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Aknaf A, Ahsan U, Baghour M, Rahhou A, Imperl J, Petrova P, Kolar M. Minerals and trace element compositions of some seaweeds from the Marchica lagoon, North-East Mediterranean coast of Morocco. MARINE POLLUTION BULLETIN 2024; 206:116795. [PMID: 39121592 DOI: 10.1016/j.marpolbul.2024.116795] [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: 05/24/2024] [Revised: 07/28/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024]
Abstract
The objective of the present study was to evaluate the mineral and heavy metals composition of different seaweeds growing in Marchica lagoon. To this end, green seaweeds, red seaweeds, and brown seaweeds were collected from three different stations in the Marchica lagoon. The highest concentration of Ca was measured in Centroceras clavulatum (17.12 ± 0.60), K in Caulerpa prolifera (15.17 ± 0.20), Na in Gracilaria dura (4.16 ± 0.03) and Hypnea musciformis (4.09 ± 0.03), Mg in Ulva rigida (2.80 ± 0.06), and the highest concentration of P was registered in Ulva intestinalis (3658 ± 14). Centroceras clavulatum and Gracilaria dura had the highest Al, Fe, and Sr levels. Cystoseira compressa had the highest As (53.8 mg/kg) and Rb (43 mg/kg). These findings suggest that seaweeds collected from Marchica lagoon could be used as potential sources of minerals and trace elements in seaweed-based products for human and animal nutrition alike.
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Affiliation(s)
- Asmae Aknaf
- Laboratory of Biology, Geosciences, Physics and Environment (OLMAN-LBGPE) Multidisciplinary Faculty of Nador, Mohammed the First University, Oujda, Morocco.
| | - Umair Ahsan
- Department of Plant and Animal Production, Burdur Vocational School of Food, Agriculture and Livestock, Burdur Mehmet Akif Ersoy University, Istiklal Campus, 15030 Burdur, Turkey; Center for Agriculture, Livestock and Food Research, Burdur Mehmet Akif Ersoy University, Istiklal Campus, 15030 Burdur, Turkey
| | - Mourad Baghour
- Laboratory of Biology, Geosciences, Physics and Environment (OLMAN-LBGPE) Multidisciplinary Faculty of Nador, Mohammed the First University, Oujda, Morocco
| | - Abderrahmane Rahhou
- Laboratory of Biology, Geosciences, Physics and Environment (OLMAN-LBGPE) Multidisciplinary Faculty of Nador, Mohammed the First University, Oujda, Morocco
| | - Jernej Imperl
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Petranka Petrova
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, South-West University, NeofitRilski, 2700 Blagoevgrad, Bulgaria
| | - Mitja Kolar
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
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2
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Kim M, Cha IT, Li M, Park SJ. Unraveling interspecies cross-feeding during anaerobic lignin degradation for bioenergy applications. CHEMOSPHERE 2024; 361:142588. [PMID: 38866340 DOI: 10.1016/j.chemosphere.2024.142588] [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: 04/30/2024] [Revised: 06/04/2024] [Accepted: 06/10/2024] [Indexed: 06/14/2024]
Abstract
Lignin, a major component of plant biomass, remains underutilized for renewable biofuels due to its complex and heterogeneous structure. Although investigations into depolymerizing lignin using fungi are well-established, studies of microbial pathways that enable anaerobic lignin breakdown linked with methanogenesis are limited. Through an enrichment cultivation approach with inoculation of freshwater sediment, we enriched a microbial community capable of producing methane during anaerobic lignin degradation. We reconstructed the near-complete population genomes of key lignin degraders and methanogens using metagenome-assembled genomes finally selected in this study (MAGs; 92 bacterial and 4 archaeal MAGs affiliated into 45 and 2 taxonomic groups, respectively). This study provides genetic evidence of microbial interdependence in conversion of lignin to methane in a syntrophic community. Metagenomic analysis revealed metabolic linkages, with lignin-hydrolyzing and/or fermentative bacteria such as the genera Alkalibaculum and Propionispora transforming lignin breakdown products into compounds such as acetate to feed methanogens (two archaeal MAGs classified into the genus Methanosarcina or UBA6 of the family Methanomassiliicoccaceae). Understanding the synergistic relationships between microbes that convert lignin could inform strategies for producing renewable bioenergy and treating aromatic-contaminated environments through anaerobic biodegradation processes. Overall, this study offers fundamental insights into complex community-level anaerobic lignin metabolism, highlighting hitherto unknown players, interactions, and pathways in this biotechnologically valuable process.
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Affiliation(s)
- Minji Kim
- Department of Biology, Jeju National University, 102 Jejudaehak-ro, Jeju, 63243, South Korea
| | - In-Tae Cha
- Climate Change and Environmental Biology Research Division, National Institute of Biological Resources, Incheon, 22689, South Korea
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China; Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, Guangdong, China
| | - Soo-Je Park
- Department of Biology, Jeju National University, 102 Jejudaehak-ro, Jeju, 63243, South Korea.
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3
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Bandyopadhyay A, Sengupta A, Elvitigala T, Pakrasi HB. Endogenous clock-mediated regulation of intracellular oxygen dynamics is essential for diazotrophic growth of unicellular cyanobacteria. Nat Commun 2024; 15:3712. [PMID: 38697963 PMCID: PMC11065991 DOI: 10.1038/s41467-024-48039-0] [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: 02/24/2023] [Accepted: 04/16/2024] [Indexed: 05/05/2024] Open
Abstract
The discovery of nitrogen fixation in unicellular cyanobacteria provided the first clues for the existence of a circadian clock in prokaryotes. However, recalcitrance to genetic manipulation barred their use as model systems for deciphering the clock function. Here, we explore the circadian clock in the now genetically amenable Cyanothece 51142, a unicellular, nitrogen-fixing cyanobacterium. Unlike non-diazotrophic clock models, Cyanothece 51142 exhibits conspicuous self-sustained rhythms in various discernable phenotypes, offering a platform to directly study the effects of the clock on the physiology of an organism. Deletion of kaiA, an essential clock component in the cyanobacterial system, impacted the regulation of oxygen cycling and hindered nitrogenase activity. Our findings imply a role for the KaiA component of the clock in regulating the intracellular oxygen dynamics in unicellular diazotrophic cyanobacteria and suggest that its addition to the KaiBC clock was likely an adaptive strategy that ensured optimal nitrogen fixation as microbes evolved from an anaerobic to an aerobic atmosphere under nitrogen constraints.
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Affiliation(s)
| | - Annesha Sengupta
- Department of Biology, Washington University, St. Louis, MO, USA
- Department of Chemical Engineering, University of Toronto, Toronto, ON, Canada
| | - Thanura Elvitigala
- Department of Biology, Washington University, St. Louis, MO, USA
- General Motors Research and Development, Warren, MI, 48092, USA
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4
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Suzuki N, Iwamura Y, Kato K, Ishioka H, Konta Y, Sato K, Uchida N, Koida N, Sekine H, Tanaka T, Kumagai N, Nakai T. Crosstalk between oxygen signaling and iron metabolism in renal interstitial fibroblasts. J Clin Biochem Nutr 2024; 74:179-184. [PMID: 38799135 PMCID: PMC11111471 DOI: 10.3164/jcbn.24-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 02/23/2024] [Indexed: 05/29/2024] Open
Abstract
To maintain the oxygen supply, the production of red blood cells (erythrocytes) is promoted under low-oxygen conditions (hypoxia). Oxygen is carried by hemoglobin in erythrocytes, in which the majority of the essential element iron in the body is contained. Because iron metabolism is strictly controlled in a semi-closed recycling system to protect cells from oxidative stress caused by iron, hypoxia-inducible erythropoiesis is closely coordinated by regulatory systems that mobilize stored iron for hemoglobin synthesis. The erythroid growth factor erythropoietin (EPO) is mainly secreted by interstitial fibroblasts in the renal cortex, which are known as renal EPO-producing (REP) cells, and promotes erythropoiesis and iron mobilization. Intriguingly, EPO production is strongly induced by hypoxia through iron-dependent pathways in REP cells. Here, we summarize recent studies on the network mechanisms linking hypoxia-inducible EPO production, erythropoiesis and iron metabolism. Additionally, we introduce disease mechanisms related to disorders in the network mediated by REP cell functions. Furthermore, we propose future studies regarding the application of renal cells derived from the urine of kidney disease patients to investigate the molecular pathology of chronic kidney disease and develop precise and personalized medicine for kidney disease.
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Affiliation(s)
- Norio Suzuki
- Applied Oxygen Physiology Project, New Industry Creation Hatchery Center, Tohoku University, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
- Division of Oxygen Biology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Yuma Iwamura
- Division of Oxygen Biology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Koichiro Kato
- Applied Oxygen Physiology Project, New Industry Creation Hatchery Center, Tohoku University, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
- Division of Oxygen Biology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Hirotaka Ishioka
- Division of Oxygen Biology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
- Department of Nephrology, Rheumatology and Endocrinology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Yusuke Konta
- Division of Oxygen Biology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
- Department of Nephrology, Rheumatology and Endocrinology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Koji Sato
- Division of Oxygen Biology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
- Department of Nephrology, Juntendo University Faculty of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Nao Uchida
- Department of Pediatrics, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Noa Koida
- Division of Oxygen Biology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Hiroki Sekine
- Division of Oxygen Biology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
- Department of Gene Expression Regulation, Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Tetsuhiro Tanaka
- Department of Nephrology, Rheumatology and Endocrinology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Naonori Kumagai
- Department of Pediatrics, Fujita Health University School of Medicine, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
| | - Taku Nakai
- Division of Oxygen Biology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
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5
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Qu CL, Jin H, Zhang B, Chen WJ, Zhang Y, Xu YY, Wang R, Lao YM. Haematococcus lacustris Carotenogensis: A Historical Event of Primary to Secondary Adaptations to Earth's Oxygenation. Life (Basel) 2024; 14:576. [PMID: 38792597 PMCID: PMC11121925 DOI: 10.3390/life14050576] [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: 11/22/2023] [Revised: 02/21/2024] [Accepted: 02/28/2024] [Indexed: 05/26/2024] Open
Abstract
(1) Background: Oxygen has exerted a great effect in shaping the environment and driving biological diversity in Earth's history. Green lineage has evolved primary and secondary carotenoid biosynthetic systems to adapt to Earth's oxygenation, e.g., Haematococcus lacustris, which accumulates the highest amount of secondary astaxanthin under stresses. The two systems are controlled by lycopene ε-cyclase (LCYE) and β-cyclase (LCYB), which leave an important trace in Earth's oxygenation. (2) Objectives: This work intends to disclose the underlying molecular evolutionary mechanism of Earth's oxygenation in shaping green algal carotenogensis with a special focus on lycopene cyclases. (3) Methods: The two kinds of cyclases were analyzed by site-directed mutagenesis, phylogeny, divergence time and functional divergence. (4) Results: Green lineage LCYEs appeared at ~1.5 Ga after the first significant appearance and accumulation of atmospheric oxygen, the so-called Great Oxygenation Event (GOE), from which LCYBs diverged by gene duplication. Bacterial β-bicyclases evolved from β-monocyclase. Enhanced catalytic activity accompanied evolutionary transformation from ε-/β-monocyclase to β-bicyclase. Strong positive selection occurred in green lineage LCYEs after the GOE and in algal LCYBs during the second oxidation, the Neoproterozoic Oxygenation Event (NOE). Positively selected sites in the catalytic cavities of the enzymes controlled the mono-/bicyclase activity, respectively. Carotenoid profiling revealed that oxidative adaptation has been wildly preserved in evolution. (5) Conclusions: the functionalization of the two enzymes is a result of primary to secondary adaptations to Earth's oxygenation.
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Affiliation(s)
- Cui Lan Qu
- Shenzhen Institute of Quality & Safety Inspection and Research, Shenzhen 518055, China
| | - Hui Jin
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China;
| | - Bing Zhang
- Shenzhen Institute of Quality & Safety Inspection and Research, Shenzhen 518055, China
| | - Wei Jian Chen
- Shenzhen Institute of Quality & Safety Inspection and Research, Shenzhen 518055, China
| | - Yang Zhang
- Shenzhen Institute of Quality & Safety Inspection and Research, Shenzhen 518055, China
| | - Yuan Yuan Xu
- Shenzhen Institute of Quality & Safety Inspection and Research, Shenzhen 518055, China
| | - Rui Wang
- Shenzhen Institute of Quality & Safety Inspection and Research, Shenzhen 518055, China
| | - Yong Min Lao
- Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
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6
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Liu Y, Ge H, Lu D. Functional proteomics reveals that Slr0237 is a SigE-regulated glycogen debranching enzyme pivotal for glycogen breakdown. Proteomics 2024:e2300222. [PMID: 38581091 DOI: 10.1002/pmic.202300222] [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: 05/15/2023] [Revised: 03/04/2024] [Accepted: 03/14/2024] [Indexed: 04/08/2024]
Abstract
The group 2 σ factor for RNA polymerase SigE plays important role in regulating central carbon metabolism in cyanobacteria. However, the regulation of SigE for these pathways at a proteome level remains unknown. Using a sigE-deficient strain (ΔsigE) of Synechocystis sp. PCC 6803 and quantitative proteomics, we found that SigE depletion induces differential protein expression for sugar catabolic pathways including glycolysis, oxidative pentose phosphate (OPP) pathway, and glycogen catabolism. Two glycogen debranching enzyme homologues Slr1857 and Slr0237 are found differentially expressed in ΔsigE. Glycogen determination indicated that Δslr0237 accumulated glycogen under photomixotrophic condition but was unable to utilize these reserves in the dark, whereas Δslr1857 accumulates and utilizes glycogen in a similar way as the WT strain does in the same condition. These results suggest that Slr0237 plays the major role as the glycogen debranching enzyme in Synechocystis.
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Affiliation(s)
- Ye Liu
- Science & Technology Department of Sichuan Province, Chengdu, Sichuan, China
| | - Haitao Ge
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Dandan Lu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, Henan, China
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7
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Fernandes KA, Fadul JC, Fiore MF, Pinto E. A systematic review on guanitoxin: General characteristics and ecological risks. CHEMOSPHERE 2024; 352:141277. [PMID: 38307340 DOI: 10.1016/j.chemosphere.2024.141277] [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: 05/30/2023] [Revised: 11/17/2023] [Accepted: 01/20/2024] [Indexed: 02/04/2024]
Abstract
Guanitoxin (GNT) is a potent cyanotoxin, with a relatively low number of publications (n = 51) compared to other cyanotoxins. Among the published studies, 35 % were on the effect of the toxin in animals, mainly in rodents and in vitro testing, followed by studies that identified species of cyanobacteria that produce GNT in aquatic systems and consequently accidental poisoning in wild and domestic animals (27 %). Studies that developed or tested methods for identifying the molecule, based on colorimetric and analytical techniques, represented 14 %, while 8 % were on GNT biosynthesis. Review articles and chemical isolation (6 %) and on the stability of the molecule (4 %) were the topics with the lowest number of publications. The results show the occurrence of GNT was identified mainly in eutrophic environments with a higher incidence in the American continent. Chemical characteristics of the molecule, such as short half-life in the environment, instability in solutions with alkaline pH values, temperature >23 °C, added to the lack of an analytical standard, are factors that make it difficult to identify and quantify it. However, GNT monitoring can be performed using LC-MS-MRM methods or genes specific to the newly discovered molecule.
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Affiliation(s)
- Kelly Afonsina Fernandes
- Center for Nuclear Energy in Agriculture, University of São Paulo. Piracicaba, São Paulo, Brazil.
| | - Jéssica Chaves Fadul
- Center for Nuclear Energy in Agriculture, University of São Paulo. Piracicaba, São Paulo, Brazil
| | - Marli Fátima Fiore
- Center for Nuclear Energy in Agriculture, University of São Paulo. Piracicaba, São Paulo, Brazil
| | - Ernani Pinto
- Center for Nuclear Energy in Agriculture, University of São Paulo. Piracicaba, São Paulo, Brazil
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8
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Zhou K, Su H, Gao J, Li H, Liu S, Yi X, Zhang Z, Wang W. Deciphering the Kinetics of Spontaneous Generation of H 2O 2 in Individual Water Microdroplets. J Am Chem Soc 2024; 146:2445-2451. [PMID: 38230586 DOI: 10.1021/jacs.3c09864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
Spontaneous generation of H2O2 in sub-10 μm-sized water microdroplets has received increasing interest since its first discovery in 2019. On the other hand, due to the short lifetime of these microdroplets (rapid evaporation) and lack of suitable tools to real-time monitor the generation of H2O2 in individual microdroplets, such a seemingly thermodynamically unfavorable process has also raised vigorous debates on the origin of H2O2 and the underlying mechanism. Herein, we prepared water microdroplets with a long lifetime (>1 h) by virtue of microwell confinement and dynamically monitored the spontaneous generation of H2O2 in individual microdroplets via time-lapsed fluorescence imaging. It was unveiled that H2O2 was continuously generated in the as-prepared water microdroplets and an apparent equilibrium concentration of ∼3 μM of H2O2 in the presence of a H2O2-consuming reaction can be obtained. Through engineering the geometry of these microdroplets, we further revealed that the generation rates of H2O2 in individual microdroplets were positively proportional to their surface-to-volume ratios. This also allowed us to extract a maximal H2O2 generation rate of 7.7 nmol m-2 min-1 in the presence of a H2O2-consuming reaction and derive the corresponding probability of spontaneous conversion of interfacial H2O into H2O2 for the first time, that is, ∼1 of 65,000 water molecules in 1 s. These findings delivered strong evidence that the spontaneous generation of H2O2 indeed occurs at the surface of microdroplets and provided us with an important starting point to further enhance the yield of H2O2 in water microdroplets for future applications.
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Affiliation(s)
- Kai Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hua Su
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Jia Gao
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Haoran Li
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Shasha Liu
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xuannuo Yi
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Zhibing Zhang
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education (MOE), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Wei Wang
- State Key Laboratory of Analytical Chemistry for Life Science, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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9
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Lu B, Cheng H, Qu L. Inorganic Hydrogel Based on Low-Dimensional Nanomaterials. ACS NANO 2024; 18:2730-2749. [PMID: 38221737 DOI: 10.1021/acsnano.3c11262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Composed of three-dimensional (3D) nanoscale inorganic bones and up to 99% water, inorganic hydrogels have attracted much attention and undergone significant growth in recent years. The basic units of inorganic hydrogels could be metal nanoparticles, metal nanowires, SiO2 nanowires, graphene nanosheets, and MXene nanosheets, which are then assembled into the special porous structures by the sol-gel process or gelation via either covalent or noncovalent interactions. The high electrical and thermal conductivity, resistance to corrosion, stability across various temperatures, and high surface area make them promising candidates for diverse applications, such as energy storage, catalysis, adsorption, sensing, and solar steam generation. Besides, some interesting derivatives, such as inorganic aerogels and xerogels, can be produced through further processing, diversifying their functionalities and application domains greatly. In this context, we primarily provide a comprehensive overview of the current status of inorganic hydrogels and their derivatives, including the structures of inorganic hydrogels with various compositions, their gelation mechanisms, and their exceptional practical performance in fields related to energy and environmental applications.
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Affiliation(s)
- Bing Lu
- Key Laboratory of Organic Optoelectronics and Molecular Engineering, Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
- Laboratory of Flexible Electronics Technology, State Key Laboratory of Tribology in Advanced Equipment (SKLT), Tsinghua University, Beijing 100084, P. R. China
| | - Huhu Cheng
- Key Laboratory of Organic Optoelectronics and Molecular Engineering, Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
- Laboratory of Flexible Electronics Technology, State Key Laboratory of Tribology in Advanced Equipment (SKLT), Tsinghua University, Beijing 100084, P. R. China
| | - Liangti Qu
- Key Laboratory of Organic Optoelectronics and Molecular Engineering, Ministry of Education, Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
- Laboratory of Flexible Electronics Technology, State Key Laboratory of Tribology in Advanced Equipment (SKLT), Tsinghua University, Beijing 100084, P. R. China
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10
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Li H, Zhang H, Li H, Duan L, Zhang X, Gao Y, Hall IR, Hemming SR, LeVay LJ. Sedimentary DNA reveals the link between microbial community dynamics and climate during the late last glaciation in the offshore region of the Zambezi River, Southwest Indian Ocean. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167787. [PMID: 37844644 DOI: 10.1016/j.scitotenv.2023.167787] [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: 06/29/2023] [Revised: 10/04/2023] [Accepted: 10/10/2023] [Indexed: 10/18/2023]
Abstract
Reconstructing the relationship between microbial communities and past abrupt climate change is of great importance for understanding current biodiversity patterns and predicting changes under future climate scenarios. However, little is currently known about how microbial communities respond to changes in key environmental stages due to a lack of research in this area. Here, we examine the variability in the communities of bacteria, archaea, and fungi from sediments deposited offshore region of the Zambezi River between 21.7 and 9.6 thousand years ago (ka) (covering the last glacial maximum, or LGM, and the early Holocene) using DNA metabarcoding approach via high-throughput sequencing. The results showed that (1) microbial assemblages differed across three key time intervals, with the last deglaciation having the most homogeneous prokaryotic assemblages, while for fungal communities in the LGM, and the early Holocene and LGM differing the most; (2) the warm early Holocene showed the highest diversity, whereas the lowest diversity was found in the LGM; and (3) the selected indicator species better reflected the climatic characteristics of different environmental stages. These results highlight the power of ancient sedimentary DNA to refine our understanding of microbial dynamics in marine sedimentary systems near large rivers, thus providing a basis for better modeling ecological processes in further research.
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Affiliation(s)
- Haoyu Li
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, 650500 Kunming, China
| | - Hucai Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, 650500 Kunming, China.
| | - Huayong Li
- School of Resource Environment and Tourism, Anyang Normal University, Anyang 455000, China
| | - Lizeng Duan
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, 650500 Kunming, China
| | - Xiaonan Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, 650500 Kunming, China
| | - Youhong Gao
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, 650500 Kunming, China
| | - Ian R Hall
- Department of Earth Sciences, Cardiff University, Main College, Park Place, PO Box 914, Cardiff, Wales CF10 3AT, United Kingdom
| | - Sidney R Hemming
- Lamont-Doherty Earth Observatory, Columbia University, 61 Route 9W, Palisades, NY, 10964, USA
| | - Leah J LeVay
- International Ocean Discovery Program, Texas A&M University, College Station, TX 77845, USA
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11
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Faluweki MK, Cammann J, Mazza MG, Goehring L. Active Spaghetti: Collective Organization in Cyanobacteria. PHYSICAL REVIEW LETTERS 2023; 131:158303. [PMID: 37897773 DOI: 10.1103/physrevlett.131.158303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 08/30/2023] [Indexed: 10/30/2023]
Abstract
Filamentous cyanobacteria can show fascinating examples of nonequilibrium self-organization, which, however, are not well understood from a physical perspective. We investigate the motility and collective organization of colonies of these simple multicellular lifeforms. As their area density increases, linear chains of cells gliding on a substrate show a transition from an isotropic distribution to bundles of filaments arranged in a reticulate pattern. Based on our experimental observations of individual behavior and pairwise interactions, we introduce a nonreciprocal model accounting for the filaments' large aspect ratio, fluctuations in curvature, motility, and nematic interactions. This minimal model of active filaments recapitulates the observations, and rationalizes the appearance of a characteristic length scale in the system, based on the Péclet number of the cyanobacteria filaments.
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Affiliation(s)
- Mixon K Faluweki
- School of Science and Technology, Nottingham Trent University, Nottingham NG11 8NS, United Kingdom
- Malawi Institute of Technology, Malawi University of Science and Technology, S150 Road, Thyolo 310105, Malawi
| | - Jan Cammann
- Interdisciplinary Centre for Mathematical Modelling and Department of Mathematical Sciences, Loughborough University, Loughborough, Leicestershire LE11 3TU, United Kingdom
| | - Marco G Mazza
- Interdisciplinary Centre for Mathematical Modelling and Department of Mathematical Sciences, Loughborough University, Loughborough, Leicestershire LE11 3TU, United Kingdom
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), Am Faßberg 17, 37077 Göttingen, Germany
| | - Lucas Goehring
- School of Science and Technology, Nottingham Trent University, Nottingham NG11 8NS, United Kingdom
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12
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Ambrosino A, Chianese A, Zannella C, Piccolella S, Pacifico S, Giugliano R, Franci G, De Natale A, Pollio A, Pinto G, De Filippis A, Galdiero M. Galdieria sulphuraria: An Extremophilic Alga as a Source of Antiviral Bioactive Compounds. Mar Drugs 2023; 21:383. [PMID: 37504915 PMCID: PMC10381441 DOI: 10.3390/md21070383] [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: 06/09/2023] [Revised: 06/24/2023] [Accepted: 06/26/2023] [Indexed: 07/29/2023] Open
Abstract
In the last decades, the interest in bioactive compounds derived from natural sources including bacteria, fungi, plants, and algae has significantly increased. It is well-known that aquatic or terrestrial organisms can produce, in special conditions, secondary metabolites with a wide range of biological properties, such as anticancer, antioxidant, anti-inflammatory, and antimicrobial activities. In this study, we focused on the extremophilic microalga Galdieria sulphuraria as a possible producer of bioactive compounds with antiviral activity. The algal culture was subjected to organic extraction with acetone. The cytotoxicity effect of the extract was evaluated by the 2,5-diphenyl-2H-tetrazolium bromide (MTT) assay. The antiviral activity was assessed through a plaque assay against herpesviruses and coronaviruses as enveloped viruses and poliovirus as a naked one. The monolayer was treated with different concentrations of extract, ranging from 1 µg/mL to 200 µg/mL, and infected with viruses. The algal extract displayed strong antiviral activity at non-toxic concentrations against all tested enveloped viruses, in particular in the virus pre-treatment against HSV-2 and HCoV-229E, with IC50 values of 1.7 µg/mL and IC90 of 1.8 µg/mL, respectively. However, no activity against the non-enveloped poliovirus has been detected. The inhibitory effect of the algal extract was confirmed by the quantitative RT-PCR of viral genes. Preliminary chemical profiling of the extract was performed using ultra-high-performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC-HRMS), revealing the enrichment in primary fatty acid amides (PFAA), such as oleamide, palmitamide, and pheophorbide A. These promising results pave the way for the further purification of the mixture to explore its potential role as an antiviral agent.
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Affiliation(s)
- Annalisa Ambrosino
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Annalisa Chianese
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Carla Zannella
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Simona Piccolella
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Severina Pacifico
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", 81100 Caserta, Italy
| | - Rosa Giugliano
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Gianluigi Franci
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, 84081 Baronissi, Italy
| | - Antonino De Natale
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, 80126 Naples, Italy
| | - Antonino Pollio
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, 80126 Naples, Italy
| | - Gabriele Pinto
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, 80126 Naples, Italy
| | - Anna De Filippis
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Massimiliano Galdiero
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
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13
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Shapiro AV, Brühl C, Klingmüller K, Steil B, Shapiro AI, Witzke V, Kostogryz N, Gizon L, Solanki SK, Lelieveld J. Metal-rich stars are less suitable for the evolution of life on their planets. Nat Commun 2023; 14:1893. [PMID: 37072387 PMCID: PMC10113254 DOI: 10.1038/s41467-023-37195-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 03/03/2023] [Indexed: 04/20/2023] Open
Abstract
Atmospheric ozone and oxygen protect the terrestrial biosphere against harmful ultraviolet (UV) radiation. Here, we model atmospheres of Earth-like planets hosted by stars with near-solar effective temperatures (5300 to 6300 K) and a broad range of metallicities covering known exoplanet host stars. We show that paradoxically, although metal-rich stars emit substantially less ultraviolet radiation than metal-poor stars, the surface of their planets is exposed to more intense ultraviolet radiation. For the stellar types considered, metallicity has a larger impact than stellar temperature. During the evolution of the universe, newly formed stars have progressively become more metal-rich, exposing organisms to increasingly intense ultraviolet radiation. Our findings imply that planets hosted by stars with low metallicity are the best targets to search for complex life on land.
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Affiliation(s)
- Anna V Shapiro
- Max Planck Institute for Solar System Research, Göttingen, Germany.
| | | | | | | | | | - Veronika Witzke
- Max Planck Institute for Solar System Research, Göttingen, Germany
| | - Nadiia Kostogryz
- Max Planck Institute for Solar System Research, Göttingen, Germany
| | - Laurent Gizon
- Max Planck Institute for Solar System Research, Göttingen, Germany
- Institute for Astrophysics, Georg-August-Universität Göttingen, Göttingen, Germany
- Center for Space Science, NYUAD Institute, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Sami K Solanki
- Max Planck Institute for Solar System Research, Göttingen, Germany
- School of Space Research, Kyung Hee University, Yongin, Republic of Korea
| | - Jos Lelieveld
- Max Planck Institute for Chemistry, Mainz, Germany
- The Cyprus Institute, Climate and Atmosphere Research Center, Nicosia, Cyprus
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14
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Boyd ES, Spietz RL, Kour M, Colman DR. A naturalist perspective of microbiology: Examples from methanogenic archaea. Environ Microbiol 2023; 25:184-198. [PMID: 36367391 DOI: 10.1111/1462-2920.16285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 11/09/2022] [Indexed: 11/13/2022]
Abstract
Storytelling has been the primary means of knowledge transfer over human history. The effectiveness and reach of stories are improved when the message is appropriate for the target audience. Oftentimes, the stories that are most well received and recounted are those that have a clear purpose and that are told from a variety of perspectives that touch on the varied interests of the target audience. Whether scientists realize or not, they are accustomed to telling stories of their own scientific discoveries through the preparation of manuscripts, presentations, and lectures. Perhaps less frequently, scientists prepare review articles or book chapters that summarize a body of knowledge on a given subject matter, meant to be more holistic recounts of a body of literature. Yet, by necessity, such summaries are often still narrow in their scope and are told from the perspective of a particular discipline. In other words, interdisciplinary reviews or book chapters tend to be the rarity rather than the norm. Here, we advocate for and highlight the benefits of interdisciplinary perspectives on microbiological subjects.
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Affiliation(s)
- Eric S Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Rachel L Spietz
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Manjinder Kour
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
| | - Daniel R Colman
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, Montana, USA
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15
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Xiao Z, Huang C, Ge H, Wang Y, Duan X, Wang G, Zheng L, Dong J, Huang X, Zhang Y, An H, Xu W, Wang Y. Proximity Labeling Facilitates Defining the Proteome Neighborhood of Photosystem II Oxygen Evolution Complex in a Model Cyanobacterium. Mol Cell Proteomics 2022; 21:100440. [PMID: 36356940 PMCID: PMC9764255 DOI: 10.1016/j.mcpro.2022.100440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/29/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
Ascorbate peroxidase (APEX)-based proximity labeling coupled with mass spectrometry has a great potential for spatiotemporal identification of proteins proximal to a protein complex of interest. Using this approach is feasible to define the proteome neighborhood of important protein complexes in a popular photosynthetic model cyanobacterium Synechocystis sp. PCC6803 (hereafter named as Synechocystis). To this end, we developed a robust workflow for APEX2-based proximity labeling in Synechocystis and used the workflow to identify proteins proximal to the photosystem II (PS II) oxygen evolution complex (OEC) through fusion APEX2 with a luminal OEC subunit, PsbO. In total, 38 integral membrane proteins (IMPs) and 93 luminal proteins were identified as proximal to the OEC. A significant portion of these proteins are involved in PS II assembly, maturation, and repair, while the majority of the rest were not previously implicated with PS II. The IMPs include subunits of PS II and cytochrome b6/f, but not of photosystem I (except for PsaL) and ATP synthases, suggesting that the latter two complexes are spatially separated from the OEC with a distance longer than the APEX2 labeling radius. Besides, the topologies of six IMPs were successfully predicted because their lumen-facing regions exclusively contain potential APEX2 labeling sites. The luminal proteins include 66 proteins with a predicted signal peptide and 57 proteins localized also in periplasm, providing important targets to study the regulation and selectivity of protein translocation. Together, we not only developed a robust workflow for the application of APEX2-based proximity labeling in Synechocystis and showcased the feasibility to define the neighborhood proteome of an important protein complex with a short radius but also discovered a set of the proteins that potentially interact with and regulate PS II structure and function.
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Affiliation(s)
- Zhen Xiao
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chengcheng Huang
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Haitao Ge
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yan Wang
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoxiao Duan
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Gaojie Wang
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Limin Zheng
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jinghui Dong
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xiahe Huang
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yuanya Zhang
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Hongyu An
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wu Xu
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, Louisiana, USA
| | - Yingchun Wang
- State Key Laboratory of Molecular Developmental Biology, Innovation Academy for Seed Design, CAS, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
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16
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Spietz RL, Payne D, Szilagyi R, Boyd ES. Reductive biomining of pyrite by methanogens. Trends Microbiol 2022; 30:1072-1083. [PMID: 35624031 DOI: 10.1016/j.tim.2022.05.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 01/13/2023]
Abstract
Pyrite (FeS2) is the most abundant iron sulfide mineral in Earth's crust. Until recently, FeS2 has been considered a sink for iron (Fe) and sulfur (S) at low temperature in the absence of oxygen or oxidative weathering, making these elements unavailable to biology. However, anaerobic methanogens can transfer electrons extracellularly to reduce FeS2 via direct contact with the mineral. Reduction of FeS2 occurs through a multistep process that generates aqueous sulfide (HS-) and FeS2-associated pyrrhotite (Fe1-xS). Subsequent dissolution of Fe1-xS provides Fe(II)(aq), but not HS-, that rapidly complexes with HS-(aq) generated from FeS2 reduction to form soluble iron sulfur clusters [nFeS(aq)]. Cells assimilate nFeS(aq) to meet Fe/S nutritional demands by mobilizing and hyperaccumulating Fe and S from FeS2. As such, reductive dissolution of FeS2 by methanogens has important implications for element cycling in anoxic habitats, both today and in the geologic past.
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Affiliation(s)
- Rachel L Spietz
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - Devon Payne
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - Robert Szilagyi
- Department of Chemistry, University of British Columbia - Okanagan, Kelowna, BC V1V 1V7, Canada
| | - Eric S Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA.
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17
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Liu W, Cong B, Lin J, Zhao L, Liu S. Complete genome sequencing and comparison of two nitrogen-metabolizing bacteria isolated from Antarctic deep-sea sediment. BMC Genomics 2022; 23:713. [PMID: 36261793 PMCID: PMC9580203 DOI: 10.1186/s12864-022-08942-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 10/13/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacteria are an essential component of the earth`s biota and affect circulation of matters through their metabolic activity. They also play an important role in the carbon and nitrogen cycle in the deep-sea environment. In this paper, two strains from deep-sea sediments were investigated in order to understand nitrogen cycling involved in the deep-sea environment. RESULTS In this paper, the basic genomic information of two strains was obtained by whole genome sequencing. The Cobetia amphilecti N-80 and Halomonas profundus 13 genome sizes are 4,160,095 bp with a GC content of 62.5% and 5,251,450 bp with a GC content of 54.84%. Through a comparison of functional analyses, we predicted the possible C and N metabolic pathways of the two strains and determined that Halomonas profundus 13 could use more carbon sources than Cobetia amphilecti N-80. The main genes associated with N metabolism in Halomonas profundus 13 are narG, narY, narI, nirS, norB, norC, nosZ, and nirD. On the contrast, nirD, using NH4+ for energy, plays a main role in Cobetia amphilecti N-80. Both of them have the same genes for fixing inorganic carbon: icd, ppc, fdhA, accC, accB, accD, and accA. CONCLUSION In this study, the whole genomes of two strains were sequenced to clarify the basic characteristics of their genomes, laying the foundation for further studying nitrogen-metabolizing bacteria. Halomonas profundus 13 can utilize more carbon sources than Cobetia amphilecti N-80, as indicated by API as well as COG and KEGG prediction results. Finally, through the analysis of the nitrification and denitrification abilities as well as the inorganic carbon fixation ability of the two strains, the related genes were identified, and the possible metabolic pathways were predicted. Together, these results provide molecular markers and theoretical support for the mechanisms of inorganic carbon fixation by deep-sea microorganisms.
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Affiliation(s)
- Wenqi Liu
- School of Advanced Manufacturing, Fuzhou University, Fuzhou, 350108, China
| | - Bailin Cong
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China.
| | - Jing Lin
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Linlin Zhao
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Shenghao Liu
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
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18
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Garcia PS, Gribaldo S, Borrel G. Diversity and Evolution of Methane-Related Pathways in Archaea. Annu Rev Microbiol 2022; 76:727-755. [PMID: 35759872 DOI: 10.1146/annurev-micro-041020-024935] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Methane is one of the most important greenhouse gases on Earth and holds an important place in the global carbon cycle. Archaea are the only organisms that use methanogenesis to produce energy and rely on the methyl-coenzyme M reductase (Mcr) complex. Over the last decade, new results have significantly reshaped our view of the diversity of methane-related pathways in the Archaea. Many new lineages that synthesize or use methane have been identified across the whole archaeal tree, leading to a greatly expanded diversity of substrates and mechanisms. In this review, we present the state of the art of these advances and how they challenge established scenarios of the origin and evolution of methanogenesis, and we discuss the potential trajectories that may have led to this strikingly wide range of metabolisms.Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Pierre Simon Garcia
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Evolutionary Biology of the Microbial Cell, Paris, France; ,
| | - Simonetta Gribaldo
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Evolutionary Biology of the Microbial Cell, Paris, France; ,
| | - Guillaume Borrel
- Institut Pasteur, Université Paris Cité, UMR CNRS 6047, Evolutionary Biology of the Microbial Cell, Paris, France; ,
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19
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Navotnaya P, Sohoni S, Lloyd LT, Abdulhadi SM, Ting PC, Higgins JS, Engel GS. Annihilation of Excess Excitations along Phycocyanin Rods Precedes Downhill Flow to Allophycocyanin Cores in the Phycobilisome of Synechococcus elongatus PCC 7942. J Phys Chem B 2022; 126:23-29. [PMID: 34982932 PMCID: PMC8762654 DOI: 10.1021/acs.jpcb.1c06509] [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] [Indexed: 11/30/2022]
Abstract
![]()
Cyanobacterial phycobilisome
complexes absorb visible sunlight
and funnel photogenerated excitons to the photosystems where charge
separation occurs. In the phycobilisome complex of Synechococcus
elongatus PCC 7942, phycocyanin protein rods that absorb
bluer wavelengths are assembled on allophycocyanin cores that absorb
redder wavelengths. This arrangement creates a natural energy gradient
toward the reaction centers of the photosystems. Here, we employ broadband
pump–probe spectroscopy to observe the fate of excess excitations
in the phycobilisome complex of this organism. We show that excess
excitons are quenched through exciton–exciton annihilation
along the phycocyanin rods prior to transfer to the allophycocyanin
cores. Our observations are especially relevant in comparison to other
antenna proteins, where exciton annihilation primarily occurs in the
lowest-energy chlorophylls. The observed effect could play a limited
photoprotective role in physiological light fluences. The exciton
decay dynamics is faster in the intact phycobilisome than in isolated
C-phycocyanin trimers studied in earlier work, confirming that this
effect is an emergent property of the complex assembly. Using the
obtained annihilation data, we calculate exciton hopping times of
2.2–6.4 ps in the phycocyanin rods. This value agrees with
earlier FRET calculations of exciton hopping times along phycocyanin
hexamers by Sauer and Scheer.
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Affiliation(s)
- Polina Navotnaya
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Siddhartha Sohoni
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Lawson T Lloyd
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Sami M Abdulhadi
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Po-Chieh Ting
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Jacob S Higgins
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
| | - Gregory S Engel
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States
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20
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Wang J, Huang X, Ge H, Wang Y, Chen W, Zheng L, Huang C, Yang H, Li L, Sui N, Wang Y, Zhang Y, Lu D, Fang L, Xu W, Jiang Y, Huang F, Wang Y. The Quantitative Proteome Atlas of a Model Cyanobacterium. J Genet Genomics 2021; 49:96-108. [PMID: 34775074 DOI: 10.1016/j.jgg.2021.09.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 09/23/2021] [Accepted: 09/25/2021] [Indexed: 12/17/2022]
Abstract
Cyanobacteria are a group of oxygenic photosynthetic bacteria with great potentials in biotechnological applications and advantages as models for photosynthesis research. The subcellular locations of the majority of proteins in any cyanobacteria remain undetermined, representing a major challenge in using cyanobacteria for both basic and industrial researches. Here, using label free quantitative proteomics we mapped 2027 proteins of Synechocystis sp. PCC6803, a model cyanobacterium, to different subcellular compartments, and generated a proteome atlas with such information. The atlas leads to numerous unexpected but important findings, including the predominant localization of the histidine kinases Hik33 and Hik27 on the thylakoid but not the plasma membrane. Such information completely changes the concept regarding how the two kinases are activated. Together, the atlas provides subcellular localization information for nearly 60% proteome of a model cyanobacterium, and will serve as an important resource for the cyanobacterial research community.
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Affiliation(s)
- Jinlong Wang
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Xiahe Huang
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Haitao Ge
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Wang
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiyang Chen
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Limin Zheng
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chengcheng Huang
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haomeng Yang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Bejing 100093, China
| | - Lingyu Li
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Bejing 100093, China
| | - Na Sui
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Science, Shandong Normal University, Jinan 250014, China
| | - Yu Wang
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuanya Zhang
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Dandan Lu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Longfa Fang
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wu Xu
- Department of Chemistry, University of Louisiana at Lafayette, Lafayette, LA 70504, USA
| | - Yuqiang Jiang
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Huang
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Bejing 100093, China.
| | - Yingchun Wang
- State Key Laboratory of Molecular Developmental Biology, The Innovative Academy of Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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21
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Kim P, Thati N, Peshori S, Jang HI, Kim YI. Shift in Conformational Equilibrium Underlies the Oscillatory Phosphoryl Transfer Reaction in the Circadian Clock. Life (Basel) 2021; 11:life11101058. [PMID: 34685430 PMCID: PMC8538168 DOI: 10.3390/life11101058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 11/26/2022] Open
Abstract
Oscillatory phosphorylation/dephosphorylation can be commonly found in a biological system as a means of signal transduction though its pivotal presence in the workings of circadian clocks has drawn significant interest: for example in a significant portion of the physiology of Synechococcus elongatus PCC 7942. The biological oscillatory reaction in the cyanobacterial circadian clock can be visualized through its reconstitution in a test tube by mixing three proteins—KaiA, KaiB and KaiC—with adenosine triphosphate and magnesium ions. Surprisingly, the oscillatory phosphorylation/dephosphorylation of the hexameric KaiC takes place spontaneously and almost indefinitely in a test tube as long as ATP is present. This autonomous post-translational modification is tightly regulated by the conformational change of the C-terminal peptide of KaiC called the “A-loop” between the exposed and the buried states, a process induced by the time-course binding events of KaiA and KaiB to KaiC. There are three putative hydrogen-bond forming residues of the A-loop that are important for stabilizing its buried conformation. Substituting the residues with alanine enabled us to observe KaiB’s role in dephosphorylating hyperphosphorylated KaiC, independent of KaiA’s effect. We found a novel role of KaiB that its binding to KaiC induces the A-loop toward its buried conformation, which in turn activates the autodephosphorylation of KaiC. In addition to its traditional role of sequestering KaiA, KaiB’s binding contributes to the robustness of cyclic KaiC phosphorylation by inhibiting it during the dephosphorylation phase, effectively shifting the equilibrium toward the correct phase of the clock.
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Affiliation(s)
- Pyonghwa Kim
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ 07102, USA;
| | - Neha Thati
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ 07102, USA; (N.T.); (S.P.)
| | - Shreya Peshori
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ 07102, USA; (N.T.); (S.P.)
| | - Hye-In Jang
- School of Cosmetic Science and Beauty Biotechnology, Semyung University, Jecheon 27136, Korea
- Correspondence: (H.-I.J.); (Y.-I.K.)
| | - Yong-Ick Kim
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ 07102, USA;
- Institute for Brain and Neuroscience Research, New Jersey Institute of Technology, Newark, NJ 07102, USA
- Correspondence: (H.-I.J.); (Y.-I.K.)
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22
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Pleil JD, Wallace MAG, Davis MD, Matty CM. The physics of human breathing: flow, timing, volume, and pressure parameters for normal, on-demand, and ventilator respiration. J Breath Res 2021; 15:10.1088/1752-7163/ac2589. [PMID: 34507310 PMCID: PMC8672270 DOI: 10.1088/1752-7163/ac2589] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/10/2021] [Indexed: 11/12/2022]
Abstract
Normal breathing for healthy humans is taken for granted; it occurs without conscious effort using ambient (1-atmosphere) pressure with 21% oxygen (O2) concentration. The body automatically adjusts for stress, exercise, altitude, and mild disease by increasing the volume and frequency of breathing. Longer term adaptations for exercise and altitude include increases in red blood cell counts and higher concentrations of capillaries in muscle tissue. When more challenging external environmental conditions or pulmonary illnesses exceed the capability for these adaptations, the human system requires technology to maintain sufficient ventilation to preserve life. On the environmental side there are two conditions to be addressed: toxicity of the surrounding atmosphere and changes in external pressure and O2concentration. On the medical side, mechanisms for assisting breathing include O2supplementation at ambient pressure, positive pressure/flow without additional O2, or a combination of both. This overview describes the various technologies applied to maintaining a safe breathing environment. Topics for environmental intervention include filter-based and flowing air-supply masks for toxic environments (occupational and laboratory protection), and on-demand gas supply systems for firefighters, self-contained underwater breathing apparatus divers, and altitude (high performance aircraft, spacecraft) applications. The topics for medical intervention include nasal cannula, continuous positive airway pressure, and medical ventilators. The primary purpose of this article is to provide a basic understanding of normal human breathing and the adaptation of breathing in different environments using available technologies.
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Affiliation(s)
- Joachim D. Pleil
- Gillings School of Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - M. Ariel Geer Wallace
- Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Michael D. Davis
- Herman B. Wells Center for Pediatrics Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Christopher M. Matty
- Johnson Space Center, National Aeronautics and Space Administration, Houston, TX, USA
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23
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Schapheer C, Pellens R, Scherson R. Arthropod-Microbiota Integration: Its Importance for Ecosystem Conservation. Front Microbiol 2021; 12:702763. [PMID: 34408733 PMCID: PMC8365148 DOI: 10.3389/fmicb.2021.702763] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/02/2021] [Indexed: 01/10/2023] Open
Abstract
Recent reports indicate that the health of our planet is getting worse and that genuine transformative changes are pressing. So far, efforts to ameliorate Earth's ecosystem crises have been insufficient, as these often depart from current knowledge of the underlying ecological processes. Nowadays, biodiversity loss and the alterations in biogeochemical cycles are reaching thresholds that put the survival of our species at risk. Biological interactions are fundamental for achieving biological conservation and restoration of ecological processes, especially those that contribute to nutrient cycles. Microorganism are recognized as key players in ecological interactions and nutrient cycling, both free-living and in symbiotic associations with multicellular organisms. This latter assemblage work as a functional ecological unit called "holobiont." Here, we review the emergent ecosystem properties derived from holobionts, with special emphasis on detritivorous terrestrial arthropods and their symbiotic microorganisms. We revisit their relevance in the cycling of recalcitrant organic compounds (e.g., lignin and cellulose). Finally, based on the interconnection between biodiversity and nutrient cycling, we propose that a multicellular organism and its associates constitute an Ecosystem Holobiont (EH). This EH is the functional unit characterized by carrying out key ecosystem processes. We emphasize that in order to meet the challenge to restore the health of our planet it is critical to reduce anthropic pressures that may threaten not only individual entities (known as "bionts") but also the stability of the associations that give rise to EH and their ecological functions.
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Affiliation(s)
- Constanza Schapheer
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur Universidad de Chile, Santiago, Chile
- Laboratorio de Sistemática y Evolución, Departamento de Silvicultura y Conservación de la Naturaleza, Universidad de Chile, Santiago, Chile
| | - Roseli Pellens
- UMR 7205, Muséum National d’Histoire Naturelle, Centre National de la Recherche Scientifique, Ecole Pratique de Hautes Etudes, Institut de Systématique, Évolution, Biodiversité, Sorbonne Université, Université des Antilles, Paris, France
| | - Rosa Scherson
- Laboratorio de Sistemática y Evolución, Departamento de Silvicultura y Conservación de la Naturaleza, Universidad de Chile, Santiago, Chile
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24
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Kaur I, Goyal D. Cartap hydrochloride induced stress response in Anabaena variabilis ARM 441. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2021; 177:104904. [PMID: 34301365 DOI: 10.1016/j.pestbp.2021.104904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 05/19/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
Cartap hydrochloride is a moderately hazardous nereistoxin analogue insecticide that is predominantly applied in paddy fields of India, at a recommended dose of 10 μg ml-1 to kill chewing and sucking insect pests of rice crop. Toxicity of cartap hydrochloride was studied on non-target free-living nitrogen fixing cyanobacterium Anabaena variabilis ARM 441 commonly used as algal biofertilizer in rice cultivation. Anabaena sp. could tolerate commercial grade insecticide up to 30 μg ml-1. However, at the recommended dose of 10 μg ml-1, it caused reduction in algal growth, total nitrogen and heterocyst frequency by 47.28, 24.29 and 17.72% respectively, as well as photosynthetic pigments under pure culture conditions. Scanning electron micrographs revealed cell rupture and breakage in filaments due to cartap exposure with the formation of akinetes. Cartap hydrochloride induced stress, since level of superoxide dismutase, peroxidase and catalase were increased by 108.57, 187.5 and 117% respectively. Generation of superoxide radicals and hydrogen peroxide were also increased by 152.48 and 34% respectively. Lipid peroxidation was increased by 31.03%, whereas there was decline in ascorbate content by 48.45%, however the glutathione content was increased by 128.57%. Increase in osmolytes such as proline from 8.6 to 32.8% and sucrose from 61.22 to 90.13% indicates their possible role in overcoming cartap induced oxidative stress and can be helpful in assessing its detrimental effect on Anabaena variabilis ARM 441, since cyanobacterial biofertilizers are purposely used in paddy fields as nitrogen contributors.
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Affiliation(s)
- Ishtpreet Kaur
- Department of Biotechnology, Thapar institute of engineering and technology, Punjab, India
| | - Dinesh Goyal
- Department of Biotechnology, Thapar institute of engineering and technology, Punjab, India.
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25
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Tian X, Liu H, Chen HF. Catalytic mechanism of butane anaerobic oxidation for alkyl-coenzyme M reductase. Chem Biol Drug Des 2021; 98:701-712. [PMID: 34328701 DOI: 10.1111/cbdd.13931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/02/2021] [Accepted: 07/24/2021] [Indexed: 12/18/2022]
Abstract
Methane is among the most potent of the greenhouse gases, which plays a key role in global climate change. As an excellent carbon and energy source, methane can be utilized by anaerobic methane oxidizing archaea and aerobic methane oxidizing bacteria. The previous work shows that an anaerobic thermophilic enrichment culture composed of dense consortia of archaea and bacteria apparently uses partly similar pathways to oxidize the C4 hydrocarbon butane. However, the catalytic mechanism of butane anaerobic oxidation for alkyl-coenzyme M reductase is still unknown. Therefore, molecular dynamics (MD) simulation was used to investigate the dynamics differences of catalytic mechanism between methane coenzyme M reductase (MCR) and alkyl-coenzyme M reductase (ACR). At first, the binding pocket of ACR is larger than that of MCR. Then, the complex of butane and ACR is more stable than that of methane and ACR. Protein conformation cloud suggests that the position of methane is dynamics and methane escapes from the binding pocket of ACR during most of the simulation time, while butane tightly binds in the pocket of ACR. The hydrophobic interactions between butane and ACR are more and stronger than those between methane and ACR. At the same time, the binding free energy between butane and ACR is significantly lower than that between methane and ACR. The dynamics correlation network indicates that the transformation of information flow for ACR-butane is smoother than that for ACR-methane. The shortest pathway for ACR-butane is from Gln144, Ala141, Hie135, Ile133, Ala160, Arg206, Asp97, Met94, Tyr347 to Phe345 with synergistic effect for two butane molecules. This study can insight into the catalytic mechanism for butane/ACR complex.
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Affiliation(s)
- Xiaopian Tian
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hao Liu
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Center for Bioinformation Technology, Shanghai, China
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26
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Mubeen M, Khalid MA, Mukhtar M, Shahrum S, Zahra S, Shabbir S, Iqbal A. Elucidating the Photoluminescence Quenching in Ensulizole: an Artificial Water Soluble Sunscreen. J Fluoresc 2021; 31:1055-1063. [PMID: 33956267 DOI: 10.1007/s10895-021-02736-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/03/2021] [Indexed: 10/21/2022]
Abstract
Employing natural or artificial sunscreens is essential to protect the skin from ultraviolet radiations that cause premature aging and develop melanoma and other forms of skin cancer. The 2-Phenylbenzimidazole-5-sulfonic acid, commonly known as ensulizole is a water-soluble artificial sunscreen that absorb UV-B (280 nm - 315 nm) radiations and protects the skin against the harmful effects of these radiations. We have measured steady-state photoluminescence (SSPL) spectra and photoluminescence (PL) kinetics of this compound in various conditions. Steady-state absorption indicates a strong absorption feature at 303 nm and a weak one at 316 nm that have been identified as π → π* and n → π* transitions, respectively. The spectra of PL induced by these absorptions indicate that the PL of ensulizole is less Stokes-shifted in polar solvents and more Stokes-shifted in non-polar solvents. The average PL lifetime of ensulizole is longer in non-polar solvents than in polar solvents and it exhibits the shortest PL lifetime in aqueous medium that maximize its transition efficiency in water. This suggests in non-polar solvents intersystem crossing is the dominant mode of relaxation of the excited ππ* state. Furthermore, an increase of pH of ensulizole solution decreases the PL intensity and the lifetime. Stern-Volmer equation is employed to evaluate bimolecular quenching rate constant kq. The evaluation result suggests the diffusional dynamic mode of PL quenching is operative.
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Affiliation(s)
- Muhammad Mubeen
- Department of Chemistry, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | | | - Maria Mukhtar
- Department of Chemistry, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Saba Shahrum
- Department of Chemistry, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Shanila Zahra
- Department of Chemistry, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Saima Shabbir
- Department of Materials Science and Engineering, Institute of Space Technology, 44000, Islamabad, Pakistan
| | - Azhar Iqbal
- Department of Chemistry, Quaid-I-Azam University, Islamabad, 45320, Pakistan.
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27
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Wang Y, Wegener G, Williams TA, Xie R, Hou J, Tian C, Zhang Y, Wang F, Xiao X. A methylotrophic origin of methanogenesis and early divergence of anaerobic multicarbon alkane metabolism. SCIENCE ADVANCES 2021; 7:eabj1453. [PMID: 34215592 PMCID: PMC11057702 DOI: 10.1126/sciadv.abj1453] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 05/21/2021] [Indexed: 06/13/2023]
Abstract
Methanogens are considered as one of the earliest life forms on Earth, and together with anaerobic methane-oxidizing archaea, they have crucial effects on climate stability. However, the origin and evolution of anaerobic alkane metabolism in the domain Archaea remain controversial. Here, we present evidence that methylotrophic methanogenesis was the ancestral form of this metabolism. Carbon dioxide-reducing methanogenesis developed later through the evolution of tetrahydromethanopterin S-methyltransferase, which linked methanogenesis to the Wood-Ljungdahl pathway for energy conservation. Anaerobic multicarbon alkane metabolisms in Archaea also originated early, with genes coding for the activation of short-chain or even long-chain alkanes likely evolving from an ethane-metabolizing ancestor. These genes were likely horizontally transferred to multiple archaeal clades including Candidatus (Ca) Bathyarchaeia, Ca. Lokiarchaeia, Ca. Hadarchaeia, and the methanogenic Ca. Methanoliparia.
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Affiliation(s)
- Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Gunter Wegener
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, BS8 1TH Bristol, UK
| | - Ruize Xie
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jialin Hou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chen Tian
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yu Zhang
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
- State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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28
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Rodríguez-Berbel N, Soria R, Ortega R, Bastida F, Miralles I. Quarry restoration treatments from recycled waste modify the physicochemical soil properties, composition and activity of bacterial communities and priming effect in semi-arid areas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 774:145693. [PMID: 33607438 DOI: 10.1016/j.scitotenv.2021.145693] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/01/2021] [Accepted: 02/03/2021] [Indexed: 06/12/2023]
Abstract
The selection of a suitable organic amendment for recovery of semi-arid soils degraded by mining is key to the success of an ecological restoration. The aim of this research is to study the short-term responses of physicochemical, biochemical and biological properties, as well as the changes of a soil bacterial community at the genus level after application of five types of organic amendments in a limestone quarry in Almería (SE, Spain). The relationship among bacterial taxa with biochemical and physicochemical properties and priming effect from restored soils was also analysed. Six months after the application of organic amendments, the values of different soil status, such as total organic carbon, total nitrogen, assimilable phosphorus and labile organic matter forms (carbohydrates and polyphenols), basal respiration (BR) and enzymatic activities increased significantly with respect to unrestored soils. Similarly, a positive priming effect of soil organic matter mineralisation was produced by all organic amendments, being significantly higher (p < 0.05) in sewage sludge-treated soils. Bacterial diversity was higher in restored than in control soils. The restoration caused changes in soil bacterial communities' composition at the phylum and genus levels. It was observed that soil bacterial communities were significantly related to several physical, chemical and biochemical soil properties, establishing two different co-occurrence patterns between restored and unrestored soils. A first bacterial co-occurrence pattern showed significant positive correlations to pH and C/N ratio and negativity with the rest of the soil properties. The second bacterial pattern was positively correlated with carbohydrates, μg of C, priming effect, BR, β-glucosidase and phosphatase and negatively with pH and C/N ratio. It was concluded that soil bacterial communities are clearly influenced by the types of organic amendments applied. Bacterial taxa such as Taibaiella or Pseudomonas could perform key functions in the carbon cycle in restored soils.
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Affiliation(s)
- N Rodríguez-Berbel
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, E-04120 Almería, Spain
| | - R Soria
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, E-04120 Almería, Spain
| | - R Ortega
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, E-04120 Almería, Spain
| | - F Bastida
- CEBAS-CSIC, Department of Soil and Water Conservation, Campus Universitario de Espinardo, E-30100, Espinardo, Murcia, Spain
| | - I Miralles
- Department of Agronomy & Center for Intensive Mediterranean Agrosystems and Agri-food Biotechnology (CIAIMBITAL), University of Almeria, E-04120 Almería, Spain.
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29
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Billings SA, Lajtha K, Malhotra A, Berhe AA, de Graaff MA, Earl S, Fraterrigo J, Georgiou K, Grandy S, Hobbie SE, Moore JAM, Nadelhoffer K, Pierson D, Rasmussen C, Silver WL, Sulman BN, Weintraub S, Wieder W. Soil organic carbon is not just for soil scientists: measurement recommendations for diverse practitioners. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2021; 31:e02290. [PMID: 33426701 DOI: 10.1002/eap.2290] [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] [Received: 04/09/2020] [Revised: 08/05/2020] [Accepted: 10/05/2020] [Indexed: 06/12/2023]
Abstract
Soil organic carbon (SOC) regulates terrestrial ecosystem functioning, provides diverse energy sources for soil microorganisms, governs soil structure, and regulates the availability of organically bound nutrients. Investigators in increasingly diverse disciplines recognize how quantifying SOC attributes can provide insight about ecological states and processes. Today, multiple research networks collect and provide SOC data, and robust, new technologies are available for managing, sharing, and analyzing large data sets. We advocate that the scientific community capitalize on these developments to augment SOC data sets via standardized protocols. We describe why such efforts are important and the breadth of disciplines for which it will be helpful, and outline a tiered approach for standardized sampling of SOC and ancillary variables that ranges from simple to more complex. We target scientists ranging from those with little to no background in soil science to those with more soil-related expertise, and offer examples of the ways in which the resulting data can be organized, shared, and discoverable.
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Affiliation(s)
- S A Billings
- Department of Ecology and Evolutionary Biology and Kansas Biological Survey, University of Kansas, Lawrence, Kansas, 66047, USA
| | - K Lajtha
- Department of Crop and Soil Sciences, Oregon State University, Corvallis, Oregon, 97331, USA
| | - A Malhotra
- Department of Earth System Science, Stanford University, Stanford, California, 94305, USA
| | - A A Berhe
- Department of Life and Environmental Sciences, University of California, Merced, Merced, California, 95344, USA
| | - M-A de Graaff
- Department of Biological Sciences, Boise State University, Boise, Idaho, 83725, USA
| | - S Earl
- Global Institute of Sustainability, Arizona State University, Tempe, Arizona, 85281, USA
| | - J Fraterrigo
- Department of Natural Resources and Environmental Sciences, and Program in Ecology, Evolution and Conservation Biology, University of Illinois, Urbana, Illinois, 61820, USA
| | - K Georgiou
- Department of Earth System Science, Stanford University, Stanford, California, 94305, USA
| | - S Grandy
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, 03824, USA
| | - S E Hobbie
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, 55455, USA
| | - J A M Moore
- Bioscience Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37830, USA
| | - K Nadelhoffer
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - D Pierson
- Department of Crop and Soil Sciences, Oregon State University, Corvallis, Oregon, 97331, USA
| | - C Rasmussen
- Department of Environmental Science, University of Arizona, Tucson, Arizona, 85721, USA
| | - W L Silver
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, California, 94720, USA
| | - B N Sulman
- Climate Change Science Institute and Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, 37830, USA
| | - S Weintraub
- National Ecological Observatory Network, Batelle, Boulder, Colorado, 80309, USA
| | - W Wieder
- Climate and Global Dynamics Laboratory, National Center for Atmospheric Research, Boulder, Colorado, 80307, USA
- Institute of Arctic and Alpine Research, University of Colorado Boulder, Boulder, Colorado, 80303, USA
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30
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Durall C, Kukil K, Hawkes JA, Albergati A, Lindblad P, Lindberg P. Production of succinate by engineered strains of Synechocystis PCC 6803 overexpressing phosphoenolpyruvate carboxylase and a glyoxylate shunt. Microb Cell Fact 2021; 20:39. [PMID: 33557832 PMCID: PMC7871529 DOI: 10.1186/s12934-021-01529-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/25/2021] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Cyanobacteria are promising hosts for the production of various industrially important compounds such as succinate. This study focuses on introduction of the glyoxylate shunt, which is naturally present in only a few cyanobacteria, into Synechocystis PCC 6803. In order to test its impact on cell metabolism, engineered strains were evaluated for succinate accumulation under conditions of light, darkness and anoxic darkness. Each condition was complemented by treatments with 2-thenoyltrifluoroacetone, an inhibitor of succinate dehydrogenase enzyme, and acetate, both in nitrogen replete and deplete medium. RESULTS We were able to introduce genes encoding the glyoxylate shunt, aceA and aceB, encoding isocitrate lyase and malate synthase respectively, into a strain of Synechocystis PCC 6803 engineered to overexpress phosphoenolpyruvate carboxylase. Our results show that complete expression of the glyoxylate shunt results in higher extracellular succinate accumulation compared to the wild type control strain after incubation of cells in darkness and anoxic darkness in the presence of nitrate. Addition of the inhibitor 2-thenoyltrifluoroacetone increased succinate titers in all the conditions tested when nitrate was available. Addition of acetate in the presence of the inhibitor further increased the succinate accumulation, resulting in high levels when phosphoenolpyruvate carboxylase was overexpressed, compared to control strain. However, the highest succinate titer was obtained after dark incubation of an engineered strain with a partial glyoxylate shunt overexpressing isocitrate lyase in addition to phosphoenolpyruvate carboxylase, with only 2-thenoyltrifluoroacetone supplementation to the medium. CONCLUSIONS Heterologous expression of the glyoxylate shunt with its central link to the tricarboxylic acid cycle (TCA) for acetate assimilation provides insight on the coordination of the carbon metabolism in the cell. Phosphoenolpyruvate carboxylase plays an important role in directing carbon flux towards the TCA cycle.
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Affiliation(s)
- Claudia Durall
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Box 523, 751 20, Uppsala, Sweden
| | - Kateryna Kukil
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Box 523, 751 20, Uppsala, Sweden
| | - Jeffrey A Hawkes
- Analytical Chemistry, Department of Chemistry-BMC, Uppsala University, Box 599, 751 20, Uppsala, Sweden
| | - Alessia Albergati
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Box 523, 751 20, Uppsala, Sweden
| | - Peter Lindblad
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Box 523, 751 20, Uppsala, Sweden
| | - Pia Lindberg
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Box 523, 751 20, Uppsala, Sweden.
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Wang Y, Wegener G, Williams TA, Xie R, Hou J, Wang F, Xiao X. A methylotrophic origin of methanogenesis and early divergence of anaerobic multicarbon alkane metabolism. SCIENCE ADVANCES 2021; 7:eabd7180. [PMID: 33568477 PMCID: PMC7875538 DOI: 10.1126/sciadv.abd7180] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 12/23/2020] [Indexed: 05/17/2023]
Abstract
Methanogens are considered as one of the earliest life forms on Earth, and together with anaerobic methane-oxidizing archaea, they have crucial effects on climate stability. Yet, the origin and evolution of anaerobic alkane metabolism in the domain Archaea remain controversial. Here, we show that methanogenesis was already present in the common ancestor of Euryarchaeota, TACK archaea, and Asgard archaea likely in the late Hadean or early Archean eon and that the ancestral methanogen was dependent on methylated compounds and hydrogen. Carbon dioxide-reducing methanogenesis developed later through the evolution of tetrahydromethanopterin S-methyltransferase, which linked methanogenesis to the Wood-Ljungdahl pathway for energy conservation. Multicarbon alkane metabolisms in Archaea also originated early, with genes coding for the activation of short- or even long-chain alkanes likely evolving from an ethane-metabolizing ancestor. These genes were likely horizontally transferred to multiple archaeal clades including Candidatus (Ca) Bathyarchaeota, Ca. Helarchaeota, Ca Hadesarchaeota, and the methanogenic Ca. Methanoliparia.
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Affiliation(s)
- Yinzhao Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Gunter Wegener
- Max Planck Institute for Marine Microbiology, 28359 Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, BS8 1TH Bristol, UK
| | - Ruize Xie
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jialin Hou
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai 200240, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
- State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean & Civil Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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Roussou S, Albergati A, Liang F, Lindblad P. Engineered cyanobacteria with additional overexpression of selected Calvin-Benson-Bassham enzymes show further increased ethanol production. Metab Eng Commun 2021; 12:e00161. [PMID: 33520653 PMCID: PMC7820548 DOI: 10.1016/j.mec.2021.e00161] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/21/2020] [Accepted: 01/06/2021] [Indexed: 12/20/2022] Open
Abstract
Cyanobacteria are one of the most promising microorganisms to produce biofuels and renewable chemicals due to their oxygenic autotrophic growth properties. However, to rely on photosynthesis, which is one of the main reasons for slow growth, low carbon assimlation rate and low production, is a bottleneck. To address this challenge, optimizing the Calvin-Benson-Bassham (CBB) cycle is one of the strategies since it is the main carbon fixation pathway. In a previous study, we showed that overexpression of either aldolase (FBA), transketolase (TK), or fructose-1,6/sedoheptulose-1,7-bisphosphatase (FBP/SBPase), enzymes responsible for RuBP regeneration and vital for controlling the CBB carbon flux, led to higher production rates and titers in ethanol producing strains of Synechocystis PCC 6803. In the present study, we investigated the combined effects of the above enzymes on ethanol production in Synechocystis PCC 6803. The ethanol production of the strains overexpressing two CBB enzymes (FBA + TK, FBP/SBPase + FBA or FBP/SBPase + TK) was higher than the respective control strains, overexpressing either FBA or TK. The co-overexpression of FBA and TK led to more than 9 times higher ethanol production compared to the overexpression of FBA. Compared to TK the respective increase is 4 times more ethanol production. Overexpression of FBP/SBPase in combination with FBA showed 2.5 times higher ethanol production compared to FBA. Finally, co-overexpression of FBP/SBPase and TK reached about twice the production of ethanol compared to overexpression of only TK. This study clearly demonstrates that overexpression of two selected CBB enzymes leads to significantly increased ethanol production compared to overexpression of a single CBB enzyme.
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Affiliation(s)
- Stamatina Roussou
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Box 523, SE-751 20, Uppsala, Sweden
| | - Alessia Albergati
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Box 523, SE-751 20, Uppsala, Sweden
| | - Feiyan Liang
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Box 523, SE-751 20, Uppsala, Sweden
| | - Peter Lindblad
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Box 523, SE-751 20, Uppsala, Sweden
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33
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Price C, Williams E, Elhalel G, Sentman D. Natural ELF fields in the atmosphere and in living organisms. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2021; 65:85-92. [PMID: 32034466 DOI: 10.1007/s00484-020-01864-6] [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] [Received: 10/13/2019] [Revised: 01/09/2020] [Accepted: 01/13/2020] [Indexed: 05/24/2023]
Abstract
Most electrical activity in vertebrates and invertebrates occurs at extremely low frequencies (ELF), with characteristic maxima below 50 Hz. The origin of these frequency maxima is unknown and remains a mystery. We propose that over billions of years during the evolutionary history of living organisms on Earth, the natural electromagnetic resonant frequencies in the atmosphere, continuously generated by global lightning activity, provided the background electric fields for the development of cellular electrical activity. In some animals, the electrical spectrum is difficult to differentiate from the natural background atmospheric electric field produced by lightning. In this paper, we present evidence for the link between the natural ELF fields and those found in many living organisms, including humans.
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Affiliation(s)
- Colin Price
- Deparment of Geophysics, Porter School of the Environment and Earth Sciences, Tel Aviv University, Tel Aviv-Yafo, Israel.
| | | | - Gal Elhalel
- Deparment of Geophysics, Porter School of the Environment and Earth Sciences, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Dave Sentman
- Department of Geophysics, University of Alaska, Fairbanks, AK, USA
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34
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Hunting ER, Matthews J, de Arróyabe Hernáez PF, England SJ, Kourtidis K, Koh K, Nicoll K, Harrison RG, Manser K, Price C, Dragovic S, Cifra M, Odzimek A, Robert D. Challenges in coupling atmospheric electricity with biological systems. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2021; 65:45-58. [PMID: 32666310 PMCID: PMC7782408 DOI: 10.1007/s00484-020-01960-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 05/29/2020] [Accepted: 06/26/2020] [Indexed: 05/24/2023]
Abstract
The atmosphere is host to a complex electric environment, ranging from a global electric circuit generating fluctuating atmospheric electric fields to local lightning strikes and ions. While research on interactions of organisms with their electrical environment is deeply rooted in the aquatic environment, it has hitherto been confined to interactions with local electrical phenomena and organismal perception of electric fields. However, there is emerging evidence of coupling between large- and small-scale atmospheric electrical phenomena and various biological processes in terrestrial environments that even appear to be tied to continental waters. Here, we synthesize our current understanding of this connectivity, discussing how atmospheric electricity can affect various levels of biological organization across multiple ecosystems. We identify opportunities for research, highlighting its complexity and interdisciplinary nature and draw attention to both conceptual and technical challenges lying ahead of our future understanding of the relationship between atmospheric electricity and the organization and functioning of biological systems.
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Affiliation(s)
- Ellard R Hunting
- School of Biological Sciences, University of Bristol, Bristol, UK.
| | | | | | - Sam J England
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Konstantinos Kourtidis
- Department of Environmental Engineering, Demokritus University of Thrace, Xanthi, Greece
- ISLP Xanthi Branch, ENTA Unit, ATHENA Research and Innovation Center, Xanthi, Greece
| | - Kuang Koh
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Keri Nicoll
- Department of Electronic and Electrical Engineering, University of Bath, Bath, UK
- Department of Meteorology, University of Reading, Reading, UK
| | | | | | - Colin Price
- Department of Geophysics. Porter School of the Environment and Earth Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Snezana Dragovic
- Vinča Institute of Nuclear Sciences, University of Belgrade, Belgrade, Serbia
| | - Michal Cifra
- Institute of Photonics and Electronics, Czech Academy of Sciences, Prague, Czechia
| | - Anna Odzimek
- Institute of Geophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Daniel Robert
- School of Biological Sciences, University of Bristol, Bristol, UK.
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35
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Natural components in sunscreens: Topical formulations with sun protection factor (SPF). Biomed Pharmacother 2020; 134:111161. [PMID: 33360043 DOI: 10.1016/j.biopha.2020.111161] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/07/2020] [Accepted: 12/14/2020] [Indexed: 02/05/2023] Open
Abstract
Artificial sunscreens are already gaining traction in order to protect the skin from sunburns, photoaging and photocarcinogenesis. However, the efficacy and safety of most artificial sunscreen constituents are hindered by their photostability, toxicity and damage to marine ecosystems. Natural selection and evolution have ensured that plants and animals have developed effective protective mechanisms against the deleterious side effects of oxidative stress and ultraviolet radiation (UV). Hence, natural antioxidants such as sun blockers are drawing considerable attention. The exact mechanism by which natural components act as sunscreen molecules has not been clearly established. However, conjugated π system is reported to play an important role in protecting the vital genetic material within the organism. Compared to artificial sunscreens, natural sunscreens with strong UV absorptive capacities are largely limited by low specific extinction value and by their inability to spread in large-scale sunscreen cosmetic applications. Previous studies have documented that natural components exert their photoprotective effects (such as improved skin elasticity and hydration, skin texture, and wrinkles) through their antioxidant effects, and through the regulation of UV-induced skin inflammation, barrier impairment and aging. This review focuses on natural antioxidant topical formulations with sun protection factor (SPF). Lignin, melanin, silymarin and other ingredients have been added to high sun protection nature sunscreens without any physical or chemical UV filters. This paper also provides a reference for adopting novel technical measures (extracting high content components, changing the type of solution, optimizing formulation, applying Nano technology, et al) to design and prepare nature sunscreen formulations equated with commercial sunscreen formulations. Another strategy is to add natural antioxidants from plants, animals, microorganisms and marine organisms as special enhancer or modifier ingredients to reinforce SPF values. Although the photoprotective effects of natural components have been established, their deleterious side effects have not been elucidated.
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36
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Kim P, Kaur M, Jang HI, Kim YI. The Circadian Clock-A Molecular Tool for Survival in Cyanobacteria. Life (Basel) 2020; 10:life10120365. [PMID: 33419320 PMCID: PMC7766417 DOI: 10.3390/life10120365] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 11/16/2022] Open
Abstract
Cyanobacteria are photosynthetic organisms that are known to be responsible for oxygenating Earth’s early atmosphere. Having evolved to ensure optimal survival in the periodic light/dark cycle on this planet, their genetic codes are packed with various tools, including a sophisticated biological timekeeping system. Among the cyanobacteria is Synechococcus elongatus PCC 7942, the simplest clock-harboring organism with a powerful genetic tool that enabled the identification of its intricate timekeeping mechanism. The three central oscillator proteins—KaiA, KaiB, and KaiC—drive the 24 h cyclic gene expression rhythm of cyanobacteria, and the “ticking” of the oscillator can be reconstituted inside a test tube just by mixing the three recombinant proteins with ATP and Mg2+. Along with its biochemical resilience, the post-translational rhythm of the oscillation can be reset through sensing oxidized quinone, a metabolite that becomes abundant at the onset of darkness. In addition, the output components pick up the information from the central oscillator, tuning the physiological and behavioral patterns and enabling the organism to better cope with the cyclic environmental conditions. In this review, we highlight our understanding of the cyanobacterial circadian clock and discuss how it functions as a molecular chronometer that readies the host for predictable changes in its surroundings.
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Affiliation(s)
- Pyonghwa Kim
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ 07102, USA; (P.K.); (M.K.)
| | - Manpreet Kaur
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ 07102, USA; (P.K.); (M.K.)
| | - Hye-In Jang
- School of Cosmetic Science and Beauty Biotechnology, Semyung University, Jecheon 27136, Korea
- Correspondence: (H.-I.J.); (Y.-I.K.)
| | - Yong-Ick Kim
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ 07102, USA; (P.K.); (M.K.)
- Institute for Brain and Neuroscience Research, New Jersey Institute of Technology, Newark, NJ 07102, USA
- Correspondence: (H.-I.J.); (Y.-I.K.)
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37
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Lee JK, Han HS, Chaikasetsin S, Marron DP, Waymouth RM, Prinz FB, Zare RN. Condensing water vapor to droplets generates hydrogen peroxide. Proc Natl Acad Sci U S A 2020; 117:30934-30941. [PMID: 33229543 PMCID: PMC7733789 DOI: 10.1073/pnas.2020158117] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
It was previously shown [J. K. Lee et al., Proc. Natl. Acad. Sci. U.S.A, 116, 19294-19298 (2019)] that hydrogen peroxide (H2O2) is spontaneously produced in micrometer-sized water droplets (microdroplets), which are generated by atomizing bulk water using nebulization without the application of an external electric field. Here we report that H2O2 is spontaneously produced in water microdroplets formed by dropwise condensation of water vapor on low-temperature substrates. Because peroxide formation is induced by a strong electric field formed at the water-air interface of microdroplets, no catalysts or external electrical bias, as well as precursor chemicals, are necessary. Time-course observations of the H2O2 production in condensate microdroplets showed that H2O2 was generated from microdroplets with sizes typically less than ∼10 µm. The spontaneous production of H2O2 was commonly observed on various different substrates, including silicon, plastic, glass, and metal. Studies with substrates with different surface conditions showed that the nucleation and the growth processes of condensate water microdroplets govern H2O2 generation. We also found that the H2O2 production yield strongly depends on environmental conditions, including relative humidity and substrate temperature. These results show that the production of H2O2 occurs in water microdroplets formed by not only atomizing bulk water but also condensing water vapor, suggesting that spontaneous water oxidation to form H2O2 from water microdroplets is a general phenomenon. These findings provide innovative opportunities for green chemistry at heterogeneous interfaces, self-cleaning of surfaces, and safe and effective disinfection. They also may have important implications for prebiotic chemistry.
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Affiliation(s)
- Jae Kyoo Lee
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Hyun Soo Han
- Department of Mechanical Engineering, Stanford University, Stanford, CA 94305
- Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305
| | | | - Daniel P Marron
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | | | - Fritz B Prinz
- Department of Mechanical Engineering, Stanford University, Stanford, CA 94305;
- Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305
| | - Richard N Zare
- Department of Chemistry, Stanford University, Stanford, CA 94305;
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38
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Gomes Gradíssimo D, Pereira Xavier L, Valadares Santos A. Cyanobacterial Polyhydroxyalkanoates: A Sustainable Alternative in Circular Economy. Molecules 2020; 25:E4331. [PMID: 32971731 PMCID: PMC7571216 DOI: 10.3390/molecules25184331] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/16/2020] [Accepted: 07/21/2020] [Indexed: 01/11/2023] Open
Abstract
Conventional petrochemical plastics have become a serious environmental problem. Its unbridled use, especially in non-durable goods, has generated an accumulation of waste that is difficult to measure, threatening aquatic and terrestrial ecosystems. The replacement of these plastics with cleaner alternatives, such as polyhydroxyalkanoates (PHA), can only be achieved by cost reductions in the production of microbial bioplastics, in order to compete with the very low costs of fossil fuel plastics. The biggest costs are carbon sources and nutrients, which can be appeased with the use of photosynthetic organisms, such as cyanobacteria, that have a minimum requirement for nutrients, and also using agro-industrial waste, such as the livestock industry, which in turn benefits from the by-products of PHA biotechnological production, for example pigments and nutrients. Circular economy can help solve the current problems in the search for a sustainable production of bioplastic: reducing production costs, reusing waste, mitigating CO2, promoting bioremediation and making better use of cyanobacteria metabolites in different industries.
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Affiliation(s)
- Diana Gomes Gradíssimo
- Post Graduation Program in Biotechnology, Institute of Biological Sciences, Universidade Federal do Pará, Augusto Corrêa Street, Guamá, Belém, PA 66075-110, Brazil
- Laboratory of Biotechnology of Enzymes and Biotransformations, Institute of Biological Sciences, Universidade Federal do Pará, Augusto Corrêa Street, Guamá, Belém, PA 66075-110, Brazil;
| | - Luciana Pereira Xavier
- Laboratory of Biotechnology of Enzymes and Biotransformations, Institute of Biological Sciences, Universidade Federal do Pará, Augusto Corrêa Street, Guamá, Belém, PA 66075-110, Brazil;
| | - Agenor Valadares Santos
- Post Graduation Program in Biotechnology, Institute of Biological Sciences, Universidade Federal do Pará, Augusto Corrêa Street, Guamá, Belém, PA 66075-110, Brazil
- Laboratory of Biotechnology of Enzymes and Biotransformations, Institute of Biological Sciences, Universidade Federal do Pará, Augusto Corrêa Street, Guamá, Belém, PA 66075-110, Brazil;
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39
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Li Z, Liu B, Li SHJ, King CG, Gitai Z, Wingreen NS. Modeling microbial metabolic trade-offs in a chemostat. PLoS Comput Biol 2020; 16:e1008156. [PMID: 32857772 PMCID: PMC7482850 DOI: 10.1371/journal.pcbi.1008156] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 09/10/2020] [Accepted: 07/16/2020] [Indexed: 02/06/2023] Open
Abstract
Microbes face intense competition in the natural world, and so need to wisely allocate their resources to multiple functions, in particular to metabolism. Understanding competition among metabolic strategies that are subject to trade-offs is therefore crucial for deeper insight into the competition, cooperation, and community assembly of microorganisms. In this work, we evaluate competing metabolic strategies within an ecological context by considering not only how the environment influences cell growth, but also how microbes shape their chemical environment. Utilizing chemostat-based resource-competition models, we exhibit a set of intuitive and general procedures for assessing metabolic strategies. Using this framework, we are able to relate and unify multiple metabolic models, and to demonstrate how the fitness landscape of strategies becomes intrinsically dynamic due to species-environment feedback. Such dynamic fitness landscapes produce rich behaviors, and prove to be crucial for ecological and evolutionarily stable coexistence in all the models we examined.
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Affiliation(s)
- Zhiyuan Li
- Center for Quantitative Biology, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- Center for the Physics of Biological Function, Princeton University, Princeton, New Jersey, United States of America
- Princeton Center for Theoretical Science, Princeton University, Princeton, New Jersey, United States of America
| | - Bo Liu
- Yuanpei College, Peking University, Beijing, China
| | - Sophia Hsin-Jung Li
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Christopher G. King
- Department of Physics, Princeton University, Princeton, New Jersey, United States of America
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Ned S. Wingreen
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
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40
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Qian L, Wu L, Yang L, Zhang Z. Inoculation concentration modulating the secretion and accumulation pattern of exopolysaccharides in desert cyanobacterium Microcoleus vaginatus. Biotechnol Appl Biochem 2020; 68:330-337. [PMID: 32337747 DOI: 10.1002/bab.1930] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 04/21/2020] [Indexed: 12/11/2022]
Abstract
Cyanobacterial exopolysaccharides (EPS) accumulated during microalgal cultivation have significant application potential in antioxidation, pharmaceutical products, and so on. Inoculation concentration strongly affects the cultivation cost, biomass, and EPS accumulation. In this study, a high-EPS-excreted desert cyanobacterium Microcoleus vaginatus was isolated, and the effects of inoculation concentration on biomass, photosynthetic activity, and EPS accumulation were explored. The results showed that the original fluorescence (Fo ) provided a good indication to cyanobacterial biomass, when Chl-a concentration was lower than 10 mg L-1 . Inoculation concentration significantly affected cyanobacterial biomass and EPS concentration (P < 0.001), whereas did not affect photosynthetic activity (Fv /Fm ; P > 0.05). The two fractions of EPS, capsular exopolysaccharides (CPS) and released exopolysaccharides (RPS) were strongly affect by inoculation concentration. Other than forming thick sheath (CPS) surrounded the filaments, M. vaginatus excreted higher proportions of RPS to culture medium, and the ratio of RPS to CPS ranged from 1.08 to 1.58 depending on the inoculation concentration. Additionally, although the biomass and EPS accumulation increased with inoculation concentration, the increasing inoculation concentration did not bring to the proportionate increase of the final biomass and EPS yield. Altogether, comprehensively considering the EPS yield and productivity, inoculation concentration of 0.04 mg Chl-a L-1 is recommended for M. vaginatus to produce EPS, with an EPS yield of 94.32 mg L-1 and EPS productivity of 184.86 mg (mg Chl-a)-1 L-1 d-1 at the end of experiment.
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Affiliation(s)
- Long Qian
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan, People's Republic of China
| | - Li Wu
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan, People's Republic of China
| | - Lie Yang
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan, People's Republic of China
| | - Zulin Zhang
- School of Resources and Environmental Engineering, Wuhan University of Technology, Wuhan, People's Republic of China.,The James Hutton Institute, Craigiebuckler, Aberdeen, UK
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41
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Mendoza-Torres E, Cruz-Catañeda J, Negrón-Mendoza A, Heredia A. Computer and Experimental Simulation of Alloxazine Synthesis from Gamma Irradiation of Amino Acids on Iceland Spar: A Prebiotic Chemistry Perspective. J Mol Evol 2020; 88:284-291. [PMID: 32140772 DOI: 10.1007/s00239-020-09933-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 02/09/2020] [Indexed: 10/24/2022]
Abstract
On ancient Earth, environmental conditions favored prebiotic chemical reactions. In the Archean, some molecules with conjugated rings might have been synthesized, displaying structural stability in the Archean in the presence of ionizing radiation and hydration-dehydration events. Additionally, it is suggested that on ancient Earth, calcite was a common mineral promoting organic compound synthesis. In the present work a study of the interaction of amino acid mixtures with the (104) surface of calcite is presented. Our preliminary results show the abiotic synthesis of alloxazine (a flavin with relevant photochemical properties). Computer simulations were performed in HyperChem 8.0.1. by means of MM+ molecular mechanics and PM3 semi-empirical methods, in 27 possible amino acid trimers of alanine, glycine and lysine. Alloxazine formation is possible by the gamma irradiation of amino acids. The computer simulations show that trimers GGG and GGA promote the further transformation from diketopiperazines (DKP's) and KGK to alloxazine. The computer simulations with free radicals are not stable when alloxazine is interacting with the calcite surface. Experiments in anoxygenic environments with hydration-dehydration events in gamma irradiated samples allow the abiotic formation of flavins, DKP's and a heterocycle compound with possible relevance in prebiotic chemistry.
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Affiliation(s)
- Ernesto Mendoza-Torres
- Facultad de Estudios Superiores Iztacala, UNAM, Av. de los Barrios 1, Los Reyes Iztacala, 54090, Tlalnepantla de Baz, Estado de México, Mexico.,Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, Circuito exterior s/n, C.P. 04510, México, DF, Mexico
| | - Jorge Cruz-Catañeda
- Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, Circuito exterior s/n, C.P. 04510, México, DF, Mexico.,Posgrado en Ciencias Químicas, Universidad Nacional Autónoma de México, Circuito exterior s/n, Mexico, Mexico
| | - Alicia Negrón-Mendoza
- Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, Circuito exterior s/n, C.P. 04510, México, DF, Mexico
| | - Alejandro Heredia
- Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, Circuito exterior s/n, C.P. 04510, México, DF, Mexico.
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42
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Durall C, Lindberg P, Yu J, Lindblad P. Increased ethylene production by overexpressing phosphoenolpyruvate carboxylase in the cyanobacterium Synechocystis PCC 6803. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:16. [PMID: 32010220 PMCID: PMC6988332 DOI: 10.1186/s13068-020-1653-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 01/09/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND Cyanobacteria can be metabolically engineered to convert CO2 to fuels and chemicals such as ethylene. A major challenge in such efforts is to optimize carbon fixation and partition towards target molecules. RESULTS The efe gene encoding an ethylene-forming enzyme was introduced into a strain of the cyanobacterium Synechocystis PCC 6803 with increased phosphoenolpyruvate carboxylase (PEPc) levels. The resulting engineered strain (CD-P) showed significantly increased ethylene production (10.5 ± 3.1 µg mL-1 OD-1 day-1) compared to the control strain (6.4 ± 1.4 µg mL-1 OD-1 day-1). Interestingly, extra copies of the native pepc or the heterologous expression of PEPc from the cyanobacterium Synechococcus PCC 7002 (Synechococcus) in the CD-P, increased ethylene production (19.2 ± 1.3 and 18.3 ± 3.3 µg mL-1 OD-1 day-1, respectively) when the cells were treated with the acetyl-CoA carboxylase inhibitor, cycloxydim. A heterologous expression of phosphoenolpyruvate synthase (PPSA) from Synechococcus in the CD-P also increased ethylene production (16.77 ± 4.48 µg mL-1 OD-1 day-1) showing differences in the regulation of the native and the PPSA from Synechococcus in Synechocystis. CONCLUSIONS This work demonstrates that genetic rewiring of cyanobacterial central carbon metabolism can enhance carbon supply to the TCA cycle and thereby further increase ethylene production.
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Affiliation(s)
- Claudia Durall
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, P.O. Box 523, 751 20 Uppsala, Sweden
| | - Pia Lindberg
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, P.O. Box 523, 751 20 Uppsala, Sweden
| | - Jianping Yu
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO USA
| | - Peter Lindblad
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, P.O. Box 523, 751 20 Uppsala, Sweden
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Ballesteros-Torres JM, Samaniego-Moreno L, Gomez-Flores R, Tamez-Guerra RS, Rodríguez-Padilla C, Tamez-Guerra P. Amino acids and acylcarnitine production by Chlorella vulgaris and Chlorella sorokiniana microalgae from wastewater culture. PeerJ 2019; 7:e7977. [PMID: 31824754 PMCID: PMC6896938 DOI: 10.7717/peerj.7977] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 10/02/2019] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Microalgae are a widely distributed group of prokaryotic and eukaryotic photosynthetic microorganisms that use a number of substances present in wastewater to produce a variety of biotechnological and nutritional biomolecules. METHODS Production ofamino acids and acylcarnitine by Chlorella vulgaris and Chlorella sorokiniana was determined after 13 d of culture in wastewater, under various culture conditions. Wastewater was collected from "La Encantada" stream, located in Saltillo, Coahuila, Mexico. Microalgae was cultured at 23°C and natural day light, including the use of the following conditions: (1) extra light (12:12 light:dark cycles, 1,380 lumens), (2) agitation (130 rpm), and (3) both conditions, until exponential phase. Supernatant products were then analyzed by liquid chromatograph coupled to mass spectrometry. In addition, metabolomic profiles related to growing conditions were evaluated. RESULTS Amino acids and acylcarnitine production by C. sorokiniana and C. vulgaris resulted in higher Ala and Leu concentrations by C. vulgaris compared with control, where control produced Gly and Pro in higher amounts compared with C. sorokiniana. Tyr, Phe, Val, and Cit were detected in lower amounts under light and shaking culture conditions. High concentrations of C0 acylcarnitines were produced by both microalgae compared with control, where C. sorokiniana production was independent of culture conditions, whereas C. vulgaris one was stimulated by shaking. C4 production was higher by C. sorokiniana compared with control. Furthermore, C4, C6DC, C14:1, C14:2, and C18:1OH production by microalga was low in all culture conditions. CONCLUSION Microalgae produced essential amino acids and nutritionally important carnitines from wastewater. In addition, C. sorokiniana biomass has higher potential as animal nutrient supplement, as compared with that of C. vulgaris.
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Affiliation(s)
- Juan M. Ballesteros-Torres
- Facultad de Ciencias Biologicas (FCB), Departamento de Microbiología e Inmunología, Ave. Universidad s/n, Cd. Universitaria, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, Nuevo León, México
| | - Luis Samaniego-Moreno
- Departamento de Riego y Drenaje, Laboratorio de Calidad de Aguas, Universidad Autónoma Agraria “Antonio Narro” (UAAAN), Saltillo, Coahuila, México
| | - Ricardo Gomez-Flores
- Facultad de Ciencias Biologicas (FCB), Departamento de Microbiología e Inmunología, Ave. Universidad s/n, Cd. Universitaria, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, Nuevo León, México
| | - Reyes S. Tamez-Guerra
- Facultad de Ciencias Biologicas (FCB), Departamento de Microbiología e Inmunología, Ave. Universidad s/n, Cd. Universitaria, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, Nuevo León, México
| | - Cristina Rodríguez-Padilla
- Facultad de Ciencias Biologicas (FCB), Departamento de Microbiología e Inmunología, Ave. Universidad s/n, Cd. Universitaria, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, Nuevo León, México
| | - Patricia Tamez-Guerra
- Facultad de Ciencias Biologicas (FCB), Departamento de Microbiología e Inmunología, Ave. Universidad s/n, Cd. Universitaria, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, Nuevo León, México
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Garcia-Robledo JE, Barrera MC, Tobón GJ. CRISPR/Cas: from adaptive immune system in prokaryotes to therapeutic weapon against immune-related diseases. Int Rev Immunol 2019; 39:11-20. [PMID: 31625429 DOI: 10.1080/08830185.2019.1677645] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
CRISPR/Cas evolved as an adaptive immune system in bacteria and archaea to inactivate foreign viral and plasmid DNA. However, the capacities of various CRISPR/Cas systems for precise genome editing based on sequence homology also allow their use as tools for genomic and epigenomic modification in eukaryotes. Indeed, these genetic characteristics have proven useful for disease modeling and testing the specific functions of target genes under pathological conditions. Moreover, recent studies provide compelling evidence that CRISPR/Cas systems could be useful therapeutic tools against human diseases, including cancer, monogenic disorders, and autoimmune disorders.HighlightsCRISPR/Cas evolved as an adaptive immune system in bacteria and archaea.CRISPR/Cas systems are nowadays used as tools for genomic modification.CRISPR/Cas systems could be useful therapeutic tools against human disease, including autoimmune conditions.
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Affiliation(s)
| | - María Claudia Barrera
- Grupo de Investigación en Reumatología, Autoinmunidad y Medicina Traslacional; Fundación Valle Del Lili and Universidad Icesi, Cali, Colombia
| | - Gabriel J Tobón
- Grupo de Investigación en Reumatología, Autoinmunidad y Medicina Traslacional; Fundación Valle Del Lili and Universidad Icesi, Cali, Colombia
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45
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Population dynamics of chemotrophs in anaerobic conditions where the metabolic energy acquisition per redox reaction is limited. J Theor Biol 2019; 467:164-173. [DOI: 10.1016/j.jtbi.2019.01.037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 01/29/2019] [Accepted: 01/31/2019] [Indexed: 11/17/2022]
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Abstract
The Archean Eon was a time of predominantly anoxic Earth surface conditions, where anaerobic processes controlled bioessential element cycles. In contrast to "oxygen oases" well documented for the Neoarchean [2.8 to 2.5 billion years ago (Ga)], the magnitude, spatial extent, and underlying causes of possible Mesoarchean (3.2 to 2.8 Ga) surface-ocean oxygenation remain controversial. Here, we report δ15N and δ13C values coupled with local seawater redox data for Mesoarchean shales of the Mozaan Group (Pongola Supergroup, South Africa) that were deposited during an episode of enhanced Mn (oxyhydr)oxide precipitation between ∼2.95 and 2.85 Ga. Iron and Mn redox systematics are consistent with an oxygen oasis in the Mesoarchean anoxic ocean, but δ15N data indicate a Mo-based diazotrophic biosphere with no compelling evidence for a significant aerobic nitrogen cycle. We propose that in contrast to the Neoarchean, dissolved O2 levels were either too low or too limited in extent to develop a large and stable nitrate reservoir in the Mesoarchean ocean. Since biological N2 fixation was evidently active in this environment, the growth and proliferation of O2-producing organisms were likely suppressed by nutrients other than nitrogen (e.g., phosphorus), which would have limited the expansion of oxygenated conditions during the Mesoarchean.
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Sosa-Hernández JE, Romero-Castillo KD, Parra-Arroyo L, Aguilar-Aguila-Isaías MA, García-Reyes IE, Ahmed I, Parra-Saldivar R, Bilal M, Iqbal HMN. Mexican Microalgae Biodiversity and State-Of-The-Art Extraction Strategies to Meet Sustainable Circular Economy Challenges: High-Value Compounds and Their Applied Perspectives. Mar Drugs 2019; 17:E174. [PMID: 30889823 PMCID: PMC6470790 DOI: 10.3390/md17030174] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/05/2019] [Accepted: 03/09/2019] [Indexed: 02/05/2023] Open
Abstract
In recent years, the demand for naturally derived products has hiked with enormous pressure to propose or develop state-of-the-art strategies to meet sustainable circular economy challenges. Microalgae possess the flexibility to produce a variety of high-value products of industrial interests. From pigments such as phycobilins or lutein to phycotoxins and several polyunsaturated fatty acids (PUFAs), microalgae have the potential to become the primary producers for the pharmaceutical, food, and agronomical industries. Also, microalgae require minimal resources to grow due to their autotrophic nature or by consuming waste matter, while allowing for the extraction of several valuable side products such as hydrogen gas and biodiesel in a single process, following a biorefinery agenda. From a Mexican microalgae biodiversity perspective, more than 70 different local species have been characterized and isolated, whereas, only a minimal amount has been explored to produce commercially valuable products, thus ignoring their potential as a locally available resource. In this paper, we discuss the microalgae diversity present in Mexico with their current applications and potential, while expanding on their future applications in bioengineering along with other industrial sectors. In conclusion, the use of available microalgae to produce biochemically revenuable products currently represents an untapped potential that could lead to the solution of several problems through green technologies. As such, if the social, industrial and research communities collaborate to strive towards a greener economy by preserving the existing biodiversity and optimizing the use of the currently available resources, the enrichment of our society and the solution to several environmental problems could be attained.
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Affiliation(s)
- Juan Eduardo Sosa-Hernández
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Ave. Eugenio Garza Sada 2501, CP 64849, Monterrey, N.L., Mexico.
| | - Kenya D Romero-Castillo
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Ave. Eugenio Garza Sada 2501, CP 64849, Monterrey, N.L., Mexico.
| | - Lizeth Parra-Arroyo
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Ave. Eugenio Garza Sada 2501, CP 64849, Monterrey, N.L., Mexico.
| | - Mauricio A Aguilar-Aguila-Isaías
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Ave. Eugenio Garza Sada 2501, CP 64849, Monterrey, N.L., Mexico.
| | - Isaac E García-Reyes
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Ave. Eugenio Garza Sada 2501, CP 64849, Monterrey, N.L., Mexico.
| | - Ishtiaq Ahmed
- School of Medical Science, Menzies Health Institute Queensland, Griffith University (Gold Coast campus), Parklands Drive, Southport, QLD 4222, Australia.
| | - Roberto Parra-Saldivar
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Ave. Eugenio Garza Sada 2501, CP 64849, Monterrey, N.L., Mexico.
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China.
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Ave. Eugenio Garza Sada 2501, CP 64849, Monterrey, N.L., Mexico.
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48
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Kalapos B, Hlavová M, Nádai TV, Galiba G, Bišová K, Dóczi R. Early Evolution of the Mitogen-Activated Protein Kinase Family in the Plant Kingdom. Sci Rep 2019; 9:4094. [PMID: 30858468 PMCID: PMC6411719 DOI: 10.1038/s41598-019-40751-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 02/04/2019] [Indexed: 01/23/2023] Open
Abstract
Mitogen-activated protein kinase (MAPK) pathways are central cellular signalling mechanisms in all eukaryotes. They are key regulators of the cell cycle and stress responses, yet evolution of MAPK families took markedly different paths in the animal and plant kingdoms. Instead of the characteristic divergence of MAPK types in animals, in plants an expanded network of ERK-like MAPKs has emerged. To gain insight into the early evolution of the plant MAPK family we identified and analysed MAPKs in 13 representative species across green algae, a large and diverse early-diverging lineage within the plant kingdom. Our results reveal that the plant MAPK gene family emerged from three types of progenitor kinases, which are ubiquitously present in algae, implying their formation in an early ancestor. Low number of MAPKs is characteristic across algae, the few losses or duplications are associated with genome complexity rather than habitat ecology, despite the importance of MAPKs in environmental signalling in flowering plants. ERK-type MAPKs are associated with cell cycle regulation in opisthokont models, yet in plants their stress-signalling function is more prevalent. Unicellular microalgae offer an excellent experimental system to study the cell cycle, and MAPK gene expression profiles show CDKB-like peaks around S/M phase in synchronised Chlamydomonas reinhardtii cultures, suggesting their participation in cell cycle regulation, in line with the notion that the ancestral eukaryotic MAPK was a cell cycle regulator ERK-like kinase. Our work also highlights the scarcity of signalling knowledge in microalgae, in spite of their enormous ecological impact and emerging economic importance.
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Affiliation(s)
- Balázs Kalapos
- Institute of Agriculture, Centre for Agricultural Research of the Hungarian Academy of Sciences, H-2462, Martonvásár, Brunszvik u. 2, Hungary.,Festetics Doctoral School, Georgikon Faculty, University of Pannonia, 8360, Keszthely, Hungary
| | - Monika Hlavová
- Centre Algatech, Institute of Microbiology Academy of Sciences of the Czech Republic, Opatovicky mlyn, CZ 379 81, Třeboň, Czech Republic
| | - Tímea V Nádai
- Institute of Agriculture, Centre for Agricultural Research of the Hungarian Academy of Sciences, H-2462, Martonvásár, Brunszvik u. 2, Hungary.,Festetics Doctoral School, Georgikon Faculty, University of Pannonia, 8360, Keszthely, Hungary
| | - Gábor Galiba
- Institute of Agriculture, Centre for Agricultural Research of the Hungarian Academy of Sciences, H-2462, Martonvásár, Brunszvik u. 2, Hungary.,Festetics Doctoral School, Georgikon Faculty, University of Pannonia, 8360, Keszthely, Hungary
| | - Kateřina Bišová
- Centre Algatech, Institute of Microbiology Academy of Sciences of the Czech Republic, Opatovicky mlyn, CZ 379 81, Třeboň, Czech Republic
| | - Róbert Dóczi
- Institute of Agriculture, Centre for Agricultural Research of the Hungarian Academy of Sciences, H-2462, Martonvásár, Brunszvik u. 2, Hungary.
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Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea. Nat Microbiol 2019; 4:603-613. [PMID: 30833729 PMCID: PMC6453112 DOI: 10.1038/s41564-019-0363-3] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 01/07/2019] [Indexed: 12/29/2022]
Abstract
Methanogenesis is an ancient metabolism of key ecological relevance, with direct impact on the evolution of Earth’s climate. Recent results suggest that the diversity of methane metabolisms and their derivations have probably been vastly underestimated. Here, by probing thousands of publicly available metagenomes for homologues of methyl-coenzyme M reductase complex (MCR), we have obtained ten metagenome-assembled genomes (MAGs) belonging to potential methanogenic, anaerobic methanotrophic and short-chain alkane oxidizing archaea. Five of these MAGs represent under-sampled (e.g., Verstraetearchaeota, Methanonatronarchaeia, ANME-1) or previously genomically undescribed (ANME-2c) archaeal lineages. The remaining five MAGs correspond to lineages that are only distantly related to previously known methanogens and span the entire archaeal phylogeny. Comprehensive comparative annotation significantly expands the metabolic diversity and energy conservation systems of MCR-bearing archaea. It also suggests the potential existence of a yet uncharacterized type of methanogenesis linked to short-chain alkane/fatty acid oxidation in a previously undescribed class of archaea (‘Ca. Methanoliparia’). We redefine a common core of marker genes specific to methanogenic, anaerobic methanotrophic and short-chain alkane-oxidizing archaea, and propose a possible scenario for the evolutionary and functional transitions that led to the emergence of such metabolic diversity.
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50
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Fernandes CC, Kishi LT, Lopes EM, Omori WP, Souza JAMD, Alves LMC, Lemos EGDM. Bacterial communities in mining soils and surrounding areas under regeneration process in a former ore mine. Braz J Microbiol 2018; 49:489-502. [PMID: 29452849 PMCID: PMC6066727 DOI: 10.1016/j.bjm.2017.12.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 11/06/2017] [Accepted: 12/04/2017] [Indexed: 01/19/2023] Open
Abstract
Human activities on the Earth's surface change the landscape of natural ecosystems. Mining practices are one of the most severe human activities, drastically altering the chemical, physical and biological properties of the soil environment. Bacterial communities in soil play an important role in the maintenance of ecological relationships. This work shows bacterial diversity, metabolic repertoire and physiological behavior in five ecosystems samples with different levels of impact. These ecosystems belong to a historical area in Iron Quadrangle, Minas Gerais, Brazil, which suffered mining activities until its total depletion without recovery since today. The results revealed Proteobacteria as the most predominant phylum followed by Acidobacteria, Verrucomicrobia, Planctomycetes, and Bacteroidetes. Soils that have not undergone anthropological actions exhibit an increase ability to degrade carbon sources. The richest soil with the high diversity was found in ecosystems that have suffered anthropogenic action. Our study shows profile of diversity inferring metabolic profile, which may elucidate the mechanisms underlying changes in community structure in situ mining sites in Brazil. Our data comes from contributing to know the bacterial diversity, relationship between these bacteria and can explore strategies for natural bioremediation in mining areas or adjacent areas under regeneration process in iron mining areas.
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Affiliation(s)
- Camila Cesário Fernandes
- UNESP - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Tecnologia, Jaboticabal, SP, Brazil
| | - Luciano Takeshi Kishi
- UNESP - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Tecnologia, Jaboticabal, SP, Brazil
| | - Erica Mendes Lopes
- UNESP - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Tecnologia, Jaboticabal, SP, Brazil
| | - Wellington Pine Omori
- UNESP - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Biologia Aplicada à Agropecuária, Laboratório de Genética Aplicada, Jaboticabal, SP, Brazil
| | - Jackson Antonio Marcondes de Souza
- UNESP - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Biologia Aplicada à Agropecuária, Laboratório de Genética Aplicada, Jaboticabal, SP, Brazil
| | - Lucia Maria Carareto Alves
- UNESP - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Tecnologia, Jaboticabal, SP, Brazil
| | - Eliana Gertrudes de Macedo Lemos
- UNESP - Univ Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Tecnologia, Jaboticabal, SP, Brazil.
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