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Shah K, Ray S, Bose H, Pandey V, Wohlschlegel JA, Mahendra S. Proteomics insights into the fungal-mediated bioremediation of environmental contaminants. Curr Opin Biotechnol 2024; 90:103213. [PMID: 39393120 DOI: 10.1016/j.copbio.2024.103213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 08/26/2024] [Accepted: 09/15/2024] [Indexed: 10/13/2024]
Abstract
As anthropogenic activities continue to introduce various contaminants into the environment, the need for effective monitoring and bioremediation strategies is critical. Fungi, with their diverse enzymatic arsenal, offer promising solutions for the biotransformation of many pollutants. While conventional research reports on ligninolytic, oxidoreductive, and cytochrome P450 (CYP) enzymes, the vast potential of fungi, with approximately 10 345 protein sequences per species, remains largely untapped. This review describes recent advancements in fungal proteomics instruments as well as software and highlights their detoxification mechanisms and biochemical pathways. Additionally, it highlights lesser-known fungal enzymes with potential applications in environmental biotechnology. By reviewing the benefits and challenges associated with proteomics tools, we hope to summarize and promote the studies of fungi and fungal proteins relevant in the environment.
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Affiliation(s)
- Kshitija Shah
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA, USA
| | - Soham Ray
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA, USA
| | - Himadri Bose
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA, USA
| | - Vijaya Pandey
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - James A Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Shaily Mahendra
- Department of Civil and Environmental Engineering, University of California, Los Angeles, CA, USA.
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2
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Mohammadi Dargah M, Pedram P, Cabrera-Barjas G, Delattre C, Nesic A, Santagata G, Cerruti P, Moeini A. Biomimetic synthesis of nanoparticles: A comprehensive review on green synthesis of nanoparticles with a focus on Prosopis farcta plant extracts and biomedical applications. Adv Colloid Interface Sci 2024; 332:103277. [PMID: 39173272 DOI: 10.1016/j.cis.2024.103277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 06/14/2024] [Accepted: 08/12/2024] [Indexed: 08/24/2024]
Abstract
The synthesis of nanoparticles (NPs) using environmentally friendly methods has garnered significant attention in response to concerns about the environmental impact of various nanomaterial manufacturing techniques. To address this issue, natural resources like extracts from plants, fungi, and bacteria are employed as a green alternative for nanoparticle synthesis. Plant extracts, which contain active components such as terpenoids, alkaloids, phenols, tannins, and vitamins, operate as coating and reducing agents. Bacteria and fungi, on the other hand, rely on internal enzymes, sugar molecules, membrane proteins, nicotinamide adenine dinucleotide (NADH), and nicotinamide adenine dinucleotide phosphate (NADPH) dependent enzymes to play critical roles as reducing agents. This review collects recent advancements in biomimetic methods for nanoparticle synthesis, critically discussing the preparation approaches, the type of particles obtained, and their envisaged applications. A specific focus is given on using Prosopis fractal plant extracts to synthesize nanoparticles tailored for biomedical applications. The applications of this plant and its role in the biomimetic manufacturing of nanoparticles have not been reported yet, making this review a pioneering and valuable contribution to the field.
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Affiliation(s)
- Maryam Mohammadi Dargah
- Department of Pharmaceutical Chemistry, Faculty of Medicinal Chemistry, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Parisa Pedram
- Chair of Brewing and Beverage Technology, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Gustavo Cabrera-Barjas
- Facultad de Ciencias para el Cuidado de la Salud, Universidad San Sebastian, Campus Las Tres Pascualas, Lientur 1457, 4080871 Concepción, Chile
| | - Cedric Delattre
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, Institut Pascal, F-63000 Clermont-Ferrand, France; Institut Universitaire de France (IUF), 1 Rue Descartes, 75005 Paris, France
| | - Aleksandra Nesic
- University of Belgrade, Vinca Institute for Nuclear Sciences, National Institute of Republic of Serbia, Mike Petrovica Alasa 12-14, Belgrade 11000, Serbia
| | - Gabriella Santagata
- Institute of Polymers, Composites and Biomaterials (IPCB-CNR), Via Campi Flegrei 34, 80078 Pozzuoli, Italy
| | - Pierfrancesco Cerruti
- Institute of Polymers, Composites and Biomaterials (IPCB-CNR), Via Campi Flegrei 34, 80078 Pozzuoli, Italy
| | - Arash Moeini
- Chair of Brewing and Beverage Technology, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany.
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3
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Franco Cairo JPL, Almeida DV, Andrade VB, Terrasan CRF, Telfer A, Gonçalves TA, Diaz DE, Figueiredo FL, Brenelli LB, Walton PH, Damasio A, Garcia W, Squina FM. Biochemical and structural insights of a recombinant AA16 LPMO from the marine and sponge-symbiont Peniophora sp. Int J Biol Macromol 2024; 280:135596. [PMID: 39276894 DOI: 10.1016/j.ijbiomac.2024.135596] [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: 07/13/2024] [Revised: 09/10/2024] [Accepted: 09/11/2024] [Indexed: 09/17/2024]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes that oxidize polysaccharides, leading to their cleavage. LPMOs are classified into eight CAZy families (AA9-11, AA13-17), with the functionality of AA16 being poorly characterized. This study presents biochemical and structural data for an AA16 LPMO (PnAA16) from the marine sponge symbiont Peniophora sp. Phylogenetic analysis revealed that PnAA16 clusters separately from previously characterized AA16s. However, the structural modelling of PnAA16 showed the characteristic immunoglobulin-like fold of LPMOs, with a conserved his-brace motif coordinating a copper ion. The copper-bound PnAA16 showed greater thermal stability than its apo-form, highlighting copper's role in enzyme stability. Functionally, PnAA16 demonstrated oxidase activity, producing 5 μM H₂O₂ after 30 min, but showed 20 times lower peroxidase activity (0.27 U/g) compared to a fungal AA9. Specific activity assays indicated that PnAA16 acts only on cellohexaose, generating native celloligosaccharides (C3 to C5) and oxidized products with regioselective oxidation at C1 and C4 positions. Finally, PnAA16 boosted the activity of a cellulolytic cocktail for cellulose saccharification in the presence of ascorbic acid, hydrogen peroxide, or both. In conclusion, the present work provides insights into the AA16 family, expanding the understanding of their structural and functional relationships and biotechnological potential.
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Affiliation(s)
- João Paulo L Franco Cairo
- Laboratório de Ciências Moleculares (LACIMO), Universidade de Sorocaba (UNISO), Sorocaba, Brazil; Laboratory of Enzymology and Molecular Biology of Microorganisms (LEBIMO), Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil; Department of Chemistry, University of York, York, United Kingdom
| | - Dnane V Almeida
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - Viviane B Andrade
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - César R F Terrasan
- Laboratory of Enzymology and Molecular Biology of Microorganisms (LEBIMO), Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Abbey Telfer
- Department of Chemistry, University of York, York, United Kingdom
| | - Thiago A Gonçalves
- Laboratório de Ciências Moleculares (LACIMO), Universidade de Sorocaba (UNISO), Sorocaba, Brazil
| | - Daniel E Diaz
- Department of Chemistry, University of York, York, United Kingdom
| | - Fernanda L Figueiredo
- Laboratory of Enzymology and Molecular Biology of Microorganisms (LEBIMO), Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Livia B Brenelli
- Laboratory of Enzymology and Molecular Biology of Microorganisms (LEBIMO), Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Paul H Walton
- Department of Chemistry, University of York, York, United Kingdom
| | - André Damasio
- Laboratory of Enzymology and Molecular Biology of Microorganisms (LEBIMO), Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Wanius Garcia
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do ABC (UFABC), Santo André, SP, Brazil
| | - Fabio M Squina
- Laboratório de Ciências Moleculares (LACIMO), Universidade de Sorocaba (UNISO), Sorocaba, Brazil.
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Yoshinaga TT, Giovanella P, de Farias GS, Dos Santos JA, Pellizzer EP, Sette LD. Fungi from Antarctic marine sediment: characterization and assessment for textile dye decolorization and detoxification. Braz J Microbiol 2024:10.1007/s42770-024-01485-w. [PMID: 39259479 DOI: 10.1007/s42770-024-01485-w] [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: 12/26/2023] [Accepted: 05/25/2024] [Indexed: 09/13/2024] Open
Abstract
Cold-adapted microorganisms can produce enzymes with activity at low and mild temperatures, which can be applied to environmental biotechnology. This study aimed to characterize 20 Antarctic fungi to identify their genus (ITS rDNA marker) and growth temperatures and evaluate their ability to decolorize and detoxify the textile dye indigo carmine (IC). An individual screening was performed to assess the decolorization and detoxification of IC by the isolates, as well as in consortia with other fungi. The isolates were affiliated with seven ascomycete genera: Aspergillus (n = 4), Cosmospora (n = 2), Leuconeurospora (n = 2), Penicillium (n = 3), Pseudogymnoascus (n = 6), Thelebolus (n = 2), and Trichoderma (n = 1). The two isolates from the genus Leuconeurospora were characterized as psychrophilic, while the others were psychrotolerant. The Penicillium isolates were able to decolorize between 60 and 82% of IC. The isolates identified as Pseudogymnoascus showed the best detoxification capacity, with results varying from 49 to 74%. The consortium using only Antarctic ascomycetes (C1) showed 45% of decolorization, while the consortia with the addition of basidiomycetes (C1 + Peniophora and C1 + Pholiota) showed 40% and 50%, respectively. The consortia C1 with the addition of the basidiomycetes presented a lower toxicity after the treatments. In addition, a higher fungal biomass was produced in the presence of dye when compared with the experiment without the dye, which can be indicative of dye metabolization. The results highlight the potential of marine-derived Antarctic fungi in the process of textile dye degradation. The findings encourage further studies to elucidate the degradation and detoxification pathways of the dye IC by these fungal isolates.
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Affiliation(s)
- Thaís Tiemi Yoshinaga
- Instituto de Biociências, Departamento de Biologia Geral e Aplicada, Universidade Estadual Paulista (UNESP), 24A, 1515, Rio Claro, CEP 13506-900, SP, Brazil
| | - Patrícia Giovanella
- Instituto de Biociências, Departamento de Biologia Geral e Aplicada, Universidade Estadual Paulista (UNESP), 24A, 1515, Rio Claro, CEP 13506-900, SP, Brazil
- Centro de Estudos Ambientais, Universidade Estadual Paulista (UNESP), Rio Claro, CEP 13506-900, SP, Brazil
| | - Gabriele Santana de Farias
- Instituto de Biociências, Departamento de Biologia Geral e Aplicada, Universidade Estadual Paulista (UNESP), 24A, 1515, Rio Claro, CEP 13506-900, SP, Brazil
| | - Juliana Aparecida Dos Santos
- Universidade do Vale do Sapucaí (Univás), Av. Prefeito Tuany Toledo, 470 - Fatima, Pouso Alegre, 37550-000, MG, Brazil
| | - Elisa Pais Pellizzer
- Instituto de Biociências, Departamento de Biologia Geral e Aplicada, Universidade Estadual Paulista (UNESP), 24A, 1515, Rio Claro, CEP 13506-900, SP, Brazil
| | - Lara Durães Sette
- Instituto de Biociências, Departamento de Biologia Geral e Aplicada, Universidade Estadual Paulista (UNESP), 24A, 1515, Rio Claro, CEP 13506-900, SP, Brazil.
- Centro de Estudos Ambientais, Universidade Estadual Paulista (UNESP), Rio Claro, CEP 13506-900, SP, Brazil.
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Anju VT, Busi S, Mohan MS, Salim SA, Ar S, Imchen M, Kumavath R, Dyavaiah M, Prasad R. Surveillance and mitigation of soil pollution through metagenomic approaches. Biotechnol Genet Eng Rev 2024; 40:589-622. [PMID: 36881114 DOI: 10.1080/02648725.2023.2186330] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 02/23/2023] [Indexed: 03/08/2023]
Abstract
Soil pollution is one of the serious global threats causing risk to environment and humans. The major cause of accumulation of pollutants in soil are anthropogenic activities and some natural processes. There are several types of soil pollutants which deteriorate the quality of human life and animal health. They are recalcitrant hydrocarbon compounds, metals, antibiotics, persistent organic compounds, pesticides and different kinds of plastics. Due to the detrimental properties of pollutants present in soil on human life and ecosystem such as carcinogenic, genotoxic and mutagenic effects, alternate and effective methods to degrade the pollutants are recommended. Bioremediation is an effective and inexpensive method of biological degradation of pollutants using plants, microorganisms and fungi. With the advent of new detection methods, the identification and degradation of soil pollutants in different ecosystems were made easy. Metagenomic approaches are a boon for the identification of unculturable microorganisms and to explore the vast bioremediation potential for different pollutants. Metagenomics is a power tool to study the microbial load in polluted or contaminated land and its role in bioremediation. In addition, the negative ecosystem and health effect of pathogens, antibiotic and metal resistant genes found in the polluted area can be studied. Also, the identification of novel compounds/genes/proteins involved in the biotechnology and sustainable agriculture practices can be performed with the integration of metagenomics.
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Affiliation(s)
- V T Anju
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Siddhardha Busi
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Mahima S Mohan
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Simi Asma Salim
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Sabna Ar
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Madangchanok Imchen
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Ranjith Kumavath
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry, India
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kerala, India
| | - Madhu Dyavaiah
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Ram Prasad
- Department of Botany, School of Life Sciences, Mahatma Gandhi Central University, Bihar, India
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Liberato MV, Paixao DAA, Tomazetto G, Ndeh D, Bolam DN, Squina FM. Discovery, structural characterization, and functional insights into a novel apiosidase from the GH140 family, isolated from a lignocellulolytic-enriched mangrove microbial community. Biotechnol Lett 2024; 46:201-211. [PMID: 38280177 DOI: 10.1007/s10529-023-03460-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 12/08/2023] [Accepted: 12/14/2023] [Indexed: 01/29/2024]
Abstract
OBJECTIVES Apiosidases are enzymes that cleave the glycosidic bond between the monosaccharides linked to apiose, a branched chain furanose found in the cell walls of vascular plants and aquatic monocots. There is biotechnological interest in this enzyme group because apiose is the flavor-active compound of grapes, fruit juice, and wine, and the monosaccharide is found to be a plant secondary metabolite with pharmaceutical properties. However, functional and structural studies of this enzyme family are scarce. Recently, a glycoside hydrolase family member GH140 was isolated from Bacteroides thetaiotaomicron and identified as an endo-apiosidase. RESULTS The structural characterization and functional identification of a second GH140 family enzyme, termed MmApi, discovered through mangrove soil metagenomic approach, are described. Among the various substrates tested, MmApi exhibited activity on an apiose-containing oligosaccharide derived from the pectic polysaccharide rhamnogalacturonan-II. While the crystallographic model of MmApi was similar to the endo-apiosidase from Bacteroides thetaiotaomicron, differences in the shape of the binding sites indicated that MmApi could cleave apioses within oligosaccharides of different compositions. CONCLUSION This enzyme represents a novel tool for researchers interested in studying the physiology and structure of plant cell walls and developing biocatalytic strategies for drug and flavor production.
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Affiliation(s)
- Marcelo Vizona Liberato
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, Brazil
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, England
| | - Douglas Antonio Alvaredo Paixao
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Geizecler Tomazetto
- Department of Pediatrics, University of Pittsburgh School of Medicine, UPMC Children's Hospital of Pittsburgh, Pittsburgh, United States
| | - Didier Ndeh
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee, Scotland
| | - David N Bolam
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, England
| | - Fabio Marcio Squina
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, Brazil.
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Singh AK, Iqbal HMN, Cardullo N, Muccilli V, Fern'andez-Lucas J, Schmidt JE, Jesionowski T, Bilal M. Structural insights, biocatalytic characteristics, and application prospects of lignin-modifying enzymes for sustainable biotechnology-A review. Int J Biol Macromol 2023:124968. [PMID: 37217044 DOI: 10.1016/j.ijbiomac.2023.124968] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/22/2023] [Accepted: 05/17/2023] [Indexed: 05/24/2023]
Abstract
Lignin modifying enzymes (LMEs) have gained widespread recognition in depolymerization of lignin polymers by oxidative cleavage. LMEs are a robust class of biocatalysts that include lignin peroxidase (LiP), manganese peroxidase (MnP), versatile peroxidase (VP), laccase (LAC), and dye-decolorizing peroxidase (DyP). Members of the LMEs family act on phenolic, non-phenolic substrates and have been widely researched for valorization of lignin, oxidative cleavage of xenobiotics and phenolics. LMEs implementation in the biotechnological and industrial sectors has sparked significant attention, although its potential future applications remain underexploited. To understand the mechanism of LMEs in sustainable pollution mitigation, several studies have been undertaken to assess the feasibility of LMEs in correlating to diverse pollutants for binding and intermolecular interactions at the molecular level. However, further investigation is required to fully comprehend the underlying mechanism. In this review we presented the key structural and functional features of LMEs, including the computational aspects, as well as the advanced applications in biotechnology and industrial research. Furthermore, concluding remarks and a look ahead, the use of LMEs coupled with computational frameworks, built upon artificial intelligence (AI) and machine learning (ML), has been emphasized as a recent milestone in environmental research.
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Affiliation(s)
- Anil Kumar Singh
- Environmental Microbiology Laboratory, Environmental Toxicology Group CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
| | - Nunzio Cardullo
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, V.le A. Doria 6, 95125 Catania, Italy
| | - Vera Muccilli
- Dipartimento di Scienze Chimiche, Università degli Studi di Catania, V.le A. Doria 6, 95125 Catania, Italy
| | - Jesús Fern'andez-Lucas
- Applied Biotechnology Group, Universidad Europea de Madrid, Urbanizaci'on El Bosque, 28670 Villaviciosa de Od'on, Spain; Grupo de Investigaci'on en Ciencias Naturales y Exactas, GICNEX, Universidad de la Costa, CUC, Calle 58 # 55-66, 080002 Barranquilla, Colombia
| | - Jens Ejbye Schmidt
- Department of Chemical Engineering, Biotechnology and Environmental Technology, University of Southern Denmark, Odense, Denmark
| | - Teofil Jesionowski
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, PL-60965 Poznan, Poland
| | - Muhammad Bilal
- Institute of Chemical Technology and Engineering, Faculty of Chemical Technology, Poznan University of Technology, Berdychowo 4, PL-60965 Poznan, Poland.
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Shabaev AV, Moiseenko KV, Glazunova OA, Savinova OS, Fedorova TV. Comparative Analysis of Peniophora lycii and Trametes hirsuta Exoproteomes Demonstrates “Shades of Gray” in the Concept of White-Rotting Fungi. Int J Mol Sci 2022; 23:ijms231810322. [PMID: 36142233 PMCID: PMC9499651 DOI: 10.3390/ijms231810322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
White-rot basidiomycete fungi are a unique group of organisms that evolved an unprecedented arsenal of extracellular enzymes for an efficient degradation of all components of wood such as cellulose, hemicelluloses and lignin. The exoproteomes of white-rot fungi represent a natural enzymatic toolbox for white biotechnology. Currently, only exoproteomes of a narrow taxonomic group of white-rot fungi—fungi belonging to the Polyporales order—are extensively studied. In this article, two white-rot fungi, Peniophora lycii LE-BIN 2142 from the Russulales order and Trametes hirsuta LE-BIN 072 from the Polyporales order, were compared and contrasted in terms of their enzymatic machinery used for degradation of different types of wood substrates—alder, birch and pine sawdust. Our findings suggested that the studied fungi use extremely different enzymatic systems for the degradation of carbohydrates and lignin. While T. hirsuta LE-BIN 072 behaved as a typical white-rot fungus, P. lycii LE-BIN 2142 demonstrated substantial peculiarities. Instead of using cellulolytic and hemicellulolytic hydrolytic enzymes, P. lycii LE-BIN 2142 primarily relies on oxidative polysaccharide-degrading enzymes such as LPMO and GMC oxidoreductase. Moreover, exoproteomes of P. lycii LE-BIN 2142 completely lacked ligninolytic peroxidases, a well-known marker of white-rot fungi, but instead contained several laccase isozymes and previously uncharacterized FAD-binding domain-containing proteins.
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9
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Guo H, He T, Lee DJ. Contemporary proteomic research on lignocellulosic enzymes and enzymolysis: A review. BIORESOURCE TECHNOLOGY 2022; 344:126263. [PMID: 34728359 DOI: 10.1016/j.biortech.2021.126263] [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: 10/03/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
This review overviewed the current researches on the isolation of novel strains, the development of novel identification protocols, the key enzymes and their synergistic interactions with other functional enzyme systems, and the strategies for enhancing enzymolysis efficiencies. The main obstacle for realizing biorefinery of lignocellulosic biomass to biofuels or biochemicals is the high cost of enzymolysis stage. Therefore, research prospects to reduce the costs for lignocellulose hydrolysis were outlined.
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Affiliation(s)
- Hongliang Guo
- College of Forestry, Northeast Forestry University, Harbin 150040, China; College of Food Engineering, Harbin University of Commerce, Harbin 150076, China
| | - Tongyuan He
- College of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Duu-Jong Lee
- Department of Chemical Engineering, National Taiwan University, Taipei 10617, Taiwan; Department of Mechanical Engineering, City University of Hong Kong, Kowloon Tang, Hong Kong.
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10
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Li N, Su J, Wang H, Cavaco-Paulo A. Production of antimicrobial powders of guaiacol oligomers by a laccase-catalyzed synthesis reaction. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.07.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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11
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Ijoma GN, Heri SM, Matambo TS, Tekere M. Trends and Applications of Omics Technologies to Functional Characterisation of Enzymes and Protein Metabolites Produced by Fungi. J Fungi (Basel) 2021; 7:700. [PMID: 34575737 PMCID: PMC8464691 DOI: 10.3390/jof7090700] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 12/14/2022] Open
Abstract
Identifying and adopting industrial applications for proteins and enzymes derived from fungi strains have been at the focal point of several studies in recent times. To facilitate such studies, it is necessary that advancements and innovation in mycological and molecular characterisation are concomitant. This review aims to provide a detailed overview of the necessary steps employed in both qualitative and quantitative research using the omics technologies that are pertinent to fungi characterisation. This stems from the understanding that data provided from the functional characterisation of fungi and their metabolites is important towards the techno-economic feasibility of large-scale production of biological products. The review further describes how the functional gaps left by genomics, internal transcribe spacer (ITS) regions are addressed by transcriptomics and the various techniques and platforms utilised, including quantitive reverse transcription polymerase chain reaction (RT-qPCR), hybridisation techniques, and RNA-seq, and the insights such data provide on the effect of environmental changes on fungal enzyme production from an expressional standpoint. The review also offers information on the many available bioinformatics tools of analysis necessary for the analysis of the overwhelming data synonymous with the omics approach to fungal characterisation.
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Affiliation(s)
- Grace N. Ijoma
- Institute for the Development of Energy for African Sustainability (IDEAS), College of Science, Engineering and Technology, University of South Africa, P.O. Box 392, UNISA, Pretoria 0001, South Africa; (S.M.H.); (T.S.M.)
| | - Sylvie M. Heri
- Institute for the Development of Energy for African Sustainability (IDEAS), College of Science, Engineering and Technology, University of South Africa, P.O. Box 392, UNISA, Pretoria 0001, South Africa; (S.M.H.); (T.S.M.)
| | - Tonderayi S. Matambo
- Institute for the Development of Energy for African Sustainability (IDEAS), College of Science, Engineering and Technology, University of South Africa, P.O. Box 392, UNISA, Pretoria 0001, South Africa; (S.M.H.); (T.S.M.)
| | - Memory Tekere
- Department of Environmental Science, College of Agricultural and Environmental Science, University of South Africa, P.O. Box 392, UNISA, Pretoria 0001, South Africa;
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de Jesus Fontes B, Kleingesinds EK, Giovanella P, Junior AP, Sette LD. Laccases produced by Peniophora from marine and terrestrial origin: A comparative study. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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13
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Sethupathy S, Morales GM, Li Y, Wang Y, Jiang J, Sun J, Zhu D. Harnessing microbial wealth for lignocellulose biomass valorization through secretomics: a review. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:154. [PMID: 34225772 PMCID: PMC8256616 DOI: 10.1186/s13068-021-02006-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/26/2021] [Indexed: 05/10/2023]
Abstract
The recalcitrance of lignocellulosic biomass is a major constraint to its high-value use at industrial scale. In nature, microbes play a crucial role in biomass degradation, nutrient recycling and ecosystem functioning. Therefore, the use of microbes is an attractive way to transform biomass to produce clean energy and high-value compounds. The microbial degradation of lignocelluloses is a complex process which is dependent upon multiple secreted enzymes and their synergistic activities. The availability of the cutting edge proteomics and highly sensitive mass spectrometry tools make possible for researchers to probe the secretome of microbes and microbial consortia grown on different lignocelluloses for the identification of hydrolytic enzymes of industrial interest and their substrate-dependent expression. This review summarizes the role of secretomics in identifying enzymes involved in lignocelluloses deconstruction, the development of enzyme cocktails and the construction of synthetic microbial consortia for biomass valorization, providing our perspectives to address the current challenges.
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Affiliation(s)
- Sivasamy Sethupathy
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Gabriel Murillo Morales
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yixuan Li
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Yongli Wang
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jianxiong Jiang
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Jianzhong Sun
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China
| | - Daochen Zhu
- School of the Environment and Safety Engineering, Biofuels Institute, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.
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Cairns TC, Zheng X, Zheng P, Sun J, Meyer V. Turning Inside Out: Filamentous Fungal Secretion and Its Applications in Biotechnology, Agriculture, and the Clinic. J Fungi (Basel) 2021; 7:535. [PMID: 34356914 PMCID: PMC8307877 DOI: 10.3390/jof7070535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/14/2021] [Accepted: 06/25/2021] [Indexed: 12/15/2022] Open
Abstract
Filamentous fungi are found in virtually every marine and terrestrial habitat. Vital to this success is their ability to secrete a diverse range of molecules, including hydrolytic enzymes, organic acids, and small molecular weight natural products. Industrial biotechnologists have successfully harnessed and re-engineered the secretory capacity of dozens of filamentous fungal species to make a diverse portfolio of useful molecules. The study of fungal secretion outside fermenters, e.g., during host infection or in mixed microbial communities, has also led to the development of novel and emerging technological breakthroughs, ranging from ultra-sensitive biosensors of fungal disease to the efficient bioremediation of polluted environments. In this review, we consider filamentous fungal secretion across multiple disciplinary boundaries (e.g., white, green, and red biotechnology) and product classes (protein, organic acid, and secondary metabolite). We summarize the mechanistic understanding for how various molecules are secreted and present numerous applications for extracellular products. Additionally, we discuss how the control of secretory pathways and the polar growth of filamentous hyphae can be utilized in diverse settings, including industrial biotechnology, agriculture, and the clinic.
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Affiliation(s)
- Timothy C. Cairns
- Chair of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Xiaomei Zheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; (X.Z.); (P.Z.); (J.S.)
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Ping Zheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; (X.Z.); (P.Z.); (J.S.)
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Jibin Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; (X.Z.); (P.Z.); (J.S.)
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Vera Meyer
- Chair of Applied and Molecular Microbiology, Institute of Biotechnology, Technische Universität Berlin, Straße des 17. Juni 135, 10623 Berlin, Germany
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15
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Nanoparticles: Mechanism of biosynthesis using plant extracts, bacteria, fungi, and their applications. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116040] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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16
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Nikolaivits E, Siaperas R, Agrafiotis A, Ouazzani J, Magoulas A, Gioti Α, Topakas E. Functional and transcriptomic investigation of laccase activity in the presence of PCB29 identifies two novel enzymes and the multicopper oxidase repertoire of a marine-derived fungus. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 775:145818. [PMID: 33631558 DOI: 10.1016/j.scitotenv.2021.145818] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 02/04/2021] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
Polychlorinated biphenyls (PCBs) are persistent organic pollutants (POPs), that can be detected in a variety of environments including the human body, adversely affecting global health. Bioremediation is an emerging field for the detoxification and removal of environmental pollutants, with novel biocatalysts appropriate for this task being in high demand. In this study, a biobank of novel fungal strains isolated as symbionts of marine invertebrates was screened for their ability to remove 2,4,5-trichlorobiphenyl (PCB29). The most efficient strains were studied further for their ability to express laccase activity, the most commonly associated extracellular activity involved in the removal of aromatic pollutants and encoded in fungi by the enzymatic class of multicopper oxidases (MCOs). The strain expressing the highest laccase activity, Cladosporium sp. TM138-S3, was cultivated in the presence of copper ions in a 12 L bioreactor and two enzymes exhibiting laccase activity were isolated from the culture broth through ion-exchange chromatography. The two enzymes, Lac1 and Lac2, were biochemically characterized and showed similar characteristics, although an improved ability to remove PCB29 (up to 71.2%) was observed for Lac2 in the presence of mediators. In parallel, we performed RNAseq of the strain growing in presence and absence of PCB29 and reconstructed its transcriptome assembly. Functional annotation allowed identifying the MCO repertoire of the fungus, consisting of 13 enzymes. Phylogenetic analysis of Ascomycete MCOs further allowed classifying these enzymes, revealing the diversity of laccase activities in Cladosporium sp. TM138-S3.
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Affiliation(s)
- Efstratios Nikolaivits
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Romanos Siaperas
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Andreas Agrafiotis
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Jamal Ouazzani
- Institut de Chimie des Substances Naturelles, ICSN, CNRS, Gif sur Yvette, France
| | - Antonios Magoulas
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
| | - Αnastasia Gioti
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
| | - Evangelos Topakas
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece.
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Wong Chin JM, Puchooa D, Bahorun T, Jeewon R. Antimicrobial properties of marine fungi from sponges and brown algae of Mauritius. Mycology 2021; 12:231-244. [PMID: 34900379 PMCID: PMC8654394 DOI: 10.1080/21501203.2021.1895347] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/19/2021] [Indexed: 11/03/2022] Open
Abstract
Purpose of the study: Marine fungi of Mauritius have been poorly studied. There are numerous reports on the bioactive secondary metabolites that are produced by fungi around the world. Yet, research on the molecular characterisation and the pharmaceutical potential of marine fungi in Mauritius is rather scanty. Method: The samples, which consisted of three sponges Haliclona sp., Iotrochota sp. and Biemna sp. and two brown algae Turbinaria conoides and Sargassum portierianum, were collected in the North of Mauritius during winter. No sporulating structures were observed from the fungal cultures making morphological analysis impossible. The molecular characterisation of the selected isolates was carried out by the amplification of the ITS regions and phylogenetic analysis. The antimicrobial properties were then determined using the disc diffusion and the minimum inhibitory concentration (MIC) assay. Results: Genus level identification was made from molecular data and for some isolates, species-level identification was even possible. Twelve fungi that showed the best antimicrobial properties were identified as Peniophora sp., Aspergillus cristatus, Acremonium sp., Cordyceps memorabilis, Aspergillus ochraceus, Biscogniauxia sp., Aspergillus keratitidis, Exserohilum rostratum, Chromocleista sp., Nigrospora oryzae, Aspergillus flavipes and Mycosphaerella. The lowest MIC result of 0.0098 mg/mL was obtained with Chromocleista sp. mycelium extract against Staphylococcus aureus. The MIC of the mycelium extracts was lower than the broth extracts for most isolates indicating that the antimicrobial compounds are not secreted. Conclusion: Marine fungi from the Mauritian waters have immense potential in the search for natural products against antibiotic-resistant bacteria.
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Affiliation(s)
| | - Daneshwar Puchooa
- Department of Agricultural and Food Science, University of Mauritius, Réduit, Republic of Mauritius
| | - Theeshan Bahorun
- Department of Biosciences and Ocean Studies, ANDI Centre for Biomedical and Biomaterials Research (CBBR) and University of Mauritius, Réduit, Republic of Mauritius
| | - Rajesh Jeewon
- Department of Health Sciences, University of Mauritius, Réduit, Republic of Mauritius
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18
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Ben Ayed A, Saint-Genis G, Vallon L, Linde D, Turbé-Doan A, Haon M, Daou M, Bertrand E, Faulds CB, Sciara G, Adamo M, Marmeisse R, Comtet-Marre S, Peyret P, Abrouk D, Ruiz-Dueñas FJ, Marchand C, Hugoni M, Luis P, Mechichi T, Record E. Exploring the Diversity of Fungal DyPs in Mangrove Soils to Produce and Characterize Novel Biocatalysts. J Fungi (Basel) 2021; 7:jof7050321. [PMID: 33919051 PMCID: PMC8143184 DOI: 10.3390/jof7050321] [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: 03/26/2021] [Revised: 04/16/2021] [Accepted: 04/16/2021] [Indexed: 01/21/2023] Open
Abstract
The functional diversity of the New Caledonian mangrove sediments was examined, observing the distribution of fungal dye-decolorizing peroxidases (DyPs), together with the complete biochemical characterization of the main DyP. Using a functional metabarcoding approach, the diversity of expressed genes encoding fungal DyPs was investigated in surface and deeper sediments, collected beneath either Avicennia marina or Rhizophora stylosa trees, during either the wet or the dry seasons. The highest DyP diversity was observed in surface sediments beneath the R. stylosa area during the wet season, and one particular operational functional unit (OFU1) was detected as the most abundant DyP isoform. This OFU was found in all sediment samples, representing 51–100% of the total DyP-encoding sequences in 70% of the samples. The complete cDNA sequence corresponding to this abundant DyP (OFU 1) was retrieved by gene capture, cloned, and heterologously expressed in Pichia pastoris. The recombinant enzyme, called DyP1, was purified and characterized, leading to the description of its physical–chemical properties, its ability to oxidize diverse phenolic substrates, and its potential to decolorize textile dyes; DyP1 was more active at low pH, though moderately stable over a wide pH range. The enzyme was very stable at temperatures up to 50 °C, retaining 60% activity after 180 min incubation. Its ability to decolorize industrial dyes was also tested on Reactive Blue 19, Acid Black, Disperse Blue 79, and Reactive Black 5. The effect of hydrogen peroxide and sea salt on DyP1 activity was studied and compared to what is reported for previously characterized enzymes from terrestrial and marine-derived fungi.
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Affiliation(s)
- Amal Ben Ayed
- INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, 13288 Marseille, France; (A.B.A.); (A.T.-D.); (M.H.); (M.D.); (E.B.); (C.B.F.); (G.S.)
- Laboratoire de Biochimie et de Génie, Enzymatique des Lipases, Université de Sfax, Ecole Nationale d’Ingénieurs de Sfax, 3038 Sfax, Tunisia;
| | - Geoffroy Saint-Genis
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622 Villeurbanne, France; (G.S.-G.); (L.V.); (M.A.); (P.L.); (R.M.); (D.A.); (M.H.)
| | - Laurent Vallon
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622 Villeurbanne, France; (G.S.-G.); (L.V.); (M.A.); (P.L.); (R.M.); (D.A.); (M.H.)
| | - Dolores Linde
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, 28040 Madrid, Spain; (D.L.); (F.J.R.-D.)
| | - Annick Turbé-Doan
- INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, 13288 Marseille, France; (A.B.A.); (A.T.-D.); (M.H.); (M.D.); (E.B.); (C.B.F.); (G.S.)
| | - Mireille Haon
- INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, 13288 Marseille, France; (A.B.A.); (A.T.-D.); (M.H.); (M.D.); (E.B.); (C.B.F.); (G.S.)
| | - Marianne Daou
- INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, 13288 Marseille, France; (A.B.A.); (A.T.-D.); (M.H.); (M.D.); (E.B.); (C.B.F.); (G.S.)
- Department of Chemistry, Khalifa University, P.O. Box 127788, Abu Dhabi, United Arab Emirates
| | - Emmanuel Bertrand
- INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, 13288 Marseille, France; (A.B.A.); (A.T.-D.); (M.H.); (M.D.); (E.B.); (C.B.F.); (G.S.)
| | - Craig B. Faulds
- INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, 13288 Marseille, France; (A.B.A.); (A.T.-D.); (M.H.); (M.D.); (E.B.); (C.B.F.); (G.S.)
| | - Giuliano Sciara
- INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, 13288 Marseille, France; (A.B.A.); (A.T.-D.); (M.H.); (M.D.); (E.B.); (C.B.F.); (G.S.)
| | - Martino Adamo
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622 Villeurbanne, France; (G.S.-G.); (L.V.); (M.A.); (P.L.); (R.M.); (D.A.); (M.H.)
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi di Torino, 10125 Torino, Italy
| | - Roland Marmeisse
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622 Villeurbanne, France; (G.S.-G.); (L.V.); (M.A.); (P.L.); (R.M.); (D.A.); (M.H.)
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi di Torino, 10125 Torino, Italy
| | - Sophie Comtet-Marre
- Université Clermont Auvergne, INRAE, MEDiS, 63000 Clermont-Ferrand, France; (S.C.-M.); (P.P.)
| | - Pierre Peyret
- Université Clermont Auvergne, INRAE, MEDiS, 63000 Clermont-Ferrand, France; (S.C.-M.); (P.P.)
| | - Danis Abrouk
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622 Villeurbanne, France; (G.S.-G.); (L.V.); (M.A.); (P.L.); (R.M.); (D.A.); (M.H.)
| | - Francisco J. Ruiz-Dueñas
- Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, 28040 Madrid, Spain; (D.L.); (F.J.R.-D.)
| | - Cyril Marchand
- IMPMC, Institut de Recherche Pour le Développement (IRD), UPMC, CNRS, MNHN, 98851 Noumea, France;
- ISEA, EA, Université de la Nouvelle-Calédonie (UNC), 3325, BP R4, 98851 Noumea, France
| | - Mylène Hugoni
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622 Villeurbanne, France; (G.S.-G.); (L.V.); (M.A.); (P.L.); (R.M.); (D.A.); (M.H.)
| | - Patricia Luis
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, 69622 Villeurbanne, France; (G.S.-G.); (L.V.); (M.A.); (P.L.); (R.M.); (D.A.); (M.H.)
| | - Tahar Mechichi
- Laboratoire de Biochimie et de Génie, Enzymatique des Lipases, Université de Sfax, Ecole Nationale d’Ingénieurs de Sfax, 3038 Sfax, Tunisia;
| | - Eric Record
- INRAE, UMR1163, Biodiversité et Biotechnologie Fongiques, Aix-Marseille Université, 13288 Marseille, France; (A.B.A.); (A.T.-D.); (M.H.); (M.D.); (E.B.); (C.B.F.); (G.S.)
- Correspondence:
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Mat Razali N, Hisham SN, Kumar IS, Shukla RN, Lee M, Abu Bakar MF, Nadarajah K. Comparative Genomics: Insights on the Pathogenicity and Lifestyle of Rhizoctonia solani. Int J Mol Sci 2021; 22:ijms22042183. [PMID: 33671736 PMCID: PMC7926851 DOI: 10.3390/ijms22042183] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/06/2021] [Accepted: 02/15/2021] [Indexed: 12/17/2022] Open
Abstract
Proper management of agricultural disease is important to ensure sustainable food security. Staple food crops like rice, wheat, cereals, and other cash crops hold great export value for countries. Ensuring proper supply is critical; hence any biotic or abiotic factors contributing to the shortfall in yield of these crops should be alleviated. Rhizoctonia solani is a major biotic factor that results in yield losses in many agriculturally important crops. This paper focuses on genome informatics of our Malaysian Draft R. solani AG1-IA, and the comparative genomics (inter- and intra- AG) with four AGs including China AG1-IA (AG1-IA_KB317705.1), AG1-IB, AG3, and AG8. The genomic content of repeat elements, transposable elements (TEs), syntenic genomic blocks, functions of protein-coding genes as well as core orthologous genic information that underlies R. solani’s pathogenicity strategy were investigated. Our analyses show that all studied AGs have low content and varying profiles of TEs. All AGs were dominant for Class I TE, much like other basidiomycete pathogens. All AGs demonstrate dominance in Glycoside Hydrolase protein-coding gene assignments suggesting its importance in infiltration and infection of host. Our profiling also provides a basis for further investigation on lack of correlation observed between number of pathogenicity and enzyme-related genes with host range. Despite being grouped within the same AG with China AG1-IA, our Draft AG1-IA exhibits differences in terms of protein-coding gene proportions and classifications. This implies that strains from similar AG do not necessarily have to retain similar proportions and classification of TE but must have the necessary arsenal to enable successful infiltration and colonization of host. In a larger perspective, all the studied AGs essentially share core genes that are generally involved in adhesion, penetration, and host colonization. However, the different infiltration strategies will depend on the level of host resilience where this is clearly exhibited by the gene sets encoded for the process of infiltration, infection, and protection from host.
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Affiliation(s)
- Nurhani Mat Razali
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia; (N.M.R.); (S.N.H.); (I.S.K.)
| | - Siti Norvahida Hisham
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia; (N.M.R.); (S.N.H.); (I.S.K.)
| | - Ilakiya Sharanee Kumar
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia; (N.M.R.); (S.N.H.); (I.S.K.)
| | - Rohit Nandan Shukla
- Bionivid Technology Pte Ltd., 209, 4th Cross Rd, B Channasandra, East of NGEF Layout, Kasturi Nagar, Bengaluru 560043, Karnataka, India;
| | - Melvin Lee
- Codon Genomics Sdn. Bhd., No 26, Jalan Dutamas 7 Taman Dutamas Balakong, Seri Kembangan 43200, Selangor, Malaysia;
| | | | - Kalaivani Nadarajah
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia; (N.M.R.); (S.N.H.); (I.S.K.)
- Correspondence:
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20
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Purification and Characterization of Two Novel Laccases from Peniophora lycii. J Fungi (Basel) 2020; 6:jof6040340. [PMID: 33291231 PMCID: PMC7762197 DOI: 10.3390/jof6040340] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/02/2020] [Accepted: 12/03/2020] [Indexed: 01/09/2023] Open
Abstract
Although, currently, more than 100 laccases have been purified from basidiomycete fungi, the majority of these laccases were obtained from fungi of the Polyporales order, and only scarce data are available about the laccases from other fungi. In this article, laccase production by the white-rot basidiomycete fungus Peniophora lycii, belonging to the Russulales order, was investigated. It was shown that, under copper induction, this fungus secreted three different laccase isozymes. Two laccase isozymes—Lac5 and LacA—were purified and their corresponding nucleotide sequences were determined. Both purified laccases were relatively thermostable with periods of half-life at 70 °C of 10 and 8 min for Lac5 and LacA, respectively. The laccases demonstrated the highest activity toward ABTS (97 U·mg−1 for Lac5 and 121 U·mg−1 for LacA at pH 4.5); Lac5 demonstrated the lowest activity toward 2,6-DMP (2.5 U·mg−1 at pH 4.5), while LacA demonstrated this towards gallic acid (1.4 U·mg−1 at pH 4.5). Both Lac5 and LacA were able to efficiently decolorize such dyes as RBBR and Bromcresol Green. Additionally, phylogenetic relationships among laccases of Peniophora spp. were reconstructed, and groups of orthologous genes were determined. Based on these groups, all currently available data about laccases of Peniophora spp. were systematized.
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21
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de Oliveira BFR, Carr CM, Dobson ADW, Laport MS. Harnessing the sponge microbiome for industrial biocatalysts. Appl Microbiol Biotechnol 2020; 104:8131-8154. [PMID: 32827049 DOI: 10.1007/s00253-020-10817-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/29/2020] [Accepted: 08/05/2020] [Indexed: 12/31/2022]
Abstract
Within the marine sphere, host-associated microbiomes are receiving growing attention as prolific sources of novel biocatalysts. Given the known biocatalytic potential of poriferan microbial inhabitants, this review focuses on enzymes from the sponge microbiome, with special attention on their relevant properties and the wide range of their potential biotechnological applications within various industries. Cultivable bacterial and filamentous fungal isolates account for the majority of the enzymatic sources. Hydrolases, mainly glycoside hydrolases and carboxylesterases, are the predominant reported group of enzymes, with varying degrees of tolerance to alkaline pH and growing salt concentrations being common. Prospective areas for the application of these microbial enzymes include biorefinery, detergent, food and effluent treatment industries. Finally, alternative strategies to identify novel biocatalysts from the sponge microbiome are addressed, with an emphasis on modern -omics-based approaches that are currently available in the enzyme research arena. By providing this current overview of the field, we hope to not only increase the appetite of researchers to instigate forthcoming studies but also to stress how basic and applied research can pave the way for new biocatalysts from these symbiotic microbial communities in a productive fashion. KEY POINTS: • The sponge microbiome is a burgeoning source of industrial biocatalysts. • Sponge microbial enzymes have useful habitat-related traits for several industries. • Strategies are provided for the future discovery of microbial enzymes from sponges.
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Affiliation(s)
- Bruno Francesco Rodrigues de Oliveira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil. .,School of Microbiology, University College Cork, Cork, Ireland.
| | - Clodagh M Carr
- School of Microbiology, University College Cork, Cork, Ireland
| | - Alan D W Dobson
- School of Microbiology, University College Cork, Cork, Ireland.,Environmental Research Institute, University College Cork, Cork, Ireland
| | - Marinella Silva Laport
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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Li T, Huang L, Li Y, Xu Z, Ge X, Zhang Y, Wang N, Wang S, Yang W, Lu F, Liu Y. The heterologous expression, characterization, and application of a novel laccase from Bacillus velezensis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 713:136713. [PMID: 32019046 DOI: 10.1016/j.scitotenv.2020.136713] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 01/11/2020] [Accepted: 01/13/2020] [Indexed: 06/10/2023]
Abstract
Laccases have a huge potential in numerous environmental and industrial applications due to the ability to oxidized a wide range of substrates. Here, a novel laccase gene from the identified Bacillus velezensis TCCC 111904 was heterologously expressed in Escherichia coli. The optimal temperature and pH for oxidation by recombinant laccase (rLac) were 80 °C and 5.5, respectively, in the case of the substrate 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), and 80 °C and 7.0, respectively, in the case of 2,6-dimethoxyphenol (2,6-DMP). rLac exhibited high thermostability and pH stability over a wide range (pH 3.0, 7.0, and 9.0). Additionally, most of the metal ions did not inhibit the activity of rLac significantly. rLac showed great tolerance against high concentration of NaCl, and 50.8% of its initial activity remained in the reaction system containing 500 mM NaCl compared to the control. Moreover, rLac showed a high efficiency in decolorizing different types of dyes including azo, anthraquinonic, and triphenylmethane dyes at a high temperature (60 °C) and over an extensive pH range (pH 5.5, 7.0, and 9.0). These unique characteristics of rLac indicated that it could be a potential candidate for applications in treatment of dye effluents and other industrial processes.
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Affiliation(s)
- Tao Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China; College of Basic Science, Tianjin Agricultural University, Tianjin 300384, PR China
| | - Lin Huang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Yanzhen Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Zehua Xu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Xiuqi Ge
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Yuanfu Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Nan Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Shuang Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Wei Yang
- College of Basic Science, Tianjin Agricultural University, Tianjin 300384, PR China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Yihan Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
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