1
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Daniel AI, Smith E, Al-Hashimi A, Gokul A, Keyster M, Klein A. Mechanistic insight into the anti-alternaria activity of bimetallic zinc oxide and silver/zinc oxide nanoparticles. Heliyon 2024; 10:e31330. [PMID: 38803897 PMCID: PMC11129099 DOI: 10.1016/j.heliyon.2024.e31330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 05/11/2024] [Accepted: 05/14/2024] [Indexed: 05/29/2024] Open
Abstract
Alternaria alternata is an opportunistic phytopathogen that negatively impact the growth and production of a wide variety of host plants. In this study, we evaluated the antifungal potential of biogenic ZnO, and bimetallic silver and zinc oxide (Ag/ZnO) nanoparticles synthesized using seed extract of Abrus precatorious and characterized using different analytical tools. In vitro antifungal potentials of ZnO and Ag/ZnO nanoparticles were carried out using the food poison technique. Morphological and ultrastructure of the A. alternata treated with the nanoparticles were carried out using high resolution scanning and transmission electron microscopy (HRSEM and HRTEM). In addition, changes in polysaccharide production, chitin content and enzymatic (cellulase and lipase) activities of A. alternata were assayed. Double peak signifying a UVmax of 353.88 and 417.25 nm representing Ag and ZnO respectively was formed in the bimetallic nanoparticles. HRSEM and HRTEM results shows agglomerated nanoparticles with particle and crystallite size of 23.94 and 16.84 nm for ZnO nanoparticles, 35.12 and 28.99 nm for Ag/ZnO nanoparticles respectively. In vitro antifungal assay shows a significant concentration-dependent inhibition (p < 0.05) of A. alternata mycelia with highest percentage inhibition of 73.93 % (ZnO nanoparticles) and 68.26 % (Ag/ZnO nanoparticles) at 200 ppm. HRSEM and HRTEM micrographs of the treated A. alternata mycelia shows alteration of the cellular structure, clearance of the cytoplasmic organelles and localization of the nanoparticles within the cell. A. alternata treated with 200 ppm nanoparticles show a significant decrease (p < 0.05) in the polysaccharides and chitin contents, cellulase and lipase activities. The results suggests that ZnO and Ag/ZnO nanoparticles mode of action may be via alteration of the fungal cell wall through the inhibition of polysaccharides, chitin, cellulases and lipases synthesis. ZnO and Ag/ZnO nanoparticles may be a promising tool for the management and control of disease causing fungal phytopathogens.
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Affiliation(s)
- Augustine Innalegwu Daniel
- Plant Omics Laboratory, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Robert Sobukwe Road, Bellville, 7535, South Africa
- Department of Biochemistry, School of Life Sciences, Federal University of Technology, P.M.B 65, Minna, Niger State, Nigeria
| | - Enriquay Smith
- Plant Omics Laboratory, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Robert Sobukwe Road, Bellville, 7535, South Africa
| | - Ali Al-Hashimi
- Plant Omics Laboratory, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Robert Sobukwe Road, Bellville, 7535, South Africa
| | - Arun Gokul
- Department of Plant Sciences, Qwaqwa Campus, University of the Free State, Phuthadithjaba, 9866, South Africa
| | - Marshall Keyster
- Environmental Biotechnology Laboratory, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Robert Sobukwe Road, Bellville, 7535, South Africa
| | - Ashwil Klein
- Plant Omics Laboratory, Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Robert Sobukwe Road, Bellville, 7535, South Africa
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2
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Peña-Castro JM, Muñoz-Páez KM, Robledo-Narvaez PN, Vázquez-Núñez E. Engineering the Metabolic Landscape of Microorganisms for Lignocellulosic Conversion. Microorganisms 2023; 11:2197. [PMID: 37764041 PMCID: PMC10535843 DOI: 10.3390/microorganisms11092197] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/16/2023] [Accepted: 08/18/2023] [Indexed: 09/29/2023] Open
Abstract
Bacteria and yeast are being intensively used to produce biofuels and high-added-value products by using plant biomass derivatives as substrates. The number of microorganisms available for industrial processes is increasing thanks to biotechnological improvements to enhance their productivity and yield through microbial metabolic engineering and laboratory evolution. This is allowing the traditional industrial processes for biofuel production, which included multiple steps, to be improved through the consolidation of single-step processes, reducing the time of the global process, and increasing the yield and operational conditions in terms of the desired products. Engineered microorganisms are now capable of using feedstocks that they were unable to process before their modification, opening broader possibilities for establishing new markets in places where biomass is available. This review discusses metabolic engineering approaches that have been used to improve the microbial processing of biomass to convert the plant feedstock into fuels. Metabolically engineered microorganisms (MEMs) such as bacteria, yeasts, and microalgae are described, highlighting their performance and the biotechnological tools that were used to modify them. Finally, some examples of patents related to the MEMs are mentioned in order to contextualize their current industrial use.
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Affiliation(s)
- Julián Mario Peña-Castro
- Centro de Investigaciones Científicas, Instituto de Biotecnología, Universidad del Papaloapan, Tuxtepec 68301, Oaxaca, Mexico;
| | - Karla M. Muñoz-Páez
- CONAHCYT—Instituto de Ingeniería, Unidad Académica Juriquilla, Universidad Nacional Autónoma de México, Queretaro 76230, Queretaro, Mexico;
| | | | - Edgar Vázquez-Núñez
- Grupo de Investigación Sobre Aplicaciones Nano y Bio Tecnológicas para la Sostenibilidad (NanoBioTS), Departamento de Ingenierías Química, Electrónica y Biomédica, División de Ciencias e Ingenierías, Universidad de Guanajuato, Lomas del Bosque 103, Lomas del Campestre, León 37150, Guanajuato, Mexico
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3
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Kalia VC, Gong C, Shanmugam R, Lee JK. Prospecting Microbial Genomes for Biomolecules and Their Applications. Indian J Microbiol 2022; 62:516-523. [PMID: 36458216 PMCID: PMC9705627 DOI: 10.1007/s12088-022-01040-x] [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: 08/02/2022] [Accepted: 09/04/2022] [Indexed: 11/26/2022] Open
Abstract
Bioactive molecules of microbial origin are finding increasing biotechnological applications. Their sources range from the terrestrial, marine, and endophytic to the human microbiome. These biomolecules have unique chemical structures and related groups, which enable them to improve the efficiency of the bioprocesses. This review focuses on the applications of biomolecules in bioremediation, agriculture, food, pharmaceutical industries, and human health.
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Affiliation(s)
- Vipin Chandra Kalia
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
| | - Chunjie Gong
- National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan, 430068 People’s Republic of China
| | - Ramasamy Shanmugam
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul, 05029 Republic of Korea
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4
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Kukkar D, Sharma PK, Kim KH. Recent advances in metagenomic analysis of different ecological niches for enhanced biodegradation of recalcitrant lignocellulosic biomass. ENVIRONMENTAL RESEARCH 2022; 215:114369. [PMID: 36165858 DOI: 10.1016/j.envres.2022.114369] [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: 08/12/2022] [Revised: 09/06/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Lignocellulose wastes stemming from agricultural residues can offer an excellent opportunity as alternative energy solutions in addition to fossil fuels. Besides, the unrestrained burning of agricultural residues can lead to the destruction of the soil microflora and associated soil sterilization. However, the difficulties associated with the biodegradation of lignocellulose biomasses remain as a formidable challenge for their sustainable management. In this respect, metagenomics can be used as an effective option to resolve such dilemma because of its potential as the next generation sequencing technology and bioinformatics tools to harness novel microbial consortia from diverse environments (e.g., soil, alpine forests, and hypersaline/acidic/hot sulfur springs). In light of the challenges associated with the bulk-scale biodegradation of lignocellulose-rich agricultural residues, this review is organized to help delineate the fundamental aspects of metagenomics towards the assessment of the microbial consortia and novel molecules (such as biocatalysts) which are otherwise unidentifiable by conventional laboratory culturing techniques. The discussion is extended further to highlight the recent advancements (e.g., from 2011 to 2022) in metagenomic approaches for the isolation and purification of lignocellulolytic microbes from different ecosystems along with the technical challenges and prospects associated with their wide implementation and scale-up. This review should thus be one of the first comprehensive reports on the metagenomics-based analysis of different environmental samples for the isolation and purification of lignocellulose degrading enzymes.
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Affiliation(s)
- Deepak Kukkar
- Department of Biotechnology, Chandigarh University, Gharuan, Mohali - 140413, Punjab, India; University Centre for Research and Development, Chandigarh University, Gharuan, Mohali - 140413, Punjab, India.
| | | | - Ki-Hyun Kim
- Department of Civil and Environmental Engineering, Hanyang University, Seongdong-gu, Wangsimni-ro, Seoul - 04763, South Korea.
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5
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Metagenomic Approaches as a Tool to Unravel Promising Biocatalysts from Natural Resources: Soil and Water. Catalysts 2022. [DOI: 10.3390/catal12040385] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Natural resources are considered a promising source of microorganisms responsible for producing biocatalysts with great relevance in several industrial areas. However, a significant fraction of the environmental microorganisms remains unknown or unexploited due to the limitations associated with their cultivation in the laboratory through classical techniques. Metagenomics has emerged as an innovative and strategic approach to explore these unculturable microorganisms through the analysis of DNA extracted from environmental samples. In this review, a detailed discussion is presented on the application of metagenomics to unravel the biotechnological potential of natural resources for the discovery of promising biocatalysts. An extensive bibliographic survey was carried out between 2010 and 2021, covering diverse metagenomic studies using soil and/or water samples from different types and locations. The review comprises, for the first time, an overview of the worldwide metagenomic studies performed in soil and water and provides a complete and global vision of the enzyme diversity associated with each specific environment.
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6
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Thermostable cellulose saccharifying microbial enzymes: Characteristics, recent advances and biotechnological applications. Int J Biol Macromol 2021; 188:226-244. [PMID: 34371052 DOI: 10.1016/j.ijbiomac.2021.08.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/19/2021] [Accepted: 08/03/2021] [Indexed: 12/12/2022]
Abstract
Cellulases play a promising role in the bioconversion of renewable lignocellulosic biomass into fermentable sugars which are subsequently fermented to biofuels and other value-added chemicals. Besides biofuel industries, they are also in huge demand in textile, detergent, and paper and pulp industries. Low titres of cellulase production and processing are the main issues that contribute to high enzyme cost. The success of ethanol-based biorefinery depends on high production titres and the catalytic efficiency of cellulases functional at elevated temperatures with acid/alkali tolerance and the low cost. In view of their wider application in various industrial processes, stable cellulases that are active at elevated temperatures in the acidic-alkaline pH ranges, and organic solvents and salt tolerance would be useful. This review provides a recent update on the advances made in thermostable cellulases. Developments in their sources, characteristics and mechanisms are updated. Various methods such as rational design, directed evolution, synthetic & system biology and immobilization techniques adopted in evolving cellulases with ameliorated thermostability and characteristics are also discussed. The wide range of applications of thermostable cellulases in various industrial sectors is described.
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7
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Screening, cloning, enzymatic properties of a novel thermostable cellulase enzyme, and its potential application on water hyacinth utilization. Int Microbiol 2021; 24:337-349. [DOI: 10.1007/s10123-021-00170-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 02/02/2021] [Accepted: 03/02/2021] [Indexed: 01/01/2023]
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8
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Sugiharto S, Widiastuti E, Isroli I, Wahyuni HI, Yudiarti T. Effect of a Fermented Mixture of Papaya Leaf and Seed Meal on Production Traits and Intestinal Ecology of the Indonesian Indigenous Crossbred Chickens. ACTA UNIVERSITATIS AGRICULTURAE ET SILVICULTURAE MENDELIANAE BRUNENSIS 2020. [DOI: 10.11118/actaun202068040707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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9
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Simultaneous Enhancement of Thermostability and Catalytic Activity of a Metagenome-Derived β-Glucosidase Using Directed Evolution for the Biosynthesis of Butyl Glucoside. Int J Mol Sci 2019; 20:ijms20246224. [PMID: 31835569 PMCID: PMC6940790 DOI: 10.3390/ijms20246224] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/08/2019] [Accepted: 12/08/2019] [Indexed: 01/16/2023] Open
Abstract
Butyl glucoside synthesis using bioenzymatic methods at high temperatures has gained increasing interest. Protein engineering using directed evolution of a metagenome-derived β-glucosidase of Bgl1D was performed to identify enzymes with improved activity and thermostability. An interesting mutant Bgl1D187 protein containing five amino acid substitutions (S28T, Y37H, D44E, R91G, and L115N), showed catalytic efficiency (kcat/Km of 561.72 mM−1 s−1) toward ρ-nitrophenyl-β-d-glucopyranoside (ρNPG) that increased by 23-fold, half-life of inactivation by 10-fold, and further retained transglycosidation activity at 50 °C as compared with the wild-type Bgl1D protein. Site-directed mutagenesis also revealed that Asp44 residue was essential to β-glucosidase activity of Bgl1D. This study improved our understanding of the key amino acids of the novel β-glucosidases and presented a raw material with enhanced catalytic activity and thermostability for the synthesis of butyl glucosides.
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10
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Yang YJ, Lin W, Singh RP, Xu Q, Chen Z, Yuan Y, Zou P, Li Y, Zhang C. Genomic, Transcriptomic and Enzymatic Insight into Lignocellulolytic System of a Plant Pathogen Dickeya sp. WS52 to Digest Sweet Pepper and Tomato Stalk. Biomolecules 2019; 9:biom9120753. [PMID: 31756942 PMCID: PMC6995524 DOI: 10.3390/biom9120753] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/15/2019] [Accepted: 11/18/2019] [Indexed: 12/29/2022] Open
Abstract
Dickeya sp., a plant pathogen, causing soft rot with strong pectin degradation capacity was taken for the comprehensive analysis of its corresponding biomass degradative system, which has not been analyzed yet. Whole genome sequence analysis of the isolated soft-rotten plant pathogen Dickeya sp. WS52, revealed various coding genes which involved in vegetable stalk degradation-related properties. A total of 122 genes were found to be encoded for putative carbohydrate-active enzymes (CAZy) in Dickeya sp. WS52. The number of pectin degradation-related genes, was higher than that of cellulolytic bacteria as well as other Dickeya spp. strains. The CAZy in Dickeya sp.WS52 contains a complete repertoire of enzymes required for hemicellulose degradation, especially pectinases. In addition, WS52 strain possessed plenty of genes encoding potential ligninolytic relevant enzymes, such as multicopper oxidase, catalase/hydroperoxidase, glutathione S-transferase, and quinone oxidoreductase. Transcriptome analysis revealed that parts of genes encoding lignocellulolytic enzymes were significantly upregulated in the presence of minimal salt medium with vegetable stalks. However, most of the genes were related to lignocellulolytic enzymes, especially pectate lyases and were downregulated due to the slow growth and downregulated secretion systems. The assay of lignocellulolytic enzymes including CMCase and pectinase activities were identified to be more active in vegetable stalk relative to MSM + glucose. However, compared with nutrient LB medium, it needed sufficient nutrient to promote growth and to improve the secretion system. Further identification of enzyme activities of Dickeya sp.WS52 by HPLC confirmed that monosaccharides were produced during degradation of tomato stalk. This identified degradative system is valuable for the application in the lignocellulosic bioenergy industry and animal production.
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Affiliation(s)
- Ying-Jie Yang
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (Y.-J.Y.); (Y.Y.); (P.Z.); (Y.L.)
| | - Wei Lin
- Tobacco Research Institute of Nanping, Nanping, Fujian 353000, China; (W.L.); (Q.X.); (Z.C.)
| | - Raghvendra Pratap Singh
- Department of Research & Development, Biotechnology, Uttaranchal University, Dehradun 248007, India
- Correspondence: (R.P.S.); (C.Z.)
| | - Qian Xu
- Tobacco Research Institute of Nanping, Nanping, Fujian 353000, China; (W.L.); (Q.X.); (Z.C.)
| | - Zhihou Chen
- Tobacco Research Institute of Nanping, Nanping, Fujian 353000, China; (W.L.); (Q.X.); (Z.C.)
| | - Yuan Yuan
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (Y.-J.Y.); (Y.Y.); (P.Z.); (Y.L.)
| | - Ping Zou
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (Y.-J.Y.); (Y.Y.); (P.Z.); (Y.L.)
| | - Yiqiang Li
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (Y.-J.Y.); (Y.Y.); (P.Z.); (Y.L.)
| | - Chengsheng Zhang
- Marine Agriculture Research Center, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao 266101, China; (Y.-J.Y.); (Y.Y.); (P.Z.); (Y.L.)
- Correspondence: (R.P.S.); (C.Z.)
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11
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Wierzbicka-Woś A, Henneberger R, Batista-García RA, Martínez-Ávila L, Jackson SA, Kennedy J, Dobson ADW. Biochemical Characterization of a Novel Monospecific Endo-β-1,4-Glucanase Belonging to GH Family 5 From a Rhizosphere Metagenomic Library. Front Microbiol 2019; 10:1342. [PMID: 31258522 PMCID: PMC6587912 DOI: 10.3389/fmicb.2019.01342] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 05/29/2019] [Indexed: 11/16/2022] Open
Abstract
Cellulases have a broad range of different industrial applications, ranging from food and beverages to pulp and paper and the biofuels area. Here a metagenomics based strategy was used to identify the cellulolytic enzyme CelRH5 from the rhizosphere. CelRH5 is a novel monospecific endo-β-1,4-glucanase belonging to the glycosyl hydrolase family 5 (GH5). Structural based modeling analysis indicated that CelRH5 is related to endo-β-1,4-glucanases derived from thermophilic microorganisms such as Thermotoga maritima, Fervidobacterium nodosum, and Ruminiclostridium thermocellum sharing 30-40% amino acid sequence identity. The molecular weight of the enzyme was determined as 40.5 kDa. Biochemical analyses revealed that the enzyme displayed good activity with soluble forms of cellulose as a substrate such as ostazin brilliant red hydroxyethyl cellulose (OBR-HEC), carboxymethylcellulose (CMC), hydroxyethyl cellulose (HEC), and insoluble azurine cross-linked hydroxyethylcellulose (AZCL-HEC). The enzyme shows highest enzymatic activity at pH 6.5 with high pH tolerance, remaining stable in the pH range 4.5–8.5. Highest activity was observed at 40°C, but CelRH5 is psychrotolerant being active and stable at temperatures below 30°C. The presence of the final products of cellulose hydrolysis (glucose and cellobiose) or metal ions such as Na+, K+, Li+, and Mg2+, as well as ethylenediaminetetraacetic acid (EDTA), urea, dithiothreitol (DTT), dimethyl sulfoxide (DMSO), 2-mercaptoethanol (2-ME) or glycerol, did not have a marked effect on CelRH5 activity. However, the enzyme is quite sensitive to the presence of 10 mM ions Zn2+, Ni2+, Co2+, Fe3+ and reagents such as 1 M guanidine HCl, 0.1% sodium dodecyl sulfate (SDS) and 20% ethanol. Given that it is psychrotolerant and retains activity in the presence of final cellulose degradation products, metal ions and various reagents, which are common in many technological processes; CelRH5 may be potential suitability for a variety of different biotechnological applications.
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Affiliation(s)
- Anna Wierzbicka-Woś
- Environmental Research Institute, University College Cork, Cork, Ireland.,Department of Microbiology, Faculty of Biology, University of Szczecin, Szczecin, Poland
| | - Ruth Henneberger
- Environmental Research Institute, University College Cork, Cork, Ireland.,Institute for Molecular Health Sciences, ETH Zürich, Zurich, Switzerland
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Liliana Martínez-Ávila
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Stephen A Jackson
- Environmental Research Institute, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | | | - Alan D W Dobson
- Environmental Research Institute, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
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12
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Brugman S, Ikeda-Ohtsubo W, Braber S, Folkerts G, Pieterse CMJ, Bakker PAHM. A Comparative Review on Microbiota Manipulation: Lessons From Fish, Plants, Livestock, and Human Research. Front Nutr 2018; 5:80. [PMID: 30234124 PMCID: PMC6134018 DOI: 10.3389/fnut.2018.00080] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 08/17/2018] [Indexed: 12/12/2022] Open
Abstract
During recent years the impact of microbial communities on the health of their host (being plants, fish, and terrestrial animals including humans) has received increasing attention. The microbiota provides the host with nutrients, induces host immune development and metabolism, and protects the host against invading pathogens (1-6). Through millions of years of co-evolution bacteria and hosts have developed intimate relationships. Microbial colonization shapes the host immune system that in turn can shape the microbial composition (7-9). However, with the large scale use of antibiotics in agriculture and human medicine over the last decades an increase of diseases associated with so-called dysbiosis has emerged. Dysbiosis refers to either a disturbed microbial composition (outgrowth of possible pathogenic species) or a disturbed interaction between bacteria and the host (10). Instead of using more antibiotics to treat dysbiosis there is a need to develop alternative strategies to combat disturbed microbial control. To this end, we can learn from nature itself. For example, the plant root (or "rhizosphere") microbiome of sugar beet contains several bacterial species that suppress the fungal root pathogen Rhizoctonia solani, an economically important fungal pathogen of this crop (11). Likewise, commensal bacteria present on healthy human skin produce antimicrobial molecules that selectively kill skin pathogen Staphylococcus aureus. Interestingly, patients with atopic dermatitis (inflammation of the skin) lacked antimicrobial peptide secreting commensal skin bacteria (12). In this review, we will give an overview of microbial manipulation in fish, plants, and terrestrial animals including humans to uncover conserved mechanisms and learn how we might restore microbial balance increasing the resilience of the host species.
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Affiliation(s)
- Sylvia Brugman
- Cell Biology and Immunology Group, Animal Sciences Group, Wageningen University and Research, Wageningen, Netherlands
| | - Wakako Ikeda-Ohtsubo
- Food and Feed Immunology Group, Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Saskia Braber
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Sciences, Utrecht University, Utrecht, Netherlands
| | - Gert Folkerts
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Sciences, Utrecht University, Utrecht, Netherlands
| | - Corné M. J. Pieterse
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, Netherlands
| | - Peter A. H. M. Bakker
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Utrecht, Netherlands
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13
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Farias N, Almeida I, Meneses C. New Bacterial Phytase through Metagenomic Prospection. Molecules 2018; 23:E448. [PMID: 29462992 PMCID: PMC6017413 DOI: 10.3390/molecules23020448] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 02/07/2018] [Accepted: 02/15/2018] [Indexed: 11/16/2022] Open
Abstract
Alkaline phytases from uncultured microorganisms, which hydrolyze phytate to less phosphorylated myo-inositols and inorganic phosphate, have great potential as additives in agricultural industry. The development of metagenomics has stemmed from the ineluctable evidence that as-yet-uncultured microorganisms represent the vast majority of organisms in most environments on earth. In this study, a gene encoding a phytase was cloned from red rice crop residues and castor bean cake using a metagenomics strategy. The amino acid identity between this gene and its closest published counterparts is lower than 60%. The phytase was named PhyRC001 and was biochemically characterized. This recombinant protein showed activity on sodium phytate, indicating that PhyRC001 is a hydrolase enzyme. The enzymatic activity was optimal at a pH of 7.0 and at a temperature of 35 °C. β-propeller phytases possess great potential as feed additives because they are the only type of phytase with high activity at neutral pH. Therefore, to explore and exploit the underlying mechanism for β-propeller phytase functions could be of great benefit to biotechnology.
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Affiliation(s)
- Nathálya Farias
- Graduate Program in Agricultural Sciences, Universidade Estadual da Paraíba (UEPB), Campina Grande/PB 58429-500, Brazil.
| | - Isabela Almeida
- Department of Biology, Universidade Estadual da Paraíba (UEPB).
| | - Carlos Meneses
- Department of Biology and Graduate Program in Agricultural Sciences, Universidade Estadual da Paraíba (UEPB), Campina Grande/PB 58429-500, Brazil.
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14
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Berini F, Casciello C, Marcone GL, Marinelli F. Metagenomics: novel enzymes from non-culturable microbes. FEMS Microbiol Lett 2017; 364:4329276. [DOI: 10.1093/femsle/fnx211] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/02/2017] [Indexed: 01/02/2023] Open
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15
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Deng J, Gao H, Gao Z, Zhao H, Yang Y, Wu Q, Wu B, Jiang C. Identification and molecular characterization of a metagenome-derived L-lysine decarboxylase gene from subtropical soil microorganisms. PLoS One 2017; 12:e0185060. [PMID: 28931053 PMCID: PMC5607190 DOI: 10.1371/journal.pone.0185060] [Citation(s) in RCA: 9] [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: 04/04/2017] [Accepted: 09/06/2017] [Indexed: 11/18/2022] Open
Abstract
L-lysine decarboxylase (LDC, EC 4.1.1.18) is a key enzyme in the decarboxylation of L-lysine to 1,5-pentanediamine and efficiently contributes significance to biosynthetic capability. Metagenomic technology is a shortcut approach used to obtain new genes from uncultured microorganisms. In this study, a subtropical soil metagenomic library was constructed, and a putative LDC gene named ldc1E was isolated by function-based screening strategy through the indication of pH change by L-lysine decarboxylation. Amino acid sequence comparison and homology modeling indicated the close relation between Ldc1E and other putative LDCs. Multiple sequence alignment analysis revealed that Ldc1E contained a highly conserved motif Ser-X-His-Lys (Pxl), and molecular docking results showed that this motif was located in the active site and could combine with the cofactor pyridoxal 5'-phosphate. The ldc1E gene was subcloned into the pET-30a(+) vector and highly expressed in Escherichia coli BL21 (DE3) pLysS. The recombinant protein was purified to homogeneity. The maximum activity of Ldc1E occurred at pH 6.5 and 40°C using L-lysine monohydrochloride as the substrate. Recombinant Ldc1E had apparent Km, kcat, and kcat/Km values of 1.08±0.16 mM, 5.09±0.63 s-1, and 4.73×103 s-1 M-1, respectively. The specific activity of Ldc1E was 1.53±0.06 U mg-1 protein. Identifying a metagenome-derived LDC gene provided a rational reference for further gene modifications in industrial applications.
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Affiliation(s)
- Jie Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Hua Gao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Zhen Gao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Huaxian Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Ying Yang
- College of Ocean and Biotechnology, Guangxi University for Nationalities, Nanning, Guangxi, China
| | - Qiaofen Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
| | - Bo Wu
- College of Ocean and Biotechnology, Guangxi University for Nationalities, Nanning, Guangxi, China
| | - Chengjian Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, China
- * E-mail:
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Ábrego U, Chen Z, Wan C. Consolidated Bioprocessing Systems for Cellulosic Biofuel Production. ADVANCES IN BIOENERGY 2017. [DOI: 10.1016/bs.aibe.2017.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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