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Guevara-Martínez SJ, Villanueva-Mejía F, Zamudio-Ojeda A, Herrera-Bucio R, Morales-Palacios FG. Isolation of the Antifungal Compound Alliodorin from the Heartwood of Cordia elaeagnoides A. DC. and the In Silico Analysis of the Laccase. PLANTS (BASEL, SWITZERLAND) 2024; 13:1294. [PMID: 38794364 PMCID: PMC11125024 DOI: 10.3390/plants13101294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 05/26/2024]
Abstract
Cordia elaeagnoides A. DC. is an endemic species of Mexico valued for its timber. Renowned for its durability, resistance, and versatile applications in medicine, this tree holds significant commercial importance. Tetrahydrofuran (THF) extract from the heartwood of C. elaeagnoides was studied. Through chromatographic column purification, the compound 8-(2,5-Dihydroxyphenyl)-2,6-dimethylocta-2,6-dienal, also known as alliodorin, was successfully isolated. Identification of alliodorin was confirmed through comprehensive analysis utilizing NMR, IR, and mass spectrometry techniques. Inhibition tests were conducted using both the THF extract and alliodorin against the rotting fungus Trametes versicolor (L.) Lloyd, employing the agar well diffusion assay. Remarkably, alliodorin exhibited 100% inhibition with a median lethal concentration of 0.079 mg/mL and a total lethal concentration of 0.127 mg/mL, in comparison to the commercial fungicide benomyl, which requires a concentration of 1 mg/mL. In silico analysis through molecular docking on the laccase enzyme was proposed in order to explain the inhibitory activity against the fungus T. versicolor, as this enzyme is one of the main sources of nutrients and development for the fungus. Based on these findings, we deduced that alliodorin holds promise as a potent antifungal agent, potentially applicable in a wide array of technological and environmentally friendly initiatives.
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Affiliation(s)
- Santiago José Guevara-Martínez
- Department of Pharmacology, School of Exact Sciences and Engineering, University of Guadalajara, Boulevard Gral. Marcelino García Barragán 1421, Olímpica, Guadalajara 44840, Jalisco, Mexico;
| | - Francisco Villanueva-Mejía
- Instituto Tecnológico de Pabellón de Arteaga, Carretera a la estación de Rincón de Romos, km 1, Aguacalientes 20670, Aguascalientes, Mexico;
| | - Adalberto Zamudio-Ojeda
- Deparment of Physics, School of Exact Sciences and Engineering, University of Guadalajara, Boulevard Gral. Marcelino García Barragán 1421, Olímpica, Guadalajara 44840, Jalisco, Mexico;
| | - Rafael Herrera-Bucio
- Instituto de Investigaciones Químico Biólogicas, Universidad Michoacana de San Nicolás de Hidalgo, Francisco J. Múgica, s/n, Morelia 58030, Michoacán, Mexico
| | - Fredy Geovannini Morales-Palacios
- Instituto de Investigaciones Químico Biólogicas, Universidad Michoacana de San Nicolás de Hidalgo, Francisco J. Múgica, s/n, Morelia 58030, Michoacán, Mexico
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Schoder KA, Krümpel J, Müller J, Lemmer A. Effects of Environmental and Nutritional Conditions on Mycelium Growth of Three Basidiomycota. MYCOBIOLOGY 2024; 52:124-134. [PMID: 38690030 PMCID: PMC11057518 DOI: 10.1080/12298093.2024.2341492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 04/05/2024] [Indexed: 05/02/2024]
Abstract
In recent decades, an enormous potential of fungal-based products with characteristics equal to, or even outperforming, classic petroleum-derived products has been acknowledged. The production of these new materials uses mycelium, a root-like structure of fungi consisting of a mass of branching, thread-like hyphae. Optimizing the production of mycelium-based materials and fungal growth under technical conditions needs to be further investigated. The main objective of this study was to select fast-growing fungi and identify optimized incubation conditions to obtain a dense mycelium mat in a short time. Further, the influence of the initial substrate characteristics on hyphae expansion was determined. Fungal isolates of Ganoderma lucidum, Pleurotus ostreatus, and Trametes versicolor were cultivated for seven days on substrate mixtures consisting of various proportions of pine bark and cotton fibers. Furthermore, the substrates were mixed with 0, 2, and 5 wt.% calcium carbonate (CaCO3), and the incubator was flushed with 0, 5, and 10 vol.% carbon dioxide (CO2). All samples grew in the dark at 26 °C and a relative humidity of 80%. Evaluation of growth rate shows that cotton fiber-rich substrates performed best for all investigated fungi. Although Pleurotus ostreatus and Trametes versicolor showed comparatively high growth rates of up to 5.4 and 5.3 mm d-1, respectively, mycelium density was thin and transparent. Ganoderma lucidum showed a significantly denser mycelium at a maximum growth rate of 3.3 mm d-1 on a cotton fiber-rich substrate (75 wt.%) without CaCO3 but flushed with 5 vol.% CO2 during incubation.
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Affiliation(s)
| | - Johannes Krümpel
- State Institute of Agricultural Engineering and Bioenergy, University of Hohenheim, Stuttgart, Germany
| | - Joachim Müller
- Agricultural Engineering in the Tropics and Subtropics, University of Hohenheim, Stuttgart, Germany
| | - Andreas Lemmer
- State Institute of Agricultural Engineering and Bioenergy, University of Hohenheim, Stuttgart, Germany
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3
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Li C, Zhang Y, Zheng Y, Shi C, Lu Y, Zhang Y, Yuan S. Contaminant transformation during sediment oxygenation: Temporal variation of oxidation mechanisms mediated by hydroxyl radicals and aerobic microbes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 919:170855. [PMID: 38340822 DOI: 10.1016/j.scitotenv.2024.170855] [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: 12/04/2023] [Revised: 01/29/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
Sediment oxidation by oxygen is ubiquitous, whereas the mechanisms of concurrent contaminant oxidation, particularly the temporal variation of chemical and biological oxidation, remain inadequately understood. This study investigated the oxidation of two contaminants (phenol and trichloroethylene) with different responses during the oxygenation of four natural sediments with different redox properties. Results showed that contaminant oxidation was initially dominated by hydroxyl radicals (•OH) (first stage), stabilized for different time for different sediments (second stage), and was re-started by microbial mechanism (third stage). In the first short stage, the contribution of chemical oxidation by •OH was mainly determined by the variation of sediment electron-donating capacity (EDC). In the second long stage, the stabilization time was dependent on sediment redox properties, that is, the abundance and growth of aerobic microbes capable of degrading the target contaminants. A more reduced sediment resulted in a higher extent of oxidation by •OH and a longer stabilization time. When the third stage of aerobic microbial oxidation was started, the contaminants like phenol that can be utilized by microbes can be oxidized quickly and completely, and those refractory contaminants like trichloroethylene remained unchanged. The study differentiates chemical and biological mechanisms for contaminant oxidation during sediment oxygenation.
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Affiliation(s)
- Chengwei Li
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan, Hubei 430078, PR China
| | - Yanting Zhang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan, Hubei 430078, PR China
| | - Yunsong Zheng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan, Hubei 430078, PR China
| | - Chongwen Shi
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan, Hubei 430078, PR China
| | - Yuxi Lu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan, Hubei 430078, PR China
| | - Yaoqiang Zhang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan, Hubei 430078, PR China
| | - Songhu Yuan
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan, Hubei 430078, PR China; Hubei Key Laboratory of Yangtze Catchment Environmental Aquatic Science, School of Environmental Studies, China University of Geosciences, 68 Jincheng Street, East Lake High-Tech Development Zone, Wuhan, Hubei 430078, PR China.
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4
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Westrick NM, Dominguez EG, Bondy M, Hull CM, Smith DL, Kabbage M. A single laccase acts as a key component of environmental sensing in a broad host range fungal pathogen. Commun Biol 2024; 7:348. [PMID: 38514801 PMCID: PMC10957995 DOI: 10.1038/s42003-024-06034-7] [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: 11/05/2023] [Accepted: 03/11/2024] [Indexed: 03/23/2024] Open
Abstract
Secreted laccases are important enzymes on a broad ecological scale for their role in mediating plant-microbe interactions, but within ascomycete fungi these enzymes have been primarily associated with melanin biosynthesis. In this study, a putatively secreted laccase, Sslac2, was characterized from the broad-host-range plant pathogen Sclerotinia sclerotiorum, which is largely unpigmented and is not dependent on melanogenesis for plant infection. Gene knockouts of Sslac2 demonstrate wide ranging developmental phenotypes and are functionally non-pathogenic. These mutants also displayed indiscriminate growth behaviors and enhanced biomass formation, seemingly as a result of their inability to respond to canonical environmental growth cues, a phenomenon further confirmed through chemical stress, physiological, and transcriptomic analyses. Transmission and scanning electron microscopy demonstrate apparent differences in extracellular matrix structure between WT and mutant strains that likely explain the inability of the mutants to respond to their environment. Targeting Sslac2 using host-induced gene silencing significantly improved resistance to S. sclerotiorum, suggesting that fungal laccases could be a valuable target of disease control. Collectively, we identified a laccase critical to the development and virulence of the broad-host-range pathogen S. sclerotiorum and propose a potentially novel role for fungal laccases in modulating environmental sensing.
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Affiliation(s)
- Nathaniel M Westrick
- Valley Laboratory, Connecticut Agricultural Experiment Station, Windsor, CT, USA
| | - Eddie G Dominguez
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, USA
| | - Madeline Bondy
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Christina M Hull
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, USA
| | - Damon L Smith
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA
| | - Mehdi Kabbage
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA.
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5
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Mou B, Gong G, Wu S. Biodegradation mechanisms of polycyclic aromatic hydrocarbons: Combination of instrumental analysis and theoretical calculation. CHEMOSPHERE 2023; 341:140017. [PMID: 37657699 DOI: 10.1016/j.chemosphere.2023.140017] [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: 08/18/2023] [Accepted: 08/29/2023] [Indexed: 09/03/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are a common class of petroleum hydrocarbons, widely encountered in both environment and industrial pollution sources. Owing to their toxicity, environmental persistence, and potential bioaccumulation properties, a mounting interest has been kindled in addressing the remediation of PAHs. Biodegradation is widely employed for the removal and remediation of PAHs due to its low cost, lack of second-contamination and ease of operation. This paper reviews the degradation efficiency of degradation and the underlying mechanisms exhibited by algae, bacteria, and fungi in remediation. Additionally, it delved into the application of modern instrumental analysis techniques and theoretical investigations in the realm of PAH degradation. Advanced instrumental analysis methods such as mass spectrometry provide a powerful tool for identifying intermediates and metabolites throughout the degradation process. Meanwhile, theoretical calculations could guide the optimization of degradation processes by revealing the reaction mechanisms and energy changes in PAH degradation. The combined use of instrumental analysis and theoretical calculations allows for a comprehensive understanding of the degradation mechanisms of PAHs and provides new insights and approaches for the development of environmental remediation technologies.
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Affiliation(s)
- Bolin Mou
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Guangyi Gong
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Shimin Wu
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.
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Wang J, Yin R, Hashizume Y, Todoroki Y, Mori T, Kawagishi H, Hirai H. Ergosterol and Its Metabolites Induce Ligninolytic Activity in the Lignin-Degrading Fungus Phanerochaete sordida YK-624. J Fungi (Basel) 2023; 9:951. [PMID: 37755059 PMCID: PMC10532932 DOI: 10.3390/jof9090951] [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: 08/29/2023] [Revised: 09/19/2023] [Accepted: 09/19/2023] [Indexed: 09/28/2023] Open
Abstract
White-rot fungi are the most important group of lignin biodegraders. Phanerochaete sordida YK-624 has higher ligninolytic activity than that of model white-rot fungi. However, the underlying mechanism responsible for lignin degradation by white-rot fungi remains unknown, and the induced compounds isolated from white-rot fungi for lignin degradation have never been studied. In the present study, we tried to screen ligninolytic-inducing compounds produced by P. sordida YK-624. After large-scale incubation of P. sordida YK-624, the culture and mycelium were separated by filtration. After the separation and purification, purified compounds were analyzed by high-resolution electrospray ionization mass spectrometry and nuclear magnetic resonance. The sterilized unbleached hardwood kraft pulp was used for the initial evaluation of ligninolytic activity. Ergosterol was isolated and identified and it induced the lignin-degrading activity of this fungus. Moreover, we investigated ergosterol metabolites from P. sordida YK-624, and the ergosterol metabolites ergosta-4,7,22-triene-3,6-dione and ergosta-4,6,8(14),22-tetraen-3-one were identified and then chemically synthesized. These compounds significantly improved the lignin-degrading activity of the fungus. This is the first report on the ligninolytic-inducing compounds produced by white-rot fungi.
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Affiliation(s)
- Jianqiao Wang
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou 510006, China;
| | - Ru Yin
- Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan;
| | - Yuki Hashizume
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan; (Y.H.); (Y.T.); (T.M.); (H.K.)
| | - Yasushi Todoroki
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan; (Y.H.); (Y.T.); (T.M.); (H.K.)
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Toshio Mori
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan; (Y.H.); (Y.T.); (T.M.); (H.K.)
- Research Institute for Mushroom Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Hirokazu Kawagishi
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan; (Y.H.); (Y.T.); (T.M.); (H.K.)
- Research Institute for Mushroom Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Hirofumi Hirai
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
- Research Institute for Mushroom Science, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
- Faculty of Global Interdisciplinary Science and Innovation, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
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7
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Mori T, Takahashi S, Soga A, Arimoto M, Kishikawa R, Yama Y, Dohra H, Kawagishi H, Hirai H. Aerobic H 2 production related to formate metabolism in white-rot fungi. FRONTIERS IN FUNGAL BIOLOGY 2023; 4:1201889. [PMID: 37746127 PMCID: PMC10512323 DOI: 10.3389/ffunb.2023.1201889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 06/05/2023] [Indexed: 09/26/2023]
Abstract
Biohydrogen is mainly produced by anaerobic bacteria, anaerobic fungi, and algae under anaerobic conditions. In higher eukaryotes, it is thought that molecular hydrogen (H2) functions as a signaling molecule for physiological processes such as stress responses. Here, it is demonstrated that white-rot fungi produce H2 during wood decay. The white-rot fungus Trametes versicolor produces H2 from wood under aerobic conditions, and H2 production is completely suppressed under hypoxic conditions. Additionally, oxalate and formate supplementation of the wood culture increased the level of H2 evolution. RNA-seq analyses revealed that T. versicolor oxalate production from the TCA/glyoxylate cycle was down-regulated, and conversely, genes encoding oxalate and formate metabolism enzymes were up-regulated. Although the involvement in H2 production of a gene annotated as an iron hydrogenase was uncertain, the results of organic acid supplementation, gene expression, and self-recombination experiments strongly suggest that formate metabolism plays a role in the mechanism of H2 production by this fungus. It is expected that this novel finding of aerobic H2 production from wood biomass by a white-rot fungus will open new fields in biohydrogen research.
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Affiliation(s)
- Toshio Mori
- Faculty of Agriculture, Shizuoka University, Shizuoka, Japan
- Research Institute for Mushroom Science, Shizuoka University, Shizuoka, Japan
| | - Saaya Takahashi
- Faculty of Agriculture, Shizuoka University, Shizuoka, Japan
| | - Ayumi Soga
- Faculty of Agriculture, Shizuoka University, Shizuoka, Japan
| | - Misa Arimoto
- Faculty of Agriculture, Shizuoka University, Shizuoka, Japan
| | | | - Yuhei Yama
- Faculty of Agriculture, Shizuoka University, Shizuoka, Japan
| | - Hideo Dohra
- Research Institute for Mushroom Science, Shizuoka University, Shizuoka, Japan
- Faculty of Science, Shizuoka University, Shizuoka, Japan
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
- Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Hirokazu Kawagishi
- Faculty of Agriculture, Shizuoka University, Shizuoka, Japan
- Research Institute for Mushroom Science, Shizuoka University, Shizuoka, Japan
| | - Hirofumi Hirai
- Faculty of Agriculture, Shizuoka University, Shizuoka, Japan
- Research Institute for Mushroom Science, Shizuoka University, Shizuoka, Japan
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
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8
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Hidalgo J, Epelde L, Anza M, Becerril JM, Garbisu C. Mycoremediation with Agaricus bisporus and Pleurotus ostreatus growth substrates versus phytoremediation with Festuca rubra and Brassica sp. for the recovery of a Pb and γ-HCH contaminated soil. CHEMOSPHERE 2023; 327:138538. [PMID: 36996916 DOI: 10.1016/j.chemosphere.2023.138538] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 06/19/2023]
Abstract
Mycoremediation with mushroom growth substrates can be used for the recovery of mixed contaminated soils due to the benefits derived from the physicochemical characteristics of the substrates, the activity of extracellular enzymes secreted by the fungi, and the presence of the fungal mycelia. The objective of this work was to assess the potential of Agaricus bisporus and Pleurotus ostreatus growth substrates (inoculated mushroom substrates vs. spent mushroom substrates) for the mycoremediation of soils co-contaminated with lead and lindane (γ-HCH). We compared the efficiency of these mycoremediation strategies with the phytoremediation with Brassica spp. Or Festuca rubra plants, in terms of both reduction in contaminant levels and enhancement of soil health. An enhanced soil health was achieved as a result of the application of mycoremediation treatments, compared to phytoremediation and control (untreated) treatments. The application of P. ostreatus inoculated substrate led to the most significant reduction in γ-HCH concentration (up to 88.9% compared to corresponding controls). In the presence of inoculated mushroom substrate, P. ostreatus fruiting bodies extracted more Pb than Brassica spp. Or F. rubra plants. Mycoremediation with P. ostreatus growth substrates appears a promising strategy for the recovery of the health of soils co-contaminated with Pb and γ-HCH.
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Affiliation(s)
- June Hidalgo
- Department of Conservation of Natural Resources, Soil Microbial Ecology Group, NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, 48160, Derio, Spain.
| | - Lur Epelde
- Department of Conservation of Natural Resources, Soil Microbial Ecology Group, NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, 48160, Derio, Spain
| | - Mikel Anza
- Department of Conservation of Natural Resources, Soil Microbial Ecology Group, NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, 48160, Derio, Spain
| | - José M Becerril
- Department of Plant Biology and Ecology, University of the Basque Country, UPV/EHU, P.O. Box 644, 48080, Bilbao, Spain
| | - Carlos Garbisu
- Department of Conservation of Natural Resources, Soil Microbial Ecology Group, NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, 48160, Derio, Spain
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9
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Buratti S, Rinaldi F, Calleri E, Bernardi M, Oliva D, Malgaretti M, De Girolamo G, Barucco B, Girometta CE, Savino E. Ganoderma resinaceum and Perenniporia fraxinea: Two Promising Wood Decay Fungi for Pharmaceutical Degradation. J Fungi (Basel) 2023; 9:jof9050555. [PMID: 37233267 DOI: 10.3390/jof9050555] [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: 04/06/2023] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 05/27/2023] Open
Abstract
Wood decay fungi (WDF) are a well-known source of enzymes and metabolites which have applications in numerous fields, including myco-remediation. Pharmaceuticals are becoming more problematic as environmental water pollutants due to their widespread use. In this study, Bjerkandera adusta, Ganoderma resinaceum, Perenniporia fraxinea, Perenniporia meridionalis and Trametes gibbosa were chosen from WDF strains maintained in MicUNIPV (the fungal research collection of the University of Pavia) to test their potential to degrade pharmaceuticals. The degradation potential was tested in spiked culture medium on diclofenac, paracetamol and ketoprofen, three of the most common pharmaceuticals, and irbesartan, a particularly difficult molecule to degrade. G. resinaceum and P. fraxinea were found to be the most effective at degradation, achieving 38% and 52% (24 h) and 72% and 49% (7 d) degradations of diclofenac, 25% and 73% (24 h) and 100% (7 d) degradations of paracetamol and 19% and 31% (24 h) and 64% and 67% (7 d) degradations of ketoprofen, respectively. Irbesartan was not affected by fungal activity. The two most active fungi, G. resinaceum and P. fraxinea, were tested in a second experiment in discharge wastewater collected from two different wastewater treatment plants in northern Italy. A high degradation was found in azithromycin, clarithromycin and sulfametoxazole (from 70% up to 100% in 7 days).
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Affiliation(s)
- Simone Buratti
- Department of Earth and Environmental Sciences, University of Pavia, 27100 Pavia, Italy
| | - Francesca Rinaldi
- Department of Drug Sciences, University of Pavia, 27100 Pavia, Italy
| | - Enrica Calleri
- Department of Drug Sciences, University of Pavia, 27100 Pavia, Italy
| | - Marco Bernardi
- CAP Holding Spa, Centro Ricerche Salazzurra, Via Circonvallazione Est, 20054 Segrate, Italy
| | - Desdemona Oliva
- CAP Holding Spa, Centro Ricerche Salazzurra, Via Circonvallazione Est, 20054 Segrate, Italy
| | | | | | | | | | - Elena Savino
- Department of Earth and Environmental Sciences, University of Pavia, 27100 Pavia, Italy
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10
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Bilal M, Zdarta J, Jesionowski T, Iqbal HMN. Manganese peroxidases as robust biocatalytic tool - An overview of sources, immobilization, and biotechnological applications. Int J Biol Macromol 2023; 234:123531. [PMID: 36754266 DOI: 10.1016/j.ijbiomac.2023.123531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/10/2023]
Abstract
With robust catalytic features, manganese peroxidases (MnPs) from various sources, including fungi and bacteria, have gained much consideration in many biotechnological applications with particular emphasis on environmental remediation. MnP is a heme-containing enzyme that belongs to the oxidoreductases that can catalyze the degradation of various organic pollutants, such as chlorophenols, nitroaromatic compounds, industrial dyes, and polycyclic aromatic hydrocarbons. To spotlight the MnP as biocatalytic tool, an effort has been put forward to cover the four major compartments. For instance, following a brief introduction, first, various microbial sources of MnP are discussed with examples. Second, structural attributes and biocatalytic features of MnP are given with examples. Third, different MnP immobilization strategies, including adsorption, covalent linking, entrapment, and cross-linking, are discussed with a significant motive to strengthen the enzyme's stability against diverse deactivation agents by restricting the conformational mobility of molecules. Compared to free counterparts, immobilized MnP fractions perform well in hostile environments. Finally, various biotechnological applications, such as fuel ethanol production, de-lignification, textile industry, pulp and paper industry, degradation of phenolic and non-phenolic compounds, and pharmaceutical and pesticide degradation, are briefly discussed.
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Affiliation(s)
- Muhammad Bilal
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, PL-60965 Poznan, Poland.
| | - Jakub Zdarta
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, PL-60965 Poznan, Poland
| | - Teofil Jesionowski
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, PL-60965 Poznan, Poland
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, 64849, Mexico; Institute of Advanced Materials for Sustainable Manufacturing, Tecnologico de Monterrey, Monterrey 64849, Mexico.
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11
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Ambika, Kumar V, Chandra D, Thakur V, Sharma U, Singh D. Depolymerization of lignin using laccase from Bacillus sp. PCH94 for production of valuable chemicals: A sustainable approach for lignin valorization. Int J Biol Macromol 2023; 234:123601. [PMID: 36775222 DOI: 10.1016/j.ijbiomac.2023.123601] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/19/2023] [Accepted: 02/05/2023] [Indexed: 02/12/2023]
Abstract
Lignin is the most abundant aromatic polymer in nature, and its depolymerization offers excellent opportunities to develop renewable aromatic chemicals. In the present study, Bacillus sp. PCH94 was investigated for laccase production and lignin depolymerization. Maximum production of laccase enzyme was achieved within 6.0 h at 50 °C on a natural lignocellulosic substrate. Furthermore, Bacillus sp. PCH94 was used to bioconvert lignin dimeric and polymeric substrates, validated using FT-IR, NMR (1H, 13C), and LCMS. Genome mining of Bacillus sp. PCH94 revealed laccase gene (lacBl) as multicopper oxidase (spore coat CotA). Further, lacBl from Bacillus sp. PCH94 was cloned, expressed, and kinetically characterized. LacBl enzyme showed activity for substrates ABTS (40.64 IU/mg), guaiacol (5.43 IU/mg), and DMP (11.93 IU/mg). The LacBl was active in higher temperatures (10 to 100 °C) and showed a half-life of 36 and 27 h at 50 and 60 °C, respectively. The purified LacBl was able to depolymerize kraft lignin into valuable products (ferulic acid and acetovanillone), which have applications in the pharmaceutical and food industries. Overall, the current study demonstrated the role of bacterial laccase in the depolymerization of lignin and opened a promising prospect for the green production of valuable compounds from recalcitrant lignin.
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Affiliation(s)
- Ambika
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh- 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad- 201002, India.
| | - Vijay Kumar
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh- 176061, India.
| | - Devesh Chandra
- Chemical Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh- 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad- 201002, India.
| | - Vikas Thakur
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh- 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad- 201002, India.
| | - Upendra Sharma
- Chemical Technology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh- 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad- 201002, India.
| | - Dharam Singh
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh- 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad- 201002, India.
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12
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Lee AA, Gervasio ED, Hughes RO, Maalouf AA, Musso SA, Crisalli AM, Woolridge EM. Alginate Encapsulation Stabilizes Xylanase Toward the Laccase Mediator System. Appl Biochem Biotechnol 2022; 195:3311-3326. [PMID: 36585551 DOI: 10.1007/s12010-022-04296-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2022] [Indexed: 01/01/2023]
Abstract
Xylanase, a hydrolytic enzyme, is susceptible to inactivation by the oxidative conditions generated by the laccase mediator system (LMS). Given the impetus to develop a mixed enzyme system for application in biomass processing industries, xylanase was encapsulated with either Cu2+- or Ca2+-alginate and then exposed to the LMS with variations such as mediator type, mediator concentration, and treatment pH. Results demonstrate that alginate-encapsulated xylanase retains substantial activity (> 80%) when exposed to the LMS relative to non-encapsulated xylanase. Cu2+-alginate generally provided better protection than Ca2+-alginate for all mediators, and protection was observed even at a low pH, where the LMS is most potent. Despite encapsulation, xylanase was still capable of hydrolyzing its polymeric substrate xylan, given kcat/Km values within an order of magnitude of that for non-encapsulated xylanase. The alginate matrix does not impede the function of the oxidized mediator, since comparable Vmax values were observed for the conversion of veratryl alcohol to veratraldehyde by free and Cu2+-alginate encapsulated laccase. Overall, these results support development of a mixed enzyme system for biomass delignification and, more broadly, show potential for protecting protein function in an oxidative environment.
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Affiliation(s)
- Annemarie A Lee
- Department of Chemistry, Biochemistry, & Physics, Marist College, Poughkeepsie, NY, 12601, USA
| | - Esabelle D Gervasio
- Department of Chemistry, Biochemistry, & Physics, Marist College, Poughkeepsie, NY, 12601, USA
| | - Riley O Hughes
- Department of Chemistry, Biochemistry, & Physics, Marist College, Poughkeepsie, NY, 12601, USA
| | - Alexandra A Maalouf
- Department of Chemistry, Biochemistry, & Physics, Marist College, Poughkeepsie, NY, 12601, USA
| | - Samantha A Musso
- Department of Chemistry, Biochemistry, & Physics, Marist College, Poughkeepsie, NY, 12601, USA
| | - Alicia M Crisalli
- Department of Chemistry, Biochemistry, & Physics, Marist College, Poughkeepsie, NY, 12601, USA
| | - Elisa M Woolridge
- Department of Chemistry, Biochemistry, & Physics, Marist College, Poughkeepsie, NY, 12601, USA.
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13
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Liu ZH, Li BZ, Yuan JS, Yuan YJ. Creative biological lignin conversion routes toward lignin valorization. Trends Biotechnol 2022; 40:1550-1566. [PMID: 36270902 DOI: 10.1016/j.tibtech.2022.09.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/18/2022] [Accepted: 09/22/2022] [Indexed: 11/05/2022]
Abstract
Lignin, the largest renewable aromatic resource, is a promising alternative feedstock for the sustainable production of various chemicals, fuels, and materials. Despite this potential, lignin is characterized by heterogeneous and macromolecular structures that must be addressed. In this review, we present biological lignin conversion routes (BLCRs) that offer opportunities for overcoming these challenges, making lignin valorization feasible. Funneling heterogeneous aromatics via a 'biological funnel' offers a high-specificity bioconversion route for aromatic platform chemicals. The inherent aromaticity of lignin drives atom-economic functionalization routes toward aromatic natural product generation. By harnessing the ligninolytic capacities of specific microbial systems, powerful aromatic ring-opening routes can be developed to generate various value-added products. Thus, BLCRs hold the promise to make lignin valorization feasible and enable a lignocellulose-based bioeconomy.
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Affiliation(s)
- Zhi-Hua Liu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
| | - Bing-Zhi Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China.
| | - Joshua S Yuan
- Department of Energy, Environmental, and Chemical Engineering, The McKelvey School of Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Ying-Jin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
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14
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Xu Z, Peng B, Kitata RB, Nicora CD, Weitz KK, Pu Y, Shi T, Cort JR, Ragauskas AJ, Yang B. Understanding of bacterial lignin extracellular degradation mechanisms by Pseudomonas putida KT2440 via secretomic analysis. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:117. [PMID: 36316752 PMCID: PMC9620641 DOI: 10.1186/s13068-022-02214-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 10/12/2022] [Indexed: 11/07/2022]
Abstract
BACKGROUND Bacterial lignin degradation is believed to be primarily achieved by a secreted enzyme system. Effects of such extracellular enzyme systems on lignin structural changes and degradation pathways are still not clearly understood, which remains as a bottleneck in the bacterial lignin bioconversion process. RESULTS This study investigated lignin degradation using an isolated secretome secreted by Pseudomonas putida KT2440 that grew on glucose as the only carbon source. Enzyme assays revealed that the secretome harbored oxidase and peroxidase/Mn2+-peroxidase capacity and reached the highest activity at 120 h of the fermentation time. The degradation rate of alkali lignin was found to be only 8.1% by oxidases, but increased to 14.5% with the activation of peroxidase/Mn2+-peroxidase. Gas chromatography-mass spectrometry (GC-MS) and two-dimensional 1H-13C heteronuclear single-quantum coherence (HSQC) NMR analysis revealed that the oxidases exhibited strong C-C bond (β-β, β-5, and β-1) cleavage. The activation of peroxidases enhanced lignin degradation by stimulating C-O bond (β-O-4) cleavage, resulting in increased yields of aromatic monomers and dimers. Further mass spectrometry-based quantitative proteomics measurements comprehensively identified different groups of enzymes particularly oxidoreductases in P. putida secretome, including reductases, peroxidases, monooxygenases, dioxygenases, oxidases, and dehydrogenases, potentially contributed to the lignin degradation process. CONCLUSIONS Overall, we discovered that bacterial extracellular degradation of alkali lignin to vanillin, vanillic acid, and other lignin-derived aromatics involved a series of oxidative cleavage, catalyzed by active DyP-type peroxidase, multicopper oxidase, and other accessory enzymes. These results will guide further metabolic engineering design to improve the efficiency of lignin bioconversion.
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Affiliation(s)
- Zhangyang Xu
- grid.451303.00000 0001 2218 3491Bioproducts, Sciences & Engineering Laboratory, Department of Biological Systems Engineering, ashington State University Tri-Cities, Joint Appointment: Pacific Northwest National Laboratory, 2710 Crimson Way, Richland, WA 99354 USA
| | - Bo Peng
- grid.451303.00000 0001 2218 3491Bioproducts, Sciences & Engineering Laboratory, Department of Biological Systems Engineering, ashington State University Tri-Cities, Joint Appointment: Pacific Northwest National Laboratory, 2710 Crimson Way, Richland, WA 99354 USA
| | - Reta Birhanu Kitata
- grid.451303.00000 0001 2218 3491Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 USA
| | - Carrie D. Nicora
- grid.451303.00000 0001 2218 3491Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 USA
| | - Karl K. Weitz
- grid.451303.00000 0001 2218 3491Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 USA
| | - Yunqiao Pu
- grid.135519.a0000 0004 0446 2659Joint Institute for Biological Sciences, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Tujin Shi
- grid.451303.00000 0001 2218 3491Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 USA
| | - John R. Cort
- grid.451303.00000 0001 2218 3491Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 USA
| | - Arthur J. Ragauskas
- grid.135519.a0000 0004 0446 2659Joint Institute for Biological Sciences, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA ,grid.411461.70000 0001 2315 1184Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996 USA ,grid.411461.70000 0001 2315 1184Department of Forestry, Wildlife, and Fisheries, Center for Renewable Carbon, University of Tennessee Institute of Agriculture, Knoxville, TN 37996 USA
| | - Bin Yang
- grid.451303.00000 0001 2218 3491Bioproducts, Sciences & Engineering Laboratory, Department of Biological Systems Engineering, ashington State University Tri-Cities, Joint Appointment: Pacific Northwest National Laboratory, 2710 Crimson Way, Richland, WA 99354 USA ,grid.451303.00000 0001 2218 3491Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352 USA
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15
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Shinde R, Shahi DK, Mahapatra P, Naik SK, Thombare N, Singh AK. Potential of lignocellulose degrading microorganisms for agricultural residue decomposition in soil: A review. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 320:115843. [PMID: 36056484 DOI: 10.1016/j.jenvman.2022.115843] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 07/16/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Lignocellulosic crop residues (LCCRs) hold a significant share of the terrestrial biomass, estimated at 5 billion Mg per annum globally. A massive amount of these LCCRs are burnt in many countries resulting in immense environmental pollution; hence, its proper disposal in a cost-effective and eco-friendly manner is a significant challenge. Among the different options for management of LCCRs, the use of lignocellulose degrading microorganisms (LCDMOs), like fungi and bacteria, has emerged as an eco-friendly and effective way for its on-site disposal. LCDMOs achieve degradation through various mechanisms, including multiple supportive enzymes, causing oxidative attacks by which recalcitrance of lignocellulose material is reduced, paving the way to further activity by depolymerizing enzymes. This improves the physical properties of soil, recycles plant nutrients, promotes plant growth and thus helps improve productivity. Rapid and proper microbial degradation may be achieved through the correct combination of the LCDMOs, supplementing nutrients and controlling different factors affecting microbial activity in the field. The review is a critical discussion of previous studies revealing the potential of individuals or a set of LCDMOs, factors controlling the rate of degradation and the key researchable areas for better understanding of the role of these decomposers for future use.
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Affiliation(s)
- Reshma Shinde
- ICAR- Research Complex for Eastern Region, Farming System Research Centre for Hill and Plateau Region, Ranchi, 834010, Jharkhand, India.
| | | | | | - Sushanta Kumar Naik
- ICAR- Research Complex for Eastern Region, Farming System Research Centre for Hill and Plateau Region, Ranchi, 834010, Jharkhand, India
| | - Nandkishore Thombare
- ICAR- Indian Institute of Natural Resin and Gums, Ranchi, 834010, Jharkhand, India
| | - Arun Kumar Singh
- ICAR- Research Complex for Eastern Region, Farming System Research Centre for Hill and Plateau Region, Ranchi, 834010, Jharkhand, India
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16
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Cribari MA, Unger MJ, Martell JD. A Horseradish Peroxidase-Mediator System for Benzylic C-H Activation. ACS Catal 2022; 12:12246-12252. [PMID: 37153120 PMCID: PMC10162642 DOI: 10.1021/acscatal.2c03424] [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] [Indexed: 11/29/2022]
Abstract
Enzyme-mediator systems generate radical intermediates that abstract hydrogen atoms under mild conditions. These systems have been employed extensively for alcohol oxidation, primarily in biomass degradation, but they are underexplored for direct activation of C(sp3)-H bonds in alkyl groups. Here, we combine horseradish peroxidase (HRP), H2O2, and redox mediator N-hydroxyphthalimide (NHPI) for C(sp3)-H functionalization of alkylbenzene-type substrates. The HRP-NHPI system is >10-fold more active than existing enzyme-mediator systems in converting alkylbenzenes to ketones and aldehydes under air, and it operates from 0-50 °C and in numerous aqueous-organic solvent mixtures. The benzylic substrate radical can be trapped through a reaction with NHPI, demonstrating the formation of benzylic products beyond ketones. Furthermore, we demonstrate a one-pot, two-step enzymatic cascade for converting alkylbenzenes to benzylic amines. Overall, the HRP-NHPI system enables the selective benzylic C-H functionalization of diverse substrates under mild conditions using a straightforward procedure.
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Affiliation(s)
- Mario A. Cribari
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI, 53706, USA
| | - Maxwell J. Unger
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI, 53706, USA
| | - Jeffrey D. Martell
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI, 53706, USA
- Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53703, USA
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17
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Sun K, Liu Q, Liu J, Li S, Qi X, Chen M, Si Y, Gao Y. New insights into humic acid-boosted conversion of bisphenol A by laccase-activated co-polyreaction: Kinetics, products, and phytotoxicity. JOURNAL OF HAZARDOUS MATERIALS 2022; 436:129269. [PMID: 35739784 DOI: 10.1016/j.jhazmat.2022.129269] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/24/2022] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
How humic acid (HA) modifies bisphenol A (BPA) conversion in exoenzyme-activated polyreaction is poorly understood. Herein, the influencing mechanism of HA on laccase-induced BPA self-polymerization was investigated, and the phytotoxicity of the produced BPA self/co-polymers was assessed for the first time. HA prominently boosted BPA elimination, and the rate constants of BPA conversion augmented from 0.61 to 1.43 h-1 as HA level raised from 0 to 50 mg·L-1. It is because the generated BPA-HA co-polymers promptly lowered the yields of long-chain BPA self-oligomers, consequently maintaining laccase activity through opening enzymatic substrate-binding pockets. Notably, a few BPA monomers were re-released from the loosely bound self-polymers and co-polymers, and the releasing amounts respectively were 13.9 - 22.4% and 0.3 - 0.5% at pH 2 - 11. Formation of self/co-polymers was greatly conducive to avoiding BPA biotoxicity. Compared with BPA self-polymers, the phytotoxicity of BPA co-polymers to germinated radish (Raphanus sativus L.) seeds was lower due to these covalently bound products were more complex and stable. It follows that laccase-mediated co-polymerization played a significant role in BPA conversion, contaminant detoxification, and carbon sequestration. These findings are not only beneficial to clarifying exoenzyme-activated the generation mechanism of BPA co-polymers in water, but to reusing these supramolecular aggregates in crop growth.
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Affiliation(s)
- Kai Sun
- College of Resources and Environment, Anhui Agricultural University, Hefei 230036, Anhui, China.
| | - Qingzhu Liu
- College of Resources and Environment, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Jie Liu
- College of Resources and Environment, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Shunyao Li
- Laboratory of Wetland Protection and Ecological Restoration, Anhui University, Hefei 230601, Anhui, China.
| | - Xuemin Qi
- College of Resources and Environment, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Meihua Chen
- College of Resources and Environment, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Youbin Si
- College of Resources and Environment, Anhui Agricultural University, Hefei 230036, Anhui, China.
| | - Yanzheng Gao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
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18
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Shao Q, Li X, Chen Y, Zhang Z, Cui Y, Fan H, Wei D. Investigations on the Fusants From Wide Cross Between White-Rot Fungi and Saccharomyces cerevisiae Reveal Unknown Lignin Degradation Mechanism. Front Microbiol 2022; 13:935462. [PMID: 35898904 PMCID: PMC9310788 DOI: 10.3389/fmicb.2022.935462] [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: 05/04/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
The degradation of lignocellulose by fungi, especially white-rot fungi, contributes a lot to carbon cycle, bio-fuel production, and many other bio-based applications. However, the existing enzymatic and non-enzymatic degradation mechanisms cannot be unequivocally supported by in vitro simulation experiment, meaning that additional mechanisms might exist. Right now, it is still very difficult to discover new mechanisms with traditional forward genetic approaches. To disclose novel lignin degradation mechanisms in white-rot fungi, a series of fusants from wide cross by protoplast fusion between Pleurotus ostreatus, a well-known lignin-degrading fungus, and Saccharomyces cerevisiae, a well-known model organism unable to degrade lignocellulose, was investigated regarding their abilities to degrade lignin. By analyzing the activity of traditional lignin-degrading enzyme, the ability to utilize pure lignin compounds and degrade corn stalk, a fusant D1-P was screened out and proved not to contain well-recognized lignin-degrading enzyme genes by whole-genome sequencing. Further investigation with two-dimension nuclear magnetic resonance (NMR) shows that D1-P was found to be able to degrade the main lignin structure β-O-4 linkage, leading to reduced level of this structure like that of the wild-type strain P. ostreatus after a 30-day semi-solid fermentation. It was also found that D1-P shows a degradation preference to β-O-4 linkage in Aβ(S)-threo. Therefore, wide cross between white-rot fungi and S. cerevisiae provides a powerful tool to uncover novel lignocellulose degradation mechanism that will contribute to green utilization of lignocellulose to produce bio-fuel and related bio-based refinery.
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Affiliation(s)
- Qi Shao
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Xin Li
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Ying Chen
- Institute of Agro-Products Preservation and Processing Technology, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Zhijun Zhang
- Institute of Agro-Products Preservation and Processing Technology, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Yong Cui
- Tianjin Tianren Century Technology Co., Ltd., Tianjin, China
| | - Huan Fan
- Institute of Animal Husbandry and Veterinary Research, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Dongsheng Wei
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
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19
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Combining Desirable Traits for a Good Biocontrol Strategy against Sclerotinia sclerotiorum. Microorganisms 2022; 10:microorganisms10061189. [PMID: 35744707 PMCID: PMC9228387 DOI: 10.3390/microorganisms10061189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/02/2022] [Accepted: 06/07/2022] [Indexed: 02/05/2023] Open
Abstract
The fungal pathogen Sclerotinia sclerotiorum (Helotiales: Sclerotiniaceae) causes white mold, a disease that leads to substantial losses on a wide variety of hosts throughout the world. This economically important fungus affects yield and seed quality, and its control mostly relies on the use of environmentally damaging fungicides. This review aimed to present the latest discoveries on microorganisms and the biocontrol mechanisms used against white mold. A special focus is put on the identification of biocontrol desirable traits required for efficient disease control. A better understanding of the mechanisms involved and the conditions required for their action is also essential to ensure a successful implementation of biocontrol under commercial field conditions. In this review, a brief introduction on the pathogen, its disease cycle, and its main pathogenicity factors is presented, followed by a thorough description of the microorganisms that have so far demonstrated biocontrol potential against white mold and the mechanisms they use to achieve control. Antibiosis, induced systemic resistance, mycoparasitism, and hypovirulence are discussed. Finally, based on our actual knowledge, the best control strategies against S. sclerotiorum that are likely to succeed commercially are discussed, including combining biocontrol desirable traits of particular interest.
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20
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Jian T, Zhou Y, Wang P, Yang W, Mu P, Zhang X, Zhang X, Chen CL. Highly stable and tunable peptoid/hemin enzymatic mimetics with natural peroxidase-like activities. Nat Commun 2022; 13:3025. [PMID: 35641490 PMCID: PMC9156750 DOI: 10.1038/s41467-022-30285-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 04/25/2022] [Indexed: 02/05/2023] Open
Abstract
Developing tunable and stable peroxidase mimetics with high catalytic efficiency provides a promising opportunity to improve and expand enzymatic catalysis in lignin depolymerization. A class of peptoid-based peroxidase mimetics with tunable catalytic activity and high stability is developed by constructing peptoids and hemins into self-assembled crystalline nanomaterials. By varying peptoid side chain chemistry to tailor the microenvironment of active sites, these self-assembled peptoid/hemin nanomaterials (Pep/hemin) exhibit highly modulable catalytic activities toward two lignin model substrates 2,2-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) and 3,3’,5,5’-tetramethylbenzidine. Among them, a Pep/hemin complex containing the pyridyl side chain showed the best catalytic efficiency (Vmax/Km = 5.81 × 10−3 s−1). These Pep/hemin catalysts are highly stable; kinetics studies suggest that they follow a peroxidase-like mechanism. Moreover, they exhibit a high efficacy on depolymerization of a biorefinery lignin. Because Pep/hemin catalysts are highly robust and tunable, we expect that they offer tremendous opportunities for lignin valorization to high value products. Peroxidase mimics are currently being investigated as catalysts for lignin depolymerisation. In this article, the authors investigate a class of self-assembled and highly stable peptoid/hemin nanomaterials as peroxidase mimics that are highly stable and tuneable for the depolymerisation of a biorefinery lignin.
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Affiliation(s)
- Tengyue Jian
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Yicheng Zhou
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.,The Voiland School of Chemical Engineering and Bioengineering, Washington State University, Richland, WA, 99354, USA
| | - Peipei Wang
- The Voiland School of Chemical Engineering and Bioengineering, Washington State University, Richland, WA, 99354, USA
| | - Wenchao Yang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.,School of Chemical Engineering and Technology, State Key Laboratory of Chemical Engineering, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Peng Mu
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.,Department of Mechanical Engineering and Materials Science and Engineering Program, State University of New York, Binghamton, NY, 13902, USA
| | - Xin Zhang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Xiao Zhang
- The Voiland School of Chemical Engineering and Bioengineering, Washington State University, Richland, WA, 99354, USA.
| | - Chun-Long Chen
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA. .,Department of Chemical Engineering, University of Washington, Seattle, WA, 98195, USA.
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21
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Barcoto MO, Rodrigues A. Lessons From Insect Fungiculture: From Microbial Ecology to Plastics Degradation. Front Microbiol 2022; 13:812143. [PMID: 35685924 PMCID: PMC9171207 DOI: 10.3389/fmicb.2022.812143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/15/2022] [Indexed: 11/13/2022] Open
Abstract
Anthropogenic activities have extensively transformed the biosphere by extracting and disposing of resources, crossing boundaries of planetary threat while causing a global crisis of waste overload. Despite fundamental differences regarding structure and recalcitrance, lignocellulose and plastic polymers share physical-chemical properties to some extent, that include carbon skeletons with similar chemical bonds, hydrophobic properties, amorphous and crystalline regions. Microbial strategies for metabolizing recalcitrant polymers have been selected and optimized through evolution, thus understanding natural processes for lignocellulose modification could aid the challenge of dealing with the recalcitrant human-made polymers spread worldwide. We propose to look for inspiration in the charismatic fungal-growing insects to understand multipartite degradation of plant polymers. Independently evolved in diverse insect lineages, fungiculture embraces passive or active fungal cultivation for food, protection, and structural purposes. We consider there is much to learn from these symbioses, in special from the community-level degradation of recalcitrant biomass and defensive metabolites. Microbial plant-degrading systems at the core of insect fungicultures could be promising candidates for degrading synthetic plastics. Here, we first compare the degradation of lignocellulose and plastic polymers, with emphasis in the overlapping microbial players and enzymatic activities between these processes. Second, we review the literature on diverse insect fungiculture systems, focusing on features that, while supporting insects' ecology and evolution, could also be applied in biotechnological processes. Third, taking lessons from these microbial communities, we suggest multidisciplinary strategies to identify microbial degraders, degrading enzymes and pathways, as well as microbial interactions and interdependencies. Spanning from multiomics to spectroscopy, microscopy, stable isotopes probing, enrichment microcosmos, and synthetic communities, these strategies would allow for a systemic understanding of the fungiculture ecology, driving to application possibilities. Detailing how the metabolic landscape is entangled to achieve ecological success could inspire sustainable efforts for mitigating the current environmental crisis.
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Affiliation(s)
- Mariana O. Barcoto
- Center for the Study of Social Insects, São Paulo State University (UNESP), Rio Claro, Brazil
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, Brazil
| | - Andre Rodrigues
- Center for the Study of Social Insects, São Paulo State University (UNESP), Rio Claro, Brazil
- Department of General and Applied Biology, São Paulo State University (UNESP), Rio Claro, Brazil
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Pacetti A, Moretti S, Perrin C, Gelhaye E, Bieler E, Kassemeyer HH, Mugnai L, Farine S, Bertsch C. Grapevine Wood-Degrading Activity of Fomitiporia mediterranea M. Fisch.: A Focus on the Enzymatic Pathway Regulation. Front Microbiol 2022; 13:844264. [PMID: 35369524 PMCID: PMC8971955 DOI: 10.3389/fmicb.2022.844264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 02/04/2022] [Indexed: 11/13/2022] Open
Abstract
Fomitiporia mediterranea is a Basidiomycetes fungus associated with some of the Esca complex diseases and responsible for decay in grapevine wood. Its role in the onset of foliar symptoms has recently been reconsidered, mainly after evidence showing a reduction in foliar symptom expression after removal of rotten wood. The study of its degradation pathways has already been approached by other authors, and with this study much information is consolidated. A microscopic observation of degraded wood provides a first approach to the characterization of F. mediterranea modalities of wood cellular structure degradation. The decay of grapevine wood was reproduced in vitro, and the measurement of each wood-forming polymer loss highlighted characteristics of F. mediterranea common to selective white rot and showed how fungal strain and vine variety are factors determining the wood degradation. All these observations were supported by the analysis of the laccase and manganese peroxidase enzyme activity, as well as by the expression of the genes coding 6 putative laccase isoforms and 3 manganese peroxidase isoforms, thereby highlighting substantial intraspecific variability.
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Affiliation(s)
- Andrea Pacetti
- Laboratoire Vigne Biotechnologies et Environnement UR-3991, Université de Haute Alsace, Colmar, France
- Department of Agricultural, Food, Environmental and Forestry Science and Technology (DAGRI), Plant Pathology and Entomology Section, University of Florence, Florence, Italy
| | - Samuele Moretti
- Laboratoire Vigne Biotechnologies et Environnement UR-3991, Université de Haute Alsace, Colmar, France
| | - Célia Perrin
- Laboratoire Vigne Biotechnologies et Environnement UR-3991, Université de Haute Alsace, Colmar, France
| | - Eric Gelhaye
- Faculté des Sciences et Technologies Boulevard des Aiguillettes, UMR IAM - Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Evi Bieler
- Swiss Nanoscience Institute (SNI) – Nano Imaging, University of Basel, Basel, Switzerland
| | - Hanns-Heinz Kassemeyer
- Swiss Nanoscience Institute (SNI) – Nano Imaging, University of Basel, Basel, Switzerland
- State Institute for Viticulture, Plant Pathology & Diagnostics, Freiburg, Germany
- Faculty of Biology, Plant Biomechanics Group and Botanic Garden, Albert-Ludwigs-Universität Freiburg, Freiburg im Breisgau, Germany
| | - Laura Mugnai
- Department of Agricultural, Food, Environmental and Forestry Science and Technology (DAGRI), Plant Pathology and Entomology Section, University of Florence, Florence, Italy
| | - Sibylle Farine
- Laboratoire Vigne Biotechnologies et Environnement UR-3991, Université de Haute Alsace, Colmar, France
| | - Christophe Bertsch
- Laboratoire Vigne Biotechnologies et Environnement UR-3991, Université de Haute Alsace, Colmar, France
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Radical generation and fate control for photocatalytic biomass conversion. Nat Rev Chem 2022; 6:197-214. [PMID: 37117437 DOI: 10.1038/s41570-022-00359-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/12/2022] [Indexed: 12/30/2022]
Abstract
Photocatalysis is an emerging approach for sustainable chemical production from renewable biomass under mild conditions. Active radicals are always generated as key intermediates, in which their high reactivity renders them versatile for various upgrading processes. However, controlling their reaction is a challenge, especially in highly functionalized biomass frameworks. In this Review, we summarize recent advanced photocatalytic systems for selective biomass valorization, with an emphasis on their distinct radical-mediated reaction patterns. The strategies for generating a specific radical intermediate and controlling its subsequent conversion towards desired chemicals are also highlighted, aiming to provide guidance for future studies. We believe that taking full advantage of the unique reactivity of radical intermediates would provide great opportunities to develop more efficient photocatalytic systems for biomass valorization.
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Sagarika MS, Parameswaran C, Senapati A, Barala J, Mitra D, Prabhukarthikeyan SR, Kumar A, Nayak AK, Panneerselvam P. Lytic polysaccharide monooxygenases (LPMOs) producing microbes: A novel approach for rapid recycling of agricultural wastes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150451. [PMID: 34607097 DOI: 10.1016/j.scitotenv.2021.150451] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/12/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Out of the huge quantity of agricultural wastes produced globally, rice straw is one of the most abundant ligno-cellulosic waste. For efficient utilization of these wastes, several cost-effective biological processes are available. The practice of field level in-situ or ex-situ decomposition of rice straw is having less degree of adoption due to its poor decomposition ability within a short time span between rice harvest and sowing of the next crop. Agricultural wastes including rice straw are in general utilized by using lignocellulose degrading microbes for industrial metabolite or compost production. However, bioconversion of crystalline cellulose and lignin present in the waste, into simple molecules is a challenging task. To resolve this issue, researchers have identified a novel new generation microbial enzyme i.e., lytic polysaccharide monooxygenases (LPMOs) and reported that the combination of LPMOs with other glycolytic enzymes are found efficient. This review explains the progress made in LPMOs and their role in lignocellulose bioconversion and the possibility of exploring LPMOs producers for rapid decomposition of agricultural wastes. Also, it provides insights to identify the knowledge gaps in improving the potential of the existing ligno-cellulolytic microbial consortium for efficient utilization of agricultural wastes at industrial and field levels.
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Affiliation(s)
- Mahapatra Smruthi Sagarika
- ICAR - National Rice Research Institute, Cuttack, Odisha 753006, India; Indira Gandhi Agricultural University, Raipur, Chhattisgarh 492012, India
| | | | - Ansuman Senapati
- ICAR - National Rice Research Institute, Cuttack, Odisha 753006, India
| | - Jatiprasad Barala
- ICAR - National Rice Research Institute, Cuttack, Odisha 753006, India
| | - Debasis Mitra
- ICAR - National Rice Research Institute, Cuttack, Odisha 753006, India
| | | | - Anjani Kumar
- ICAR - National Rice Research Institute, Cuttack, Odisha 753006, India
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Effect of ligninolytic axenic and coculture white-rot fungi on rice straw chemical composition and in vitro fermentation characteristics. Sci Rep 2022; 12:1129. [PMID: 35064211 PMCID: PMC8782829 DOI: 10.1038/s41598-022-05107-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 01/06/2022] [Indexed: 01/19/2023] Open
Abstract
The study sought to investigate the potentials of axenic cultures of Pleurotus ostreatus, Phanerochaete chrysosporium and their coculture (P. chrysosporium and P. ostreatus) to break down lignin and to enhance the rumen fermentability of rice straw. Rice straw was fermented by two lignin-degrading fungi, namely, P. ostreatus, P. chrysosporium and its coculture (P. ostreatus and P. chrysosporium) with uninoculated straw as control under solid-state fermentation employing a completely randomized research design. The coculture exhibited a mutual intermingling plus inhibition interaction. The fungi treatment increased the crude protein from (5.1%) in the control to (6.5%, 6.6%, and 6.7%) in the P. ostreatus, P. chrysosporium and coculture respectively. The coculture treated straw had a lower lignin content (5.3%) compared to the P. chrysosporium (6.2%) with the P. ostreatus recording the least (3.3%) lignin fraction. Treatment of rice straw with coculture improved the in vitro dry matter digestibility (68.1%), total volatile fatty acids (35.3 mM), and total gas (57.4 ml/200 mg) compared to P. chrysosporium (45.1%, 32.2 mM, 44.4 ml/200 mg) but was second to P. ostreatus (75.3%, 38.3 mM, 65.6 ml/200 mg). Instead of an anticipated synergistic effect from the coculture, a competitive antagonistic effect was rather observed at the end of the study, a condition that can be attributed to the coculture behavior.
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26
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Banerjee A, Show BK, Chaudhury S, Balachandran S. Biological pretreatment for enhancement of biogas production. COST EFFECTIVE TECHNOLOGIES FOR SOLID WASTE AND WASTEWATER TREATMENT 2022:101-114. [DOI: 10.1016/b978-0-12-822933-0.00020-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2023]
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27
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Bazzicalupo A, Gonçalves SC, Hébert R, Jakob S, Justo A, Kernaghan G, Lebeuf R, Malloch B, Thorn RG, Walker AK. Macrofungal conservation in Canada and target species for assessment: a starting point. Facets (Ott) 2022. [DOI: 10.1139/facets-2021-0180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Despite the ecological importance of fungi, we still know little about their diversity in Canada. One of the largest hurdles to implementing fungal conservation initiatives is the lack of fungal distribution data. As anthropogenic impacts accelerate the speed of environmental change, it is imperative that we fill this major information gap, critical for fungal protection. To gain insight on the conservation status of Canadian macrofungi, we took advantage of the large and growing body of fungal biodiversity data from government research ( Wild Species 2020), citizen science, trained independent mycologists, university, and museum biodiversity research. The majority of macrofungi are data deficient; we do not know their geographic distribution or habitat requirements, occurrence, or abundance in Canada. For mushrooms that fruit only a few days of the year and are often difficult to positively identify, there is a lot of work to overcome the uncertainty of distinguishing under-sampling from rarity. Our work stresses the importance of building a strong network of professional and amateur mycologists to develop resources, disseminate information to make educated decisions, and advance conservation actions. We found that several fungi can be prioritized; we present a short list for consideration for formal conservation assessment.
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Affiliation(s)
- Anna Bazzicalupo
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Susana C. Gonçalves
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Rémi Hébert
- Canadian Wildlife Service, Environment and Climate Change Canada, Government of Canada, Gatineau, QC K1A 0H3, Canada
| | - Sigrid Jakob
- New York Mycological Society, New York, NY 11215, USA
| | - Alfredo Justo
- New Brunswick Museum, Saint John, NB E2K 1E5, Canada
| | - Gavin Kernaghan
- Department of Biology, Mount St. Vincent University, Halifax, NS B3M 2J6, Canada
| | - Renée Lebeuf
- Cercle des Mycologues de Lanaudière et de la Mauricie, L’Assomption, QC J5W 1G6, Canada
| | - Bruce Malloch
- Department of Biology, University of Western Ontario, London, ON N6A 5B7, Canada
| | - R. Greg Thorn
- Department of Biology, University of Western Ontario, London, ON N6A 5B7, Canada
| | - Allison K. Walker
- Department of Biology, Acadia University, Wolfville, NS B4P 2R6, Canada
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Nakagaki S, Machado GS, Stival JF, Henrique dos Santos E, Silva GM, Wypych F. Natural and synthetic layered hydroxide salts (LHS): Recent advances and application perspectives emphasizing catalysis. PROG SOLID STATE CH 2021. [DOI: 10.1016/j.progsolidstchem.2021.100335] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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29
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Cajnko MM, Oblak J, Grilc M, Likozar B. Enzymatic bioconversion process of lignin: mechanisms, reactions and kinetics. BIORESOURCE TECHNOLOGY 2021; 340:125655. [PMID: 34388661 DOI: 10.1016/j.biortech.2021.125655] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
Lignin is a wasted renewable source of biomass-derived value-added chemicals. However, due to its material resistance to degradation, it remains highly underutilized. In order to develop new, catalysed and more environment friendly reaction processes for lignin valorization, science has turned a selective concentrated attention to microbial enzymes. This present work looks at the enzymes involved with the main reference focus on the different elementary mechanisms of action/conversion rate kinetics. Pathways, like with laccases/peroxidases, employ radicals, which more readily result in polymerization than de-polymerization. The β-etherase system interaction of proteins targets β-O-4 ether covalent bond, which targets lower molecular weight product species. Enzymatic activity is influenced by a wide variety of different factors which need to be considered in order to obtain the best functionality and synthesis yields.
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Affiliation(s)
- Miša Mojca Cajnko
- Department of Catalysis and Chemical Reaction Engineering, National Institute of Chemistry, NIC, Hajdrihova, 19, SI-1001 Ljubljana, Slovenia
| | - Jošt Oblak
- Department of Catalysis and Chemical Reaction Engineering, National Institute of Chemistry, NIC, Hajdrihova, 19, SI-1001 Ljubljana, Slovenia
| | - Miha Grilc
- Department of Catalysis and Chemical Reaction Engineering, National Institute of Chemistry, NIC, Hajdrihova, 19, SI-1001 Ljubljana, Slovenia
| | - Blaž Likozar
- Department of Catalysis and Chemical Reaction Engineering, National Institute of Chemistry, NIC, Hajdrihova, 19, SI-1001 Ljubljana, Slovenia.
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30
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Perez SB, Fraterrigo JM, Dalling JW. Interspecific wood trait variation predicts decreased carbon residence time in changing forests. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sierra B. Perez
- Program in Ecology, Evolution, and Conservation Biology University of Illinois at Urbana‐Champaign Urbana IL USA
| | - Jennifer M. Fraterrigo
- Program in Ecology, Evolution, and Conservation Biology University of Illinois at Urbana‐Champaign Urbana IL USA
- Department of Natural Resources and Environmental Sciences University of Illinois at Urbana‐Champaign Urbana IL USA
| | - James W. Dalling
- Program in Ecology, Evolution, and Conservation Biology University of Illinois at Urbana‐Champaign Urbana IL USA
- Department of Plant Biology University of Illinois at Urbana‐Champaign Urbana IL USA
- Smithsonian Tropical Research Institute Ancon Apartado Republic of Panama
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31
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Henn KA, Forsman N, Zou T, Österberg M. Colloidal Lignin Particles and Epoxies for Bio-Based, Durable, and Multiresistant Nanostructured Coatings. ACS APPLIED MATERIALS & INTERFACES 2021; 13:34793-34806. [PMID: 34261310 PMCID: PMC8397241 DOI: 10.1021/acsami.1c06087] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
There is a need for safe and sustainable alternatives in the coating industry. Bio-based coatings are interesting in this perspective. Although various oils and waxes have been used as traditional wood coatings, they often lack sufficient durability. Lignin is an abundant natural polyphenol that can be used to cure epoxies, but its poor water solubility has impeded the use of unmodified lignin in coatings in the past. To address this issue, water-dispersible colloidal lignin particles (CLPs) and an epoxy compound, glycerol diglycidyl ether (GDE), were used to prepare multiprotective bio-based surface coatings. With the GDE/CLP ratios of 0.65 and 0.52 g/g, the cured CLP-GDE films became highly resistant to abrasion and heat. When applied as a coating on wooden substrates, the particulate morphology enabled effective protection against water, stains, and sunlight with very thin layers (less than half the weight of commercial coatings) while retaining the wood's breathability excellently. Optimal hydrophobicity was reached with a coat weight of 6.9 g(CLP)/m2, resulting in water contact angle values of up to 120°. Due to their spherical shape and chemical structure, the CLPs acted as both a hardener and a particulate component in the coating, which removed the need for an underlying binding polymer matrix. Light interferometry measurements showed that while commercial polymeric film-forming coatings smoothened the substrate noticeably, the particulate morphology retained the substrate's roughness in lightweight coatings, allowing for a high water contact angle. This work presents new strategies for lignin applications in durable particulate coatings and their advantages compared to both currently used synthetic and bio-based coatings.
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Candotto Carniel F, Fortuna L, Zanelli D, Garrido M, Vázquez E, González VJ, Prato M, Tretiach M. Graphene environmental biodegradation: Wood degrading and saprotrophic fungi oxidize few-layer graphene. JOURNAL OF HAZARDOUS MATERIALS 2021; 414:125553. [PMID: 34030410 DOI: 10.1016/j.jhazmat.2021.125553] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 02/02/2021] [Accepted: 02/25/2021] [Indexed: 06/12/2023]
Abstract
The environmental biodegradability profile of graphene related materials (GRMs) is important to know in order to predict whether these materials will accumulate in soil or will be transformed by primary decomposers. In this study, few-layer graphene (FLG) was exposed to living and devitalized axenic cultures of two white-rot basidiomycetes (Bjerkandera adusta and Phanerochaete chrysosporium) and one soil saprotrophic ascomycete (Morchella esculenta) with or without lignin, for a period of four months. Over this time, the increase of fungal biomass and presence of H2O2 and oxidizing enzymes [laccase/peroxidase and lignin peroxidase (LiP)] in growth media was assessed by gravimetric and spectrophotometric measurements, respectively. Raman spectroscopy and transmission electron microscopy (TEM) were used to compare the structure of FLG before and after incubation. All of the test fungi decreased pH in growth media and released H2O2 and laccase/peroxidase, but only basidiomycetes released LiP. Independent of growth media composition all fungi were found to be capable to oxidize FLG to a graphene oxide-like material, including M. esculenta, which released only laccase/peroxidase, i.e. the most common enzymes among primary decomposers. These findings suggest that FLG involuntarily released into terrestrial environments would likely be oxidized by soil microflora.
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Affiliation(s)
- Fabio Candotto Carniel
- Department of Life Sciences, University of Trieste, via L. Giorgieri 10, Trieste I-34127, Italy.
| | - Lorenzo Fortuna
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, via L. Giorgieri 1, Trieste I-34127, Italy
| | - Davide Zanelli
- Department of Life Sciences, University of Trieste, via L. Giorgieri 10, Trieste I-34127, Italy
| | - Marina Garrido
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, via L. Giorgieri 1, Trieste I-34127, Italy
| | - Ester Vázquez
- Facultad de Ciencias y Tecnologías Químicas, Universidad de Castilla-La Mancha, Ciudad Real E-13071, Spain; Instituto Regional de Investigación Científica Aplicada (IRICA), Universidad de Castilla-La Mancha, Ciudad Real E-13071, Spain
| | - Viviana Jehová González
- Instituto Regional de Investigación Científica Aplicada (IRICA), Universidad de Castilla-La Mancha, Ciudad Real E-13071, Spain
| | - Maurizio Prato
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, via L. Giorgieri 1, Trieste I-34127, Italy; Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 182, Donostia San Sebastián E-20014, Spain; Basque Foundation for Science, Ikerbasque, Bilbao E-48013, Spain
| | - Mauro Tretiach
- Department of Life Sciences, University of Trieste, via L. Giorgieri 10, Trieste I-34127, Italy
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Stravoravdis S, Shipway JR, Goodell B. How Do Shipworms Eat Wood? Screening Shipworm Gill Symbiont Genomes for Lignin-Modifying Enzymes. Front Microbiol 2021; 12:665001. [PMID: 34322098 PMCID: PMC8312274 DOI: 10.3389/fmicb.2021.665001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/22/2021] [Indexed: 11/23/2022] Open
Abstract
Shipworms are ecologically and economically important mollusks that feed on woody plant material (lignocellulosic biomass) in marine environments. Digestion occurs in a specialized cecum, reported to be virtually sterile and lacking resident gut microbiota. Wood-degrading CAZymes are produced both endogenously and by gill endosymbiotic bacteria, with extracellular enzymes from the latter being transported to the gut. Previous research has predominantly focused on how these animals process the cellulose component of woody plant material, neglecting the breakdown of lignin – a tough, aromatic polymer which blocks access to the holocellulose components of wood. Enzymatic or non-enzymatic modification and depolymerization of lignin has been shown to be required in other wood-degrading biological systems as a precursor to cellulose deconstruction. We investigated the genomes of five shipworm gill bacterial symbionts obtained from the Joint Genome Institute Integrated Microbial Genomes and Microbiomes Expert Review for the production of lignin-modifying enzymes, or ligninases. The genomes were searched for putative ligninases using the Joint Genome Institute’s Function Profile tool and blastp analyses. The resulting proteins were then modeled using SWISS-MODEL. Although each bacterial genome possessed at least four predicted ligninases, the percent identities and protein models were of low quality and were unreliable. Prior research demonstrates limited endogenous ability of shipworms to modify lignin at the chemical/molecular level. Similarly, our results reveal that shipworm bacterial gill-symbiont enzymes are unlikely to play a role in lignin modification during lignocellulose digestion in the shipworm gut. This suggests that our understanding of how these keystone organisms digest and process lignocellulose is incomplete, and further research into non-enzymatic and/or other unknown mechanisms for lignin modification is required.
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Affiliation(s)
- Stefanos Stravoravdis
- Goodell Laboratory, Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, United States
| | - J Reuben Shipway
- Goodell Laboratory, Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, United States.,Centre for Enzyme Innovation, School of Biological Sciences, Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, United Kingdom
| | - Barry Goodell
- Goodell Laboratory, Department of Microbiology, University of Massachusetts Amherst, Amherst, MA, United States
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Angelova GV, Brazkova MS, Krastanov AI. Renewable mycelium based composite - sustainable approach for lignocellulose waste recovery and alternative to synthetic materials - a review. ACTA ACUST UNITED AC 2021; 76:431-442. [PMID: 34252997 DOI: 10.1515/znc-2021-0040] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 06/16/2021] [Indexed: 11/15/2022]
Abstract
The agricultural waste with lignocellulose origin is considered to be one of the major environmental pollutants which, because of their high nutritional value, represent an extremely rich resource with significant potential for the production of value added bio-products. This review discusses the applications of higher fungi to upcycle abundant agricultural by-products into more sustainable materials and to promote the transition to a circular economy. It focuses on the main factors influencing the properties and application of mycelium composites - the feedstock, the basidiomycete species and their interaction with the feedstock. During controlled solid state cultivation on various lignocellulose substrates, the basidiomycetes of class Agaricomycetes colonize their surfaces and form a three-dimensional mycelium net. Fungal mycelium secretes enzymes that break down lignocellulose over time and are partially replaced by mycelium. The mycelium adheres to the residual undegraded substrates resulting in the formation of a high-mechanical-strength bio-material called a mycelium based bio-composite. The mycelium based bio-composites are completely natural, biodegradable and can be composted after their cycle of use is completed. The physicochemical, mechanical, and thermodynamic characteristics of mycelium based bio-composites are competitive with those of synthetic polymers and allow them to be successfully used in the construction, architecture, and other industries.
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Affiliation(s)
- Galena V Angelova
- Department of Biotechnology, University of Food Technology, 26 Maritza Blvd, Plovdiv, Bulgaria
| | - Mariya S Brazkova
- Department of Biotechnology, University of Food Technology, 26 Maritza Blvd, Plovdiv, Bulgaria
| | - Albert I Krastanov
- Department of Biotechnology, University of Food Technology, 26 Maritza Blvd, Plovdiv, Bulgaria
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Mushroom Ligninolytic Enzymes―Features and Application of Potential Enzymes for Conversion of Lignin into Bio-Based Chemicals and Materials. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11136161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Mushroom ligninolytic enzymes are attractive biocatalysts that can degrade lignin through oxido-reduction. Laccase, lignin peroxidase, manganese peroxidase, and versatile peroxidase are the main enzymes that depolymerize highly complex lignin structures containing aromatic or aliphatic moieties and oxidize the subunits of monolignol associated with oxidizing agents. Among these enzymes, mushroom laccases are secreted glycoproteins, belonging to a polyphenol oxidase family, which have a powerful oxidizing capability that catalyzes the modification of lignin using synthetic or natural mediators by radical mechanisms via lignin bond cleavage. The high redox potential laccase within mediators can catalyze the oxidation of a wide range of substrates and the polymerization of lignin derivatives for value-added chemicals and materials. The chemoenzymatic process using mushroom laccases has been applied effectively for lignin utilization and the degradation of recalcitrant chemicals as an eco-friendly technology. Laccase-mediated grafting has also been employed to modify lignin and other polymers to obtain novel functional groups able to conjugate small and macro-biomolecules. In this review, the biochemical features of mushroom ligninolytic enzymes and their potential applications in catalytic reactions involving lignin and its derivatives to obtain value-added chemicals and novel materials in lignin valorization are discussed.
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Costantini I, Castro K, Rodriguez-Laso MD, Madariaga JM, Arana G. Non-Destructive Analytical Investigation of Decorative Wallpapers Samples of the Nineteenth Century before Their Restoration. SENSORS 2021; 21:s21134416. [PMID: 34203186 PMCID: PMC8272152 DOI: 10.3390/s21134416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/18/2021] [Accepted: 06/25/2021] [Indexed: 11/16/2022]
Abstract
In this work, decorative wallpapers (19th century) from an historical palace located in Oiartzun (Basque Country, Spain) were analyzed before their restoration. Micro-energy dispersive X-ray fluorescence spectroscopy, Raman spectroscopy, and attenuated total reflectance infrared spectroscopy were used to investigate the elemental and molecular composition of pigments, the presence of binders, and the state of conservation of the paper support. The aim of the investigation was trying to understand the possible degradation pathways and identify the raw materials in order to choose the best restoration protocol according to the original aspect of wallpapers. As stated from both the elemental distribution and the identification of mineral phases by Raman spectroscopy, the most used pigment was lead chromate. It was mixed with other pigments such as ultramarine blue, zinc chromate, hematite, and atacamite among others to obtain different shades and they were applied mixed with an animal glue. Brass, identified thanks to elemental micro-EDXRF maps, was employed as a shiny decorative element. In addition, a partial degradation of cellulose was detected due to its natural ageing, the acidic nature of lignin, and to a phenomenon of humidity of the walls. Probably the deposition of black particulate matter was the cause of the darkening of the painting surfaces.
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Affiliation(s)
- Ilaria Costantini
- Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country UPV/EHU, P.O. Box 644, 48080 Bilbao, Basque Country, Spain; (I.C.); (K.C.); (G.A.)
| | - Kepa Castro
- Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country UPV/EHU, P.O. Box 644, 48080 Bilbao, Basque Country, Spain; (I.C.); (K.C.); (G.A.)
| | | | - Juan Manuel Madariaga
- Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country UPV/EHU, P.O. Box 644, 48080 Bilbao, Basque Country, Spain; (I.C.); (K.C.); (G.A.)
- Correspondence:
| | - Gorka Arana
- Department of Analytical Chemistry, Faculty of Science and Technology, University of the Basque Country UPV/EHU, P.O. Box 644, 48080 Bilbao, Basque Country, Spain; (I.C.); (K.C.); (G.A.)
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Zitare UA, Habib MH, Rozeboom H, Mascotti ML, Todorovic S, Fraaije MW. Mutational and structural analysis of an ancestral fungal dye-decolorizing peroxidase. FEBS J 2021; 288:3602-3618. [PMID: 33369202 PMCID: PMC8248431 DOI: 10.1111/febs.15687] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/15/2020] [Accepted: 12/22/2020] [Indexed: 12/31/2022]
Abstract
Dye-decolorizing peroxidases (DyPs) constitute a superfamily of heme-containing peroxidases that are related neither to animal nor to plant peroxidase families. These are divided into four classes (types A, B, C, and D) based on sequence features. The active site of DyPs contains two highly conserved distal ligands, an aspartate and an arginine, the roles of which are still controversial. These ligands have mainly been studied in class A-C bacterial DyPs, largely because no effective recombinant expression systems have been developed for the fungal (D-type) DyPs. In this work, we employ ancestral sequence reconstruction (ASR) to resurrect a D-type DyP ancestor, AncDyPD-b1. Expression of AncDyPD-b1 in Escherichia coli results in large amounts of a heme-containing soluble protein and allows for the first mutagenesis study on the two distal ligands of a fungal DyP. UV-Vis and resonance Raman (RR) spectroscopic analyses, in combination with steady-state kinetics and the crystal structure, reveal fine pH-dependent details about the heme active site structure and show that both the aspartate (D222) and the arginine (R390) are crucial for hydrogen peroxide reduction. Moreover, the data indicate that these two residues play important but mechanistically different roles on the intraprotein long-range electron transfer process. DATABASE: Structural data are available in the PDB database under the accession number 7ANV.
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Affiliation(s)
- Ulises A. Zitare
- Molecular Enzymology GroupUniversity of GroningenThe Netherlands
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE)Departamento de Química Inorgánica, Analítica y Química FísicaFacultad de Ciencias Exactas y NaturalesUniversidad de Buenos Aires and CONICETArgentina
| | - Mohamed H. Habib
- Molecular Enzymology GroupUniversity of GroningenThe Netherlands
- Department of Microbiology and ImmunologyFaculty of PharmacyCairo UniversityEgypt
| | | | - Maria L. Mascotti
- Molecular Enzymology GroupUniversity of GroningenThe Netherlands
- IMIBIO‐SL CONICETFacultad de Química Bioquímica y FarmaciaUniversidad Nacional de San LuisArgentina
| | - Smilja Todorovic
- Instituto de Tecnologia Química e BiológicaUniversidade Nova de LisboaOeirasPortugal
| | - Marco W. Fraaije
- Molecular Enzymology GroupUniversity of GroningenThe Netherlands
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Ziemniak M, Zawadzka-Kazimierczuk A, Pawlędzio S, Malinska M, Sołtyka M, Trzybiński D, Koźmiński W, Skora S, Zieliński R, Fokt I, Priebe W, Woźniak K, Pająk B. Experimental and Computational Studies on Structure and Energetic Properties of Halogen Derivatives of 2-Deoxy-D-Glucose. Int J Mol Sci 2021; 22:3720. [PMID: 33918425 PMCID: PMC8038202 DOI: 10.3390/ijms22073720] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 02/01/2023] Open
Abstract
The results of structural studies on a series of halogen-substituted derivatives of 2-deoxy-D-glucose (2-DG) are reported. 2-DG is an inhibitor of glycolysis, a metabolic pathway crucial for cancer cell proliferation and viral replication in host cells, and interferes with D-glucose and D-mannose metabolism. Thus, 2-DG and its derivatives are considered as potential anticancer and antiviral drugs. X-ray crystallography shows that a halogen atom present at the C2 position in the pyranose ring does not significantly affect its conformation. However, it has a noticeable effect on the crystal structure. Fluorine derivatives exist as a dense 3D framework isostructural with the parent compound, while Cl- and I-derivatives form layered structures. Analysis of the Hirshfeld surface shows formation of hydrogen bonds involving the halogen, yet no indication for the existence of halogen bonds. Density functional theory (DFT) periodic calculations of cohesive and interaction energies (at the B3LYP level of theory) have supported these findings. NMR studies in the solution show that most of the compounds do not display significant differences in their anomeric equilibria, and that pyranose ring puckering is similar to the crystalline state. For 2-deoxy-2-fluoro-D-glucose (2-FG), electrostatic interaction energies between the ligand and protein for several existing structures of pyranose 2-oxidase were also computed. These interactions mostly involve acidic residues of the protein; single amino-acid substitutions have only a minor impact on binding. These studies provide a better understanding of the structural chemistry of halogen-substituted carbohydrates as well as their intermolecular interactions with proteins determining their distinct biological activity.
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Affiliation(s)
- Marcin Ziemniak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warszawa, Poland; (A.Z.-K.); (S.P.); (M.M.); (D.T.); (W.K.); (K.W.)
| | - Anna Zawadzka-Kazimierczuk
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warszawa, Poland; (A.Z.-K.); (S.P.); (M.M.); (D.T.); (W.K.); (K.W.)
| | - Sylwia Pawlędzio
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warszawa, Poland; (A.Z.-K.); (S.P.); (M.M.); (D.T.); (W.K.); (K.W.)
| | - Maura Malinska
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warszawa, Poland; (A.Z.-K.); (S.P.); (M.M.); (D.T.); (W.K.); (K.W.)
| | - Maja Sołtyka
- Independent Laboratory of Genetics and Molecular Biology, Kaczkowski Military Institute of Hygiene and Epidemiology, Kozielska 4, 01-163 Warsaw, Poland;
| | - Damian Trzybiński
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warszawa, Poland; (A.Z.-K.); (S.P.); (M.M.); (D.T.); (W.K.); (K.W.)
| | - Wiktor Koźmiński
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warszawa, Poland; (A.Z.-K.); (S.P.); (M.M.); (D.T.); (W.K.); (K.W.)
| | - Stanisław Skora
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, 1901 East Rd., Houston, TX 77054, USA; (S.S.); (R.Z.); (I.F.)
| | - Rafał Zieliński
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, 1901 East Rd., Houston, TX 77054, USA; (S.S.); (R.Z.); (I.F.)
| | - Izabela Fokt
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, 1901 East Rd., Houston, TX 77054, USA; (S.S.); (R.Z.); (I.F.)
| | - Waldemar Priebe
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, 1901 East Rd., Houston, TX 77054, USA; (S.S.); (R.Z.); (I.F.)
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warszawa, Poland; (A.Z.-K.); (S.P.); (M.M.); (D.T.); (W.K.); (K.W.)
| | - Beata Pająk
- Independent Laboratory of Genetics and Molecular Biology, Kaczkowski Military Institute of Hygiene and Epidemiology, Kozielska 4, 01-163 Warsaw, Poland;
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Alam R, Ardiati FC, Solihat NN, Alam MB, Lee SH, Yanto DHY, Watanabe T, Kim S. Biodegradation and metabolic pathway of anthraquinone dyes by Trametes hirsuta D7 immobilized in light expanded clay aggregate and cytotoxicity assessment. JOURNAL OF HAZARDOUS MATERIALS 2021; 405:124176. [PMID: 33131941 DOI: 10.1016/j.jhazmat.2020.124176] [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: 07/23/2020] [Revised: 09/14/2020] [Accepted: 10/01/2020] [Indexed: 06/11/2023]
Abstract
Biodegradation and metabolic pathways of three anthraquinone dyes, Reactive Blue 4 (RB4), Remazol Brilliant Blue - R (RBBR), and Acid Blue 129 (AB129) by Trametes hirsuta D7 fungus immobilized in light expanded clay aggregate (LECA) were investigated. Morphological characteristics observed with scanning electron microscope (SEM) showed successful immobilization of the fungus in LECA. Based on UV absorbance measurement, immobilized T. hirsuta D7 effectively degraded 90%, 95%, and 96% of RB4, RBBR and AB129, respectively. Metabolites were identified with high-resolution mass spectrometry (HRMS) and degradation pathway of the dyes by T. hirsuta D7 was proposed. Toxicity assay on human dermal fibroblast (HDF) showed that anthraquinone dyes exhibits significant toxicity of 35%, 40%, and 34% reduction of cell viability by RB4, RBBR, and AB129, respectively. Fungal treatment resulted in an abatement of the toxicity and cell viability was increased up to 94%. The data clearly showed the effectiveness of immobilized T. hirsuta D7 in LECA on detoxification of anthraquinone dyes. This study provides potential and fundamental understanding of wastewater treatment using the newly isolated fungus T. hirsuta D7.
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Affiliation(s)
- Rafiqul Alam
- Department of Chemistry, Kyungpook National University, 41566, Republic of Korea
| | - Fenny Clara Ardiati
- Research Center for Biomaterials, Indonesian Institute of Sciences (LIPI), Cibinong 16911, Republic of Indonesia
| | - Nissa Nurfajrin Solihat
- Research Center for Biomaterials, Indonesian Institute of Sciences (LIPI), Cibinong 16911, Republic of Indonesia
| | - Md Badrul Alam
- Department of Food Science and Biotechnology, Graduate School, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Sang Han Lee
- Department of Food Science and Biotechnology, Graduate School, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Dede Heri Yuli Yanto
- Research Center for Biomaterials, Indonesian Institute of Sciences (LIPI), Cibinong 16911, Republic of Indonesia.
| | - Takashi Watanabe
- Research Institute for Sustainable Humanosphere, Kyoto University, Kyoto 611-0011, Japan
| | - Sunghwan Kim
- Department of Chemistry, Kyungpook National University, 41566, Republic of Korea; Mass Spectrometry Converging Research Center and Green-Nano Materials Research Center, Daegu 41566, Republic of Korea.
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40
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Kumar V, Dwivedi SK. Mycoremediation of heavy metals: processes, mechanisms, and affecting factors. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:10375-10412. [PMID: 33410020 DOI: 10.1007/s11356-020-11491-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 10/30/2020] [Indexed: 05/27/2023]
Abstract
Industrial processes and mining of coal and metal ores are generating a number of threats by polluting natural water bodies. Contamination of heavy metals (HMs) in water and soil is the most serious problem caused by industrial and mining processes and other anthropogenic activities. The available literature suggests that existing conventional technologies are costly and generated hazardous waste that necessitates disposal. So, there is a need for cheap and green approaches for the treatment of such contaminated wastewater. Bioremediation is considered a sustainable way where fungi seem to be good bioremediation agents to treat HM-polluted wastewater. Fungi have high adsorption and accumulation capacity of HMs and can be potentially utilized. The most important biomechanisms which are involved in HM tolerance and removal by fungi are bioaccumulation, bioadsorption, biosynthesis, biomineralisation, bioreduction, bio-oxidation, extracellular precipitation, intracellular precipitation, surface sorption, etc. which vary from species to species. However, the time, pH, temperature, concentration of HMs, the dose of fungal biomass, and shaking rate are the most influencing factors that affect the bioremediation of HMs and vary with characteristics of the fungi and nature of the HMs. In this review, we have discussed the application of fungi, involved tolerance and removal strategies in fungi, and factors affecting the removal of HMs.
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Affiliation(s)
- Vinay Kumar
- Department of Environmental Science, Babasaheb Bhimrao Ambedkar University, Lucknow, 226025, India.
| | - Shiv Kumar Dwivedi
- Department of Environmental Science, Babasaheb Bhimrao Ambedkar University, Lucknow, 226025, India
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41
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Vos AM, Bleichrodt R, Herman KC, Ohm RA, Scholtmeijer K, Schmitt H, Lugones LG, Wösten HAB. Cycling in degradation of organic polymers and uptake of nutrients by a litter-degrading fungus. Environ Microbiol 2021; 23:224-238. [PMID: 33140552 PMCID: PMC7894533 DOI: 10.1111/1462-2920.15297] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/25/2020] [Accepted: 10/26/2020] [Indexed: 11/30/2022]
Abstract
Wood and litter degrading fungi are the main decomposers of lignocellulose and thus play a key role in carbon cycling in nature. Here, we provide evidence for a novel lignocellulose degradation strategy employed by the litter degrading fungus Agaricus bisporus (known as the white button mushroom). Fusion of hyphae allows this fungus to synchronize the activity of its mycelium over large distances (50 cm). The synchronized activity has a 13-h interval that increases to 20 h before becoming irregular and it is associated with a 3.5-fold increase in respiration, while compost temperature increases up to 2°C. Transcriptomic analysis of this burst-like phenomenon supports a cyclic degradation of lignin, deconstruction of (hemi-) cellulose and microbial cell wall polymers, and uptake of degradation products during vegetative growth of A. bisporus. Cycling in expression of the ligninolytic system, of enzymes involved in saccharification, and of proteins involved in nutrient uptake is proposed to provide an efficient way for degradation of substrates such as litter.
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Affiliation(s)
- Aurin M. Vos
- Microbiology, Department of BiologyUtrecht UniversityUtrechtthe Netherlands
- Wageningen Plant ResearchWageningen URWageningenthe Netherlands
| | | | - Koen C. Herman
- Microbiology, Department of BiologyUtrecht UniversityUtrechtthe Netherlands
| | - Robin A. Ohm
- Microbiology, Department of BiologyUtrecht UniversityUtrechtthe Netherlands
| | - Karin Scholtmeijer
- Plant BreedingWageningen University and ResearchWageningenthe Netherlands
| | - Heike Schmitt
- Institute for Risk Assessment SciencesUtrecht UniversityUtrechtthe Netherlands
| | - Luis G. Lugones
- Microbiology, Department of BiologyUtrecht UniversityUtrechtthe Netherlands
| | - Han A. B. Wösten
- Microbiology, Department of BiologyUtrecht UniversityUtrechtthe Netherlands
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42
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Microbial Enzymes in the Bioremediation of Pollutants: Emerging Potential and Challenges. Fungal Biol 2021. [DOI: 10.1007/978-3-030-54422-5_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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43
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Hamberg L, Saksa T, Hantula J. Role and function of Chondrostereum purpureum in biocontrol of trees. Appl Microbiol Biotechnol 2020; 105:431-440. [PMID: 33340337 PMCID: PMC7806553 DOI: 10.1007/s00253-020-11053-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 11/06/2020] [Accepted: 12/09/2020] [Indexed: 11/30/2022]
Abstract
Abstract A decay fungus, Chondrostereum purpureum (Pers. Ex Fr.) Pouzar, has been investigated in Europe, Northern America and New Zealand for its ability to decay hardwood stumps and thus prevent sprouting. The aim of these investigations has been to find an alternative to mechanical (cutting only) and chemical sprout control (cutting and applying chemicals to stumps in order to prevent sprouting). Mechanical sprout control is not an efficient option due to hardwood tree species’ ability to re-sprout efficiently after cutting, and therefore management costs are high. Chemicals would be efficient but due to their harmful effects on the environment, alternatives are needed. The fungal treatment, i.e., cutting accompanied with C. purpureum inoculum is an environmentally friendly and efficient option for sprout control. This mini-review comprises the role and function of C. purpureum in biocontrol of trees: the ecology of C. purpureum, its sprout control efficacy, factors affecting sprout control efficacy, devices in biological sprout control, potential risks, and the future perspectives of biological sprout control. Key points • A fungus Chondrostereum purpureum is efficient in preventing sprouting of hardwoods • C. purpureum is not sensitive to environmental conditions • Devices should be developed for cost-efficient biological sprout control
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Affiliation(s)
- Leena Hamberg
- Natural Resources Institute Finland, P.O. Box 2, (Latokartanonkaari 9), FI-00790, Helsinki, Finland.
| | - Timo Saksa
- Natural Resources Institute Finland, Juntintie 154, FI-77600, Suonenjoki, Finland
| | - Jarkko Hantula
- Natural Resources Institute Finland, P.O. Box 2, (Latokartanonkaari 9), FI-00790, Helsinki, Finland
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Wang L, O'Connor D, Rinklebe J, Ok YS, Tsang DCW, Shen Z, Hou D. Biochar Aging: Mechanisms, Physicochemical Changes, Assessment, And Implications for Field Applications. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:14797-14814. [PMID: 33138356 DOI: 10.1021/acs.est.0c04033] [Citation(s) in RCA: 170] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Biochar has triggered a black gold rush in environmental studies as a carbon-rich material with well-developed porous structure and tunable functionality. While much attention has been placed on its apparent ability to store carbon in the ground, immobilize soil pollutants, and improve soil fertility, its temporally evolving in situ performance in these roles must not be overlooked. After field application, various environmental factors, such as temperature variations, precipitation events and microbial activities, can lead to its fragmentation, dissolution, and oxidation, thus causing drastic changes to the physicochemical properties. Direct monitoring of biochar-amended soils can provide good evidence of its temporal evolution, but this requires long-term field trials. Various artificial aging methods, such as chemical oxidation, wet-dry cycling and mineral modification, have therefore been designed to mimic natural aging mechanisms. Here we evaluate the science of biochar aging, critically summarize aging-induced changes to biochar properties, and offer a state-of-the-art for artificial aging simulation approaches. In addition, the implications of biochar aging are also considered regarding its potential development and deployment as a soil amendment. We suggest that for improved simulation and prediction, artificial aging methods must shift from qualitative to quantitative approaches. Furthermore, artificial preaging may serve to synthesize engineered biochars for green and sustainable environmental applications.
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Affiliation(s)
- Liuwei Wang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - David O'Connor
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Jörg Rinklebe
- University of Wuppertal, School of Architecture and Civil Engineering, Institute of Foundation Engineering, Water- and Waste-Management, Laboratory of Soil- and Groundwater-Management, Pauluskirchstraße 7, Wuppertal, 42285, Germany
- Department of Environment, Energy and Geoinformatics, Sejong University, 98 Gunja-Dong, Seoul, Republic of Korea
| | - Yong Sik Ok
- Korea Biochar Research Center, APRU Sustainable Waste Management Program & Division of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Daniel C W Tsang
- Department of Civil and Environmental Engineering, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong China
| | - Zhengtao Shen
- School of Environment, Tsinghua University, Beijing 100084, China
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, T6G 2E3, Canada
| | - Deyi Hou
- School of Environment, Tsinghua University, Beijing 100084, China
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Grelska A, Noszczyńska M. White rot fungi can be a promising tool for removal of bisphenol A, bisphenol S, and nonylphenol from wastewater. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:39958-39976. [PMID: 32803603 PMCID: PMC7546991 DOI: 10.1007/s11356-020-10382-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 08/03/2020] [Indexed: 05/04/2023]
Abstract
Endocrine-disrupting chemicals (EDC) are a wide group of chemicals that interfere with the endocrine system. Their similarity to natural steroid hormones makes them able to attach to hormone receptors, thereby causing unfavorable health effects. Among EDC, bisphenol A (BPA), bisphenol S (BPS), and nonylphenol (NP) seem to be particularly harmful. As the industry is experiencing rapid expansion, BPA, BPS, and NP are being produced in growing amounts, generating considerable environmental pollution. White rot fungi (WRF) are an economical, ecologically friendly, and socially acceptable way to remove EDC contamination from ecosystems. WRF secrete extracellular ligninolytic enzymes such as laccase, manganese peroxidase, lignin peroxidase, and versatile peroxidase, involved in lignin deterioration. Owing to the broad substrate specificity of these enzymes, they are able to remove numerous xenobiotics, including EDC. Therefore, WRF seem to be a promising tool in the abovementioned EDC elimination during wastewater treatment processes. Here, we review WRF application for this EDC removal from wastewater and indicate several strengths and limitations of such methods.
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Affiliation(s)
- Agnieszka Grelska
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellońska 28, 40-032, Katowice, Poland
| | - Magdalena Noszczyńska
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellońska 28, 40-032, Katowice, Poland.
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Ahn H, Rehman JU, Kim T, Oh MS, Yoon HY, Kim C, Lee Y, Shin SG, Jeon JR. Fungal mycelia functionalization with halloysite nanotubes for hyphal spreading and sorption behavior regulation: A new bio-ceramic hybrid for enhanced water treatment. WATER RESEARCH 2020; 186:116380. [PMID: 32919139 DOI: 10.1016/j.watres.2020.116380] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 06/11/2023]
Abstract
Filamentous fungi are believed to remove a wide range of environmental xenobiotics due to their characteristically non-specific catabolic metabolisms. Nonetheless, irregular hyphal spreading can lead to clogging problems in treatment facilities and the dependence of pollutant bioavailability on hyphal surface features severely limits their applicability in water treatment. Here, we propose a scalable and facile methodology to structurally modify fungal hyphae, allowing for both the maximization of pollutant sorption and fungal pellet morphology self-regulation. Halloysite-doped mycelium architectures were efficiently constructed by dipping Aspergillus fumigatus pellets in halloysite nanotube-dispersed water. Ultrastructure analyses using scanning electron microscopy equipped with energy-dispersive X-ray spectroscopy revealed that the nanotubes were mainly attached to the outer surface of the pellets. Fungal viability and exoenzyme production were hardly affected by the halloysites. Notably, nanotube doping appeared to be extremely robust given that detachments rarely occurred even in high concentrations of organic solvents and salt. It was also demonstrated that the doped halloysites weakened hyphal growth-driven gelation, thus maintaining sphere-like pellet structures. The water treatment potential of the hybrid fungal mycelia was assessed through both cationic toxic organic/inorganic-contaminated water and real dye industry wastewater clean-ups. Aided by the mesoporous halloysite sites on their surface, the removal abilities of the hybrid structures were significantly enhanced. Moreover, inherent low sorption ability of HNT for heavy metals was found to be overcome by the aid of fungal mycelia. Finally, universal feature of the dipping-based doping way was confirmed by using different filamentous fungi. Given that traditional approaches to effectively implement fungus-based water treatment are based mostly on polymer-based immobilization techniques, our proposed approach provides a novel and effective alternative via simple doping of living fungi with environmentally-benign clays such as halloysite nanotubes.
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Affiliation(s)
- Hyoungjae Ahn
- Department of Agricultural Chemistry and Food Science & Technology, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Jalil Ur Rehman
- Department of Agricultural Chemistry and Food Science & Technology, Gyeongsang National University, Jinju 52828, Republic of Korea; IALS, Gyeongsang National University, Jinju 52828, Republic of Korea; Division of Applied Life Science (BK21Plus), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Taehyen Kim
- Department of Agricultural Chemistry and Food Science & Technology, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Min Seung Oh
- Department of Agricultural Chemistry and Food Science & Technology, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Ho Young Yoon
- Department of Agricultural Chemistry and Food Science & Technology, Gyeongsang National University, Jinju 52828, Republic of Korea; IALS, Gyeongsang National University, Jinju 52828, Republic of Korea; Division of Applied Life Science (BK21Plus), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Changgyo Kim
- Department of Materials Engineering and Convergence Technology, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Younki Lee
- Department of Materials Engineering and Convergence Technology, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Seung Gu Shin
- Department of Energy Engineering, Future Convergence Technology Research Institute, Gyeongnam National University of Science and Technology, Jinju 52725, Republic of Korea
| | - Jong-Rok Jeon
- Department of Agricultural Chemistry and Food Science & Technology, Gyeongsang National University, Jinju 52828, Republic of Korea; IALS, Gyeongsang National University, Jinju 52828, Republic of Korea; Division of Applied Life Science (BK21Plus), Gyeongsang National University, Jinju 52828, Republic of Korea.
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Dasgupta A, Chowdhury N, De RK. Metabolic pathway engineering: Perspectives and applications. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2020; 192:105436. [PMID: 32199314 DOI: 10.1016/j.cmpb.2020.105436] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 02/29/2020] [Accepted: 03/03/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND Metabolic engineering aims at contriving microbes as biocatalysts for enhanced and cost-effective production of countless secondary metabolites. These secondary metabolites can be treated as the resources of industrial chemicals, pharmaceuticals and fuels. Plants are also crucial targets for metabolic engineers to produce necessary secondary metabolites. Metabolic engineering of both microorganism and plants also contributes towards drug discovery. In order to implement advanced metabolic engineering techniques efficiently, metabolic engineers should have detailed knowledge about cell physiology and metabolism. Principle behind methodologies: Genome-scale mathematical models of integrated metabolic, signal transduction, gene regulatory and protein-protein interaction networks along with experimental validation can provide such knowledge in this context. Incorporation of omics data into these models is crucial in the case of drug discovery. Inverse metabolic engineering and metabolic control analysis (MCA) can help in developing such models. Artificial intelligence methodology can also be applied for efficient and accurate metabolic engineering. CONCLUSION In this review, we discuss, at the beginning, the perspectives of metabolic engineering and its application on microorganism and plant leading to drug discovery. At the end, we elaborate why inverse metabolic engineering and MCA are closely related to modern metabolic engineering. In addition, some crucial steps ensuring efficient and optimal metabolic engineering strategies have been discussed. Moreover, we explore the use of genomics data for the activation of silent metabolic clusters and how it can be integrated with metabolic engineering. Finally, we exhibit a few applications of artificial intelligence to metabolic engineering.
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Affiliation(s)
- Abhijit Dasgupta
- Department of Data Science, School of Interdisciplinary Studies, University of Kalyani, Kalyani, Nadia 741235, West Bengal, India
| | - Nirmalya Chowdhury
- Department of Computer Science & Engineering, Jadavpur University, Kolkata 700032, India
| | - Rajat K De
- Machine Intelligence Unit, Indian Statistical Institute, 203 B.T. Road, Kolkata 700108, India.
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Hilgers R, van Dam A, Zuilhof H, Vincken JP, Kabel MA. Controlling the Competition: Boosting Laccase/HBT-Catalyzed Cleavage of a β-O-4′ Linked Lignin Model. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02154] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Roelant Hilgers
- Laboratory of Food Chemistry, Wageningen University and Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Annemieke van Dam
- Laboratory of Organic Chemistry, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Han Zuilhof
- Laboratory of Organic Chemistry, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
- School of Pharmaceutical Sciences and Technology, Tianjin University, 92 Weijin Road, 300072 Tianjin, China
| | - Jean-Paul Vincken
- Laboratory of Food Chemistry, Wageningen University and Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
| | - Mirjam A. Kabel
- Laboratory of Food Chemistry, Wageningen University and Research, Bornse Weilanden 9, 6708 WG Wageningen, The Netherlands
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Chang R, Lata R, Rohindra D. Study of mechanical, enzymatic degradation and antimicrobial properties of poly(butylene succinate)/pine-resin blends. Polym Bull (Berl) 2020. [DOI: 10.1007/s00289-019-02938-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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50
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Wilkinson RC, Rahman Pour R, Jamshidi S, Fülöp V, Bugg TDH. Extracellular alpha/beta-hydrolase from Paenibacillus species shares structural and functional homology to tobacco salicylic acid binding protein 2. J Struct Biol 2020; 210:107496. [PMID: 32224091 DOI: 10.1016/j.jsb.2020.107496] [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: 11/24/2019] [Revised: 03/20/2020] [Accepted: 03/21/2020] [Indexed: 10/24/2022]
Abstract
An alpha/ beta hydrolase annotated as a putative salicylate esterase within the genome of a species of Paenibacillus previously identified from differential and selective growth on Kraft lignin was structurally and functionally characterised. Feruloyl esterases are key to the degradation of lignin in several bacterial species and although this activity was investigated, no such activity was observed. The crystal structure of the Paenibacillus esterase, here denoted as PnbE, was determined at 1.32 Å resolution, showing high similarity to Nicotiana tabacum salicylic acid binding protein 2 from the protein database. Structural similarities between these two structures across the core domains and key catalytic residues were observed, with superposition of catalytic residues giving an RMSD of 0.5 Å across equivalent Cα atoms. Conversely, the cap domains of PnbE and Nicotiana tabacum SABP2 showed greater divergence with decreased flexibility in the PnbE cap structure. Activity of PnbE as a putative methyl salicylate esterase was supported with binding studies showing affinity for salicylic acid and functional studies showing methyl salicylate esterase activity. We hypothesise that this activity could enrich Paenibacillus sp. within the rhizosphere by increasing salicylic acid concentrations within the soil.
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Affiliation(s)
| | | | - Shirin Jamshidi
- School of Cancer and Pharmaceutical Sciences, King's College London, SE1 9NH, UK
| | - Vilmos Fülöp
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Timothy D H Bugg
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK.
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