
| | - Maura Tomatis
- Department of Chemistry, University of Turin, Turin, Italy,“G. Scansetti” Interdepartmental Centre for Studies on Asbestos and Other Toxic Particulates, University of Turin, Turin, Italy
| | - Riccardo Leinardi
- Louvain Centre for Toxicology and Applied Pharmacology, Institute of Experimental and Clinical Research, Université catholique de Louvain, Brussels, Belgium
| | - Lorenzo Mino
- Department of Chemistry, University of Turin, Turin, Italy,Nanostructured Interfaces and Surfaces Interdepartmental Centre, University of Turin, Turin, Italy
| | - Francesco Turci
- Department of Chemistry, University of Turin, Turin, Italy,“G. Scansetti” Interdepartmental Centre for Studies on Asbestos and Other Toxic Particulates, University of Turin, Turin, Italy,*Correspondence: Francesco Turci,
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22
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Bauwe H. Photorespiration - Rubisco's repair crew. JOURNAL OF PLANT PHYSIOLOGY 2023; 280:153899. [PMID: 36566670 DOI: 10.1016/j.jplph.2022.153899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/11/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
The photorespiratory repair pathway (photorespiration in short) was set up from ancient metabolic modules about three billion years ago in cyanobacteria, the later ancestors of chloroplasts. These prokaryotes developed the capacity for oxygenic photosynthesis, i.e. the use of water as a source of electrons and protons (with O2 as a by-product) for the sunlight-driven synthesis of ATP and NADPH for CO2 fixation in the Calvin cycle. However, the CO2-binding enzyme, ribulose 1,5-bisphosphate carboxylase (known under the acronym Rubisco), is not absolutely selective for CO2 and can also use O2 in a side reaction. It then produces 2-phosphoglycolate (2PG), the accumulation of which would inhibit and potentially stop the Calvin cycle and subsequently photosynthetic electron transport. Photorespiration removes the 2-PG and in this way prevents oxygenic photosynthesis from poisoning itself. In plants, the core of photorespiration consists of ten enzymes distributed over three different types of organelles, requiring interorganellar transport and interaction with several auxiliary enzymes. It goes together with the release and to some extent loss of freshly fixed CO2. This disadvantageous feature can be suppressed by CO2-concentrating mechanisms, such as those that evolved in C4 plants thirty million years ago, which enhance CO2 fixation and reduce 2PG synthesis. Photorespiration itself provided a pioneer variant of such mechanisms in the predecessors of C4 plants, C3-C4 intermediate plants. This article is a review and update particularly on the enzyme components of plant photorespiration and their catalytic mechanisms, on the interaction of photorespiration with other metabolism and on its impact on the evolution of photosynthesis. This focus was chosen because a better knowledge of the enzymes involved and how they are embedded in overall plant metabolism can facilitate the targeted use of the now highly advanced methods of metabolic network modelling and flux analysis. Understanding photorespiration more than before as a process that enables, rather than reduces, plant photosynthesis, will help develop rational strategies for crop improvement.
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Affiliation(s)
- Hermann Bauwe
- University of Rostock, Plant Physiology, Albert-Einstein-Straße 3, D-18051, Rostock, Germany.
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23
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Valenti R, Jabłońska J, Tawfik DS. Characterization of ancestral Fe/Mn superoxide dismutases indicates their cambialistic origin. Protein Sci 2022; 31:e4423. [PMID: 36173172 PMCID: PMC9490801 DOI: 10.1002/pro.4423] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 06/29/2022] [Accepted: 08/09/2022] [Indexed: 11/10/2022]
Abstract
Superoxide dismutases (SODs) are critical metalloenzymes mitigating the damages of the modern oxygenated world. However, the emergence of one family of SODs, the Fe/Mn SOD, has been recurrently proposed to predate the great oxygenation event (GOE). This ancient family lacks metal binding selectivity, but displays strong catalytic selectivity. Therefore, some homologues would only be active when bound to Fe or Mn, although others, dubbed cambialistic, would function when loaded with either ion. This posed the longstanding question about the identity of the cognate metal ion of the first SODs to emerge. In this work, we utilize ancestral sequence reconstruction techniques to infer the earliest SODs. We show that the “ancestors” are active in vivo and in vitro. Further, we test their metal specificity and demonstrate that they are cambialistic in nature. Our findings shed light on how the predicted Last Common Universal Ancestor was capable of dealing with decomposition of the superoxide anion, and the early relationship between life, oxygen, and metal ion availability.
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Affiliation(s)
- Rosario Valenti
- Department of Biomolecular Sciences Weizmann Institute of Science Rehovot Israel
| | - Jagoda Jabłońska
- Department of Biomolecular Sciences Weizmann Institute of Science Rehovot Israel
| | - Dan S. Tawfik
- Department of Biomolecular Sciences Weizmann Institute of Science Rehovot Israel
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24
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Stone J, Edgar JO, Gould JA, Telling J. Tectonically-driven oxidant production in the hot biosphere. Nat Commun 2022; 13:4529. [PMID: 35941147 PMCID: PMC9360021 DOI: 10.1038/s41467-022-32129-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: 01/24/2022] [Accepted: 07/15/2022] [Indexed: 11/17/2022] Open
Abstract
Genomic reconstructions of the common ancestor to all life have identified genes involved in H2O2 and O2 cycling. Commonly dismissed as an artefact of lateral gene transfer after oxygenic photosynthesis evolved, an alternative is a geological source of H2O2 and O2 on the early Earth. Here, we show that under oxygen-free conditions high concentrations of H2O2 can be released from defects on crushed silicate rocks when water is added and heated to temperatures close to boiling point, but little is released at temperatures <80 °C. This temperature window overlaps the growth ranges of evolutionary ancient heat-loving and oxygen-respiring Bacteria and Archaea near the root of the Universal Tree of Life. We propose that the thermal activation of mineral surface defects during geological fault movements and associated stresses in the Earth’s crust was a source of oxidants that helped drive the (bio)geochemistry of hot fractures where life first evolved. Researchers at Newcastle University have discovered a mechanism by which earthquakes create bursts of hydrogen peroxide and oxygen in hot underground fractures. These may have played a vital role in the early evolution and origin of life on Earth.
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Affiliation(s)
- Jordan Stone
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
| | - John O Edgar
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
| | - Jamie A Gould
- Faculty of Science, Agriculture and Engineering, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK
| | - Jon Telling
- School of Natural and Environmental Sciences, Newcastle University, Newcastle-upon-Tyne, NE1 7RU, UK.
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25
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Oliver N, Avramov AP, Nürnberg DJ, Dau H, Burnap RL. From manganese oxidation to water oxidation: assembly and evolution of the water-splitting complex in photosystem II. PHOTOSYNTHESIS RESEARCH 2022; 152:107-133. [PMID: 35397059 DOI: 10.1007/s11120-022-00912-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 03/03/2022] [Indexed: 06/14/2023]
Abstract
The manganese cluster of photosystem II has been the focus of intense research aiming to understand the mechanism of H2O-oxidation. Great effort has also been applied to investigating its oxidative photoassembly process, termed photoactivation that involves the light-driven incorporation of metal ions into the active Mn4CaO5 cluster. The knowledge gained on these topics has fundamental scientific significance, but may also provide the blueprints for the development of biomimetic devices capable of splitting water for solar energy applications. Accordingly, synthetic chemical approaches inspired by the native Mn cluster are actively being explored, for which the native catalyst is a useful benchmark. For both the natural and artificial catalysts, the assembly process of incorporating Mn ions into catalytically active Mn oxide complexes is an oxidative process. In both cases this process appears to share certain chemical features, such as producing an optimal fraction of open coordination sites on the metals to facilitate the binding of substrate water, as well as the involvement of alkali metals (e.g., Ca2+) to facilitate assembly and activate water-splitting catalysis. This review discusses the structure and formation of the metal cluster of the PSII H2O-oxidizing complex in the context of what is known about the formation and chemical properties of different Mn oxides. Additionally, the evolutionary origin of the Mn4CaO5 is considered in light of hypotheses that soluble Mn2+ was an ancient source of reductant for some early photosynthetic reaction centers ('photomanganotrophy'), and recent evidence that PSII can form Mn oxides with structural resemblance to the geologically abundant birnessite class of minerals. A new functional role for Ca2+ to facilitate sustained Mn2+ oxidation during photomanganotrophy is proposed, which may explain proposed physiological intermediates during the likely evolutionary transition from anoxygenic to oxygenic photosynthesis.
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Affiliation(s)
- Nicholas Oliver
- Physics Department, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Anton P Avramov
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Dennis J Nürnberg
- Physics Department, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Holger Dau
- Physics Department, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Robert L Burnap
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, 74078, USA.
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Probing the Role of Cysteine Thiyl Radicals in Biology: Eminently Dangerous, Difficult to Scavenge. Antioxidants (Basel) 2022; 11:antiox11050885. [PMID: 35624747 PMCID: PMC9137623 DOI: 10.3390/antiox11050885] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/21/2022] [Accepted: 04/23/2022] [Indexed: 11/17/2022] Open
Abstract
Thiyl radicals are exceptionally interesting reactive sulfur species (RSS), but rather rarely considered in a biological or medical context. We here review the reactivity of protein thiyl radicals in aqueous and lipid phases and provide an overview of their most relevant reaction partners in biological systems. We deduce that polyunsaturated fatty acids (PUFAs) are their preferred reaction substrates in lipid phases, whereas protein side chains arguably prevail in aqueous phases. In both cellular compartments, a single, dominating thiyl radical-specific antioxidant does not seem to exist. This conclusion is rationalized by the high reaction rate constants of thiyl radicals with several highly concentrated substrates in the cell, precluding effective interception by antioxidants, especially in lipid bilayers. The intractable reactivity of thiyl radicals may account for a series of long-standing, but still startling biochemical observations surrounding the amino acid cysteine: (i) its global underrepresentation on protein surfaces, (ii) its selective avoidance in aerobic lipid bilayers, especially the inner mitochondrial membrane, (iii) the inverse correlation between cysteine usage and longevity in animals, (iv) the mitochondrial synthesis and translational incorporation of cysteine persulfide, and potentially (v) the ex post introduction of selenocysteine into the genetic code.
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Huang XL. What are the inorganic nanozymes? Artificial or inorganic enzymes! NEW J CHEM 2022. [DOI: 10.1039/d2nj02088b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The research on inorganic nanozymes remains very active since the first paper on the “intrinsic peroxidase-like properties of ferromagnetic nanoparticles” was published in Nature Nanotechnology in 2007. However, there is...
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