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Ajeje SB, Hu Y, Song G, Peter SB, Afful RG, Sun F, Asadollahi MA, Amiri H, Abdulkhani A, Sun H. Thermostable Cellulases / Xylanases From Thermophilic and Hyperthermophilic Microorganisms: Current Perspective. Front Bioeng Biotechnol 2021; 9:794304. [PMID: 34976981 PMCID: PMC8715034 DOI: 10.3389/fbioe.2021.794304] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/02/2021] [Indexed: 12/13/2022] Open
Abstract
The bioconversion of lignocellulose into monosaccharides is critical for ensuring the continual manufacturing of biofuels and value-added bioproducts. Enzymatic degradation, which has a high yield, low energy consumption, and enhanced selectivity, could be the most efficient and environmentally friendly technique for converting complex lignocellulose polymers to fermentable monosaccharides, and it is expected to make cellulases and xylanases the most demanded industrial enzymes. The widespread nature of thermophilic microorganisms allows them to proliferate on a variety of substrates and release substantial quantities of cellulases and xylanases, which makes them a great source of thermostable enzymes. The most significant breakthrough of lignocellulolytic enzymes lies in lignocellulose-deconstruction by enzymatic depolymerization of holocellulose into simple monosaccharides. However, commercially valuable thermostable cellulases and xylanases are challenging to produce in high enough quantities. Thus, the present review aims at giving an overview of the most recent thermostable cellulases and xylanases isolated from thermophilic and hyperthermophilic microbes. The emphasis is on recent advancements in manufacturing these enzymes in other mesophilic host and enhancement of catalytic activity as well as thermostability of thermophilic cellulases and xylanases, using genetic engineering as a promising and efficient technology for its economic production. Additionally, the biotechnological applications of thermostable cellulases and xylanases of thermophiles were also discussed.
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Affiliation(s)
- Samaila Boyi Ajeje
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yun Hu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Guojie Song
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Sunday Bulus Peter
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Richmond Godwin Afful
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Fubao Sun
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Mohammad Ali Asadollahi
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Hamid Amiri
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Ali Abdulkhani
- Department of Wood and Paper Science and Technology, Faculty of Natural Resources, University of Tehran, Karaj, Iran
| | - Haiyan Sun
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
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Kirubakaran R, ArulJothi KN, Revathi S, Shameem N, Parray JA. Emerging priorities for microbial metagenome research. BIORESOURCE TECHNOLOGY REPORTS 2020; 11:100485. [PMID: 32835181 PMCID: PMC7319936 DOI: 10.1016/j.biteb.2020.100485] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/23/2020] [Accepted: 06/24/2020] [Indexed: 12/20/2022]
Abstract
Overwhelming anthropogenic activities lead to deterioration of natural resources and the environment. The microorganisms are considered desirable, due to their suitability for easy genetic manipulation and handling. With the aid of modern biotechnological techniques, the culturable microorganisms have been widely exploited for the benefit of mankind. Metagenomics, a powerful tool to access the abundant biodiversity of the environmental samples including the unculturable microbes, to determine microbial diversity and population structure, their ecological roles and expose novel genes of interest. This review focuses on the microbial adaptations to the adverse environmental conditions, metagenomic techniques employed towards microbial biotechnology. Metagenomic approach helps to understand microbial ecology and to identify useful microbial derivatives like antibiotics, toxins, and enzymes with diverse and enhanced function. It also summarizes the application of metagenomics in clinical diagnosis, improving microbial ecology, therapeutics, xenobiotic degradation and impact on agricultural crops.
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Affiliation(s)
| | - K N ArulJothi
- Department of Genetic Engineering, SRM Institute of Science and Technology, Chennai, India
- Department of Human Biology, University of Cape Town, Cape Town, South Africa
| | | | - Nowsheen Shameem
- Department of Environmental Science, Cluster University Srinagar, J&K, India
| | - Javid A Parray
- Department of Environmental Science, Govt SAM Degree College Budgam, J&K, India
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López-Mondéjar R, Algora C, Baldrian P. Lignocellulolytic systems of soil bacteria: A vast and diverse toolbox for biotechnological conversion processes. Biotechnol Adv 2019; 37:107374. [DOI: 10.1016/j.biotechadv.2019.03.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/06/2019] [Accepted: 03/21/2019] [Indexed: 12/12/2022]
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Patel AK, Singhania RR, Sim SJ, Pandey A. Thermostable cellulases: Current status and perspectives. BIORESOURCE TECHNOLOGY 2019; 279:385-392. [PMID: 30685132 DOI: 10.1016/j.biortech.2019.01.049] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/09/2019] [Accepted: 01/11/2019] [Indexed: 05/18/2023]
Abstract
It is envisaged that the utilization of lignocellulosic biomass for ethanol production for transport sector, would make cellulases the most demanded industrial enzyme. The greatest potential of cellulolytic enzymes lies in ethanol production from biomass by enzymatic hydrolysis of cellulose but low thermostability and low titer of cellulase production resulting into high cost of the enzyme which is the major set-back. A number of research groups are working on cellulase to improve its thermostability so as to be able to perform hydrolysis at elevated temperatures which would eventually increase the efficiency of cellulose hydrolysis. The technologies developed from lignocellulosic biomass via cellulose hydrolysis promise environmental and economical sustainability in the long run along with non-dependence on nonrenewable energy source. This review deals with the important sources of thermostable cellulases, mechanism, its regulation, strategies to enhance the thermostability further with respect to its importance for biofuel applications.
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Affiliation(s)
- Anil K Patel
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
| | | | - Sang Jun Sim
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Ashok Pandey
- Centre for Innovation and Translational Research, Indian Institute of Toxicological Research, Lucknow 226 001, India
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Ngara TR, Zhang H. Recent Advances in Function-based Metagenomic Screening. GENOMICS PROTEOMICS & BIOINFORMATICS 2018; 16:405-415. [PMID: 30597257 PMCID: PMC6411959 DOI: 10.1016/j.gpb.2018.01.002] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/05/2018] [Accepted: 01/09/2018] [Indexed: 12/01/2022]
Abstract
Metagenomes from uncultured microorganisms are rich resources for novel enzyme genes. The methods used to screen the metagenomic libraries fall into two categories, which are based on sequence or function of the enzymes. The sequence-based approaches rely on the known sequences of the target gene families. In contrast, the function-based approaches do not involve the incorporation of metagenomic sequencing data and, therefore, may lead to the discovery of novel gene sequences with desired functions. In this review, we discuss the function-based screening strategies that have been used in the identification of enzymes from metagenomes. Because of its simplicity, agar plate screening is most commonly used in the identification of novel enzymes with diverse functions. Other screening methods with higher sensitivity are also employed, such as microtiter plate screening. Furthermore, several ultra-high-throughput methods were developed to deal with large metagenomic libraries. Among these are the FACS-based screening, droplet-based screening, and the in vivo reporter-based screening methods. The application of these novel screening strategies has increased the chance for the discovery of novel enzyme genes.
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Affiliation(s)
- Tanyaradzwa Rodgers Ngara
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, MOE Key Laboratory of Molecular Biophysics, Wuhan 430074, China
| | - Houjin Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, MOE Key Laboratory of Molecular Biophysics, Wuhan 430074, China.
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Lewin A, Zhou J, Pham VTT, Haugen T, Zeiny ME, Aarstad O, Liebl W, Wentzel A, Liles MR. Novel archaeal thermostable cellulases from an oil reservoir metagenome. AMB Express 2017; 7:183. [PMID: 28963711 PMCID: PMC5622026 DOI: 10.1186/s13568-017-0485-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 09/20/2017] [Indexed: 01/24/2023] Open
Abstract
Microbial assemblages were sampled from an offshore deep sub-surface petroleum reservoir 2.5 km below the ocean floor off the coast of Norway, providing conditions of high temperature and pressure, to identify new thermostable enzymes. In this study, we used DNA sequences obtained directly from the sample metagenome and from a derived fosmid library to survey the functional diversity of this extreme habitat. The metagenomic fosmid library containing 11,520 clones was screened using function- and sequence-based methods to identify recombinant clones expressing carbohydrate-degrading enzymes. Open reading frames (ORFs) encoding carbohydrate-degrading enzymes were predicted by BLAST against the CAZy database, and many fosmid clones expressing carbohydrate-degrading activities were discovered by functional screening using Escherichia coli as a heterologous host. Each complete ORF predicted to encode a cellulase identified from sequence- or function-based screening was subcloned in an expression vector. Five subclones was found to have significant activity using a fluorescent cellulose model substrate, and three of these were observed to be highly thermostable. Based on phylogenetic analyses, the thermostable cellulases were derived from thermophilic Archaea and are distinct from known cellulases. Cellulase F1, obtained from function-based screening, contains two distinct cellulase modules, perhaps resulting from fusion of two archaeal cellulases and with a novel protein structure that may result in enhanced activity and thermostability. This enzyme was found to exhibit exocellulase function and to have a remarkably high activity compared to commercially available enzymes. Results from this study highlight the complementarity of hybrid approaches for enzyme discovery, combining sequence- and function-based screening.
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Tiwari R, Nain L, Labrou NE, Shukla P. Bioprospecting of functional cellulases from metagenome for second generation biofuel production: a review. Crit Rev Microbiol 2017; 44:244-257. [DOI: 10.1080/1040841x.2017.1337713] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Rameshwar Tiwari
- Department of Microbiology, Laboratory of Enzyme Technology and Protein Bioinformatics, Maharshi Dayanand University, Rohtak, India
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi, India
| | - Lata Nain
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi, India
| | - Nikolaos E. Labrou
- Department of Biotechnology, School of Food, Biotechnology and Development, Laboratory of Enzyme Technology, Agricultural University of Athens, Athens, Greece
| | - Pratyoosh Shukla
- Department of Microbiology, Laboratory of Enzyme Technology and Protein Bioinformatics, Maharshi Dayanand University, Rohtak, India
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Gomes-Pepe ES, Machado Sierra EG, Pereira MR, Castellane TCL, Lemos EGDM. Bg10: A Novel Metagenomics Alcohol-Tolerant and Glucose-Stimulated GH1 ß-Glucosidase Suitable for Lactose-Free Milk Preparation. PLoS One 2016; 11:e0167932. [PMID: 28002476 PMCID: PMC5176175 DOI: 10.1371/journal.pone.0167932] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 11/22/2016] [Indexed: 11/19/2022] Open
Abstract
New ß-glucosidases with product (glucose) or ethanol tolerances are greatly desired to make industrial processes more marketable and efficient. Therefore, this report describes the in silico/vitro characterization of Bg10, a metagenomically derived homodimeric ß-glucosidase that exhibited a Vmax of 10.81 ± 0.43 μM min-1, Kcat of 175.1± 6.91 min-1, and Km of 0.49 ± 0.12 mM at a neutral pH and 37°C when pNP-ß-D-glucopyranoside was used as the substrate, and the enzyme retained greater than 80% activity within the respective pH and temperature ranges of 6.5 to 8.0 and 35 to 40°C. The enzyme was stimulated by its product, glucose; consequently, the Bg10 activity against 50 and 100 mM of glucose were increased by 36.8% and 22%, respectively, while half of the activity was retained at 350 mM. Moreover, the Bg10 was able to hydrolyse 55% (milk sample) and 100% (purified sugar) of the lactose at low (6°C) and optimum (37°C) temperatures, respectively, suggesting the possibility of further optimization of the reaction for lactose-free dairy production. In addition, the enzyme was able to fully hydrolyse 40 mM of cellobiose at one hour and was tolerant to ethanol up to concentrations of 500 mM (86% of activity), while a 1 M concentration still resulted in 41% residual activity, which could be interesting for biofuel production.
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Affiliation(s)
- Elisângela Soares Gomes-Pepe
- Department of Technology, São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal. Via de Acesso Prof. Paulo Donato Castellane S/N, km 5, CEP, Jaboticabal, São Paulo State, Brazil
- Molecular Biology Laboratory; Institute for Research in Bioenergy (IPBEN), UNESP–Jaboticabal, SP, Brazil
- Agricultural Microbiology postgraduate program of UNESP, Jaboticabal, São Paulo State, Brazil
| | - Elwi Guillermo Machado Sierra
- Department of Technology, São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal. Via de Acesso Prof. Paulo Donato Castellane S/N, km 5, CEP, Jaboticabal, São Paulo State, Brazil
- Molecular Biology Laboratory; Institute for Research in Bioenergy (IPBEN), UNESP–Jaboticabal, SP, Brazil
| | - Mariana Rangel Pereira
- Department of Technology, São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal. Via de Acesso Prof. Paulo Donato Castellane S/N, km 5, CEP, Jaboticabal, São Paulo State, Brazil
- Molecular Biology Laboratory; Institute for Research in Bioenergy (IPBEN), UNESP–Jaboticabal, SP, Brazil
| | - Tereza Cristina Luque Castellane
- Department of Technology, São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal. Via de Acesso Prof. Paulo Donato Castellane S/N, km 5, CEP, Jaboticabal, São Paulo State, Brazil
- Molecular Biology Laboratory; Institute for Research in Bioenergy (IPBEN), UNESP–Jaboticabal, SP, Brazil
| | - Eliana Gertrudes de Macedo Lemos
- Department of Technology, São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal. Via de Acesso Prof. Paulo Donato Castellane S/N, km 5, CEP, Jaboticabal, São Paulo State, Brazil
- Molecular Biology Laboratory; Institute for Research in Bioenergy (IPBEN), UNESP–Jaboticabal, SP, Brazil
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Nakamura K, Iizuka R, Nishi S, Yoshida T, Hatada Y, Takaki Y, Iguchi A, Yoon DH, Sekiguchi T, Shoji S, Funatsu T. Culture-independent method for identification of microbial enzyme-encoding genes by activity-based single-cell sequencing using a water-in-oil microdroplet platform. Sci Rep 2016; 6:22259. [PMID: 26915788 PMCID: PMC4768102 DOI: 10.1038/srep22259] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 02/10/2016] [Indexed: 12/22/2022] Open
Abstract
Environmental microbes are a great source of industrially valuable enzymes with potent and unique catalytic activities. Unfortunately, the majority of microbes remain unculturable and thus are not accessible by culture-based methods. Recently, culture-independent metagenomic approaches have been successfully applied, opening access to untapped genetic resources. Here we present a methodological approach for the identification of genes that encode metabolically active enzymes in environmental microbes in a culture-independent manner. Our method is based on activity-based single-cell sequencing, which focuses on microbial cells showing specific enzymatic activities. First, at the single-cell level, environmental microbes were encapsulated in water-in-oil microdroplets with a fluorogenic substrate for the target enzyme to screen for microdroplets that contain microbially active cells. Second, the microbial cells were recovered and subjected to whole genome amplification. Finally, the amplified genomes were sequenced to identify the genes encoding target enzymes. Employing this method, we successfully identified 14 novel β-glucosidase genes from uncultured bacterial cells in marine samples. Our method contributes to the screening and identification of genes encoding industrially valuable enzymes.
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Affiliation(s)
- Kazuki Nakamura
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ryo Iizuka
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shinro Nishi
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Takao Yoshida
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Yuji Hatada
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Yoshihiro Takaki
- Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka-shi, Kanagawa 237-0061, Japan
| | - Ayaka Iguchi
- Department of NanoscieWnce and Nanoengineering (ASE Graduate School), Waseda University, 3-4-1 Okubo, Shinju-ku, Tokyo 169-8555, Japan
| | - Dong Hyun Yoon
- Department of NanoscieWnce and Nanoengineering (ASE Graduate School), Waseda University, 3-4-1 Okubo, Shinju-ku, Tokyo 169-8555, Japan
| | - Tetsushi Sekiguchi
- Research Organization for Nano &Life Innovation, Waseda University, 513, Waseda-tsurumaki-cho, Shinjuku-ku, Tokyo, 162-0041, Japan
| | - Shuichi Shoji
- Department of NanoscieWnce and Nanoengineering (ASE Graduate School), Waseda University, 3-4-1 Okubo, Shinju-ku, Tokyo 169-8555, Japan
| | - Takashi Funatsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Xu Z, Zhang L, Yu P. Optimization of a heat-tolerant β-glucosidase production by Bacillus sp. ZJ1308 and its purification and characterization. Biotechnol Appl Biochem 2015; 63:553-63. [PMID: 26077129 DOI: 10.1002/bab.1405] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 06/04/2015] [Indexed: 11/08/2022]
Abstract
Response surface methodology was used to optimize the medium composition to improve the production of the heat-tolerant β-glucosidase from Bacillus sp. ZJ1308. Three significant factors were found to be corn cob, beef extract, and MnSO4 ·H2 O. The final medium compositions optimized were corn cob (51.8 g/L), beef extract (23.8 g/L), salicin (0.5 g/L), MnSO4 ·H2 O (0.363 g/L), MgSO4 ·7H2 O (0.4 g/L), and NaCl (5 g/L). Under the optimal conditions, the activity of β-glucosidase was up to 4.71 U/mL. β-Glucosidase was purified to homogeneity with a recovery rate of 5% and a specific activity of 110.47 U/mg. The optimal pH and temperature were 7.0 and 60 °C, respectively. β-Glucosidase was stable within a pH range of 6.0-8.0 and showed an extremely high thermostability at 80 and 90 °C, retaining 56% and 38% of its maximal activity, respectively. Ni(2+) and Ba(2+) heavily inhibited the β-glucosidase activity. The purified β-glucosidase showed a high substrate specificity. The kinetic parameters revealed that it had a high catalytic efficiency toward the substrate p-nitrophenyl-β-d-glucopyranoside (Kcat /Km = 700). It also showed a high catalytic activity toward the natural substrate salicin. This study provides a new insight into the future development and use of β-glucosidase from Bacillus sp. ZJ1308.
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Affiliation(s)
- Zhenni Xu
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Lei Zhang
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Ping Yu
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province, People's Republic of China
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Coughlan LM, Cotter PD, Hill C, Alvarez-Ordóñez A. Biotechnological applications of functional metagenomics in the food and pharmaceutical industries. Front Microbiol 2015; 6:672. [PMID: 26175729 PMCID: PMC4485178 DOI: 10.3389/fmicb.2015.00672] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Accepted: 06/19/2015] [Indexed: 12/31/2022] Open
Abstract
Microorganisms are found throughout nature, thriving in a vast range of environmental conditions. The majority of them are unculturable or difficult to culture by traditional methods. Metagenomics enables the study of all microorganisms, regardless of whether they can be cultured or not, through the analysis of genomic data obtained directly from an environmental sample, providing knowledge of the species present, and allowing the extraction of information regarding the functionality of microbial communities in their natural habitat. Function-based screenings, following the cloning and expression of metagenomic DNA in a heterologous host, can be applied to the discovery of novel proteins of industrial interest encoded by the genes of previously inaccessible microorganisms. Functional metagenomics has considerable potential in the food and pharmaceutical industries, where it can, for instance, aid (i) the identification of enzymes with desirable technological properties, capable of catalyzing novel reactions or replacing existing chemically synthesized catalysts which may be difficult or expensive to produce, and able to work under a wide range of environmental conditions encountered in food and pharmaceutical processing cycles including extreme conditions of temperature, pH, osmolarity, etc; (ii) the discovery of novel bioactives including antimicrobials active against microorganisms of concern both in food and medical settings; (iii) the investigation of industrial and societal issues such as antibiotic resistance development. This review article summarizes the state-of-the-art functional metagenomic methods available and discusses the potential of functional metagenomic approaches to mine as yet unexplored environments to discover novel genes with biotechnological application in the food and pharmaceutical industries.
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Affiliation(s)
| | - Paul D Cotter
- Teagasc Food Research Centre Cork, Ireland ; Alimentary Pharmabiotic Centre Cork, Ireland
| | - Colin Hill
- Alimentary Pharmabiotic Centre Cork, Ireland ; School of Microbiology, University College Cork Cork, Ireland
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Guazzaroni ME, Silva-Rocha R, Ward RJ. Synthetic biology approaches to improve biocatalyst identification in metagenomic library screening. Microb Biotechnol 2014; 8:52-64. [PMID: 25123225 PMCID: PMC4321373 DOI: 10.1111/1751-7915.12146] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 06/22/2014] [Accepted: 06/28/2014] [Indexed: 11/28/2022] Open
Abstract
There is a growing demand for enzymes with improved catalytic performance or tolerance to process-specific parameters, and biotechnology plays a crucial role in the development of biocatalysts for use in industry, agriculture, medicine and energy generation. Metagenomics takes advantage of the wealth of genetic and biochemical diversity present in the genomes of microorganisms found in environmental samples, and provides a set of new technologies directed towards screening for new catalytic activities from environmental samples with potential biotechnology applications. However, biased and low level of expression of heterologous proteins in Escherichia coli together with the use of non-optimal cloning vectors for the construction of metagenomic libraries generally results in an extremely low success rate for enzyme identification. The bottleneck arising from inefficient screening of enzymatic activities has been addressed from several perspectives; however, the limitations related to biased expression in heterologous hosts cannot be overcome by using a single approach, but rather requires the synergetic implementation of multiple methodologies. Here, we review some of the principal constraints regarding the discovery of new enzymes in metagenomic libraries and discuss how these might be resolved by using synthetic biology methods.
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Zhang M, Liu N, Qian C, Wang Q, Wang Q, Long Y, Huang Y, Zhou Z, Yan X. Phylogenetic and functional analysis of gut microbiota of a fungus-growing higher termite: Bacteroidetes from higher termites are a rich source of β-glucosidase genes. MICROBIAL ECOLOGY 2014; 68:416-425. [PMID: 24584416 DOI: 10.1007/s00248-014-0388-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Accepted: 02/04/2014] [Indexed: 06/03/2023]
Abstract
Fungus-growing termites, their symbiotic fungi, and microbiota inhibiting their intestinal tract comprise a highly efficient cellulose-hydrolyzing system; however, little is known about the role of gut microbiota in this system. Twelve fosmid clones with β-glucosidase activity were previously obtained by functionally screening a metagenomic library of a fungus-growing termite, Macrotermes annandalei. Ten contigs containing putative β-glucosidase genes (bgl1-10) were assembled by sequencing data of these fosmid clones. All these contigs were binned to Bacteroidetes, and all these β-glucosidase genes were phylogenetically closed to those from Bacteroides or Dysgonomonas. Six out of 10 β-glucosidase genes had predicted signal peptides, indicating a transmembrane capability of these enzymes to mediate cellulose hydrolysis within the gut of the termites. To confirm the activities of these β-glucosidase genes, three genes (bgl5, bgl7, and bgl9) were successfully expressed and purified. The optimal temperature and pH of these enzymes largely resembled the environment of the host's gut. The gut microbiota composition of the fungus-growing termite was also determined by 454 pyrosequencing, showing that Bacteroidetes was the most dominant phylum. The diversity and the enzyme properties of β-glucosidases revealed in this study suggested that Bacteroidetes as the major member in fungus-growing termites contributed to cello-oligomer degradation in cellulose-hydrolyzing process and represented a rich source for β-glucosidase genes.
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Affiliation(s)
- Meiling Zhang
- School of Life Sciences, East China Normal University, Shanghai, China
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Stroobants A, Portetelle D, Vandenbol M. New carbohydrate-active enzymes identified by screening two metagenomic libraries derived from the soil of a winter wheat field. J Appl Microbiol 2014; 117:1045-55. [PMID: 25039822 DOI: 10.1111/jam.12597] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 06/24/2014] [Accepted: 07/06/2014] [Indexed: 12/01/2022]
Abstract
AIMS Soils are rich, diversified environments where β-glucosidases abound because of their importance in organic matter degradation. The aim of this work was to discover new β-glucosidases by constructing two metagenomic DNA libraries from soil samples collected in winter and spring from a field of winter wheat. METHODS AND RESULTS Both libraries were screened on esculin-supplemented medium so as to isolate candidates showing β-glucosidase activity. Candidate analysis revealed seven putative β-glycosidases and two putative glycosyltransferases, displaying 25 to 82% identity to known enzymes. The putative β-glycosidases belong to families GH1, GH3 and GH20 and the two putative glycosyltransferases, probably, to new families. In characterization tests performed on bacteria in suspension or spread on agar plates, some candidates appeared to hydrolyse several natural and synthetic substrates. These tests also highlighted interesting industrial characteristics, such as the activity of four β-glycosidases under alkaline conditions and the esculin-hydrolysing activity of a β-glucosidase candidate in the presence of glucose. CONCLUSIONS Seven putative β-glycosidases and two putative glycosyltransferases were found by functional screening of two metagenomic DNA libraries derived from agricultural soil. SIGNIFICANCE AND IMPACT OF THE STUDY This study has identified β-glycosidases and putative glycosyltransferases that have or may have interesting industrial characteristics.
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Affiliation(s)
- A Stroobants
- Microbiology and Genomics Unit, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
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Evaluation of a pooled strategy for high-throughput sequencing of cosmid clones from metagenomic libraries. PLoS One 2014; 9:e98968. [PMID: 24911009 PMCID: PMC4049660 DOI: 10.1371/journal.pone.0098968] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 05/09/2014] [Indexed: 11/19/2022] Open
Abstract
High-throughput sequencing methods have been instrumental in the growing field of metagenomics, with technological improvements enabling greater throughput at decreased costs. Nonetheless, the economy of high-throughput sequencing cannot be fully leveraged in the subdiscipline of functional metagenomics. In this area of research, environmental DNA is typically cloned to generate large-insert libraries from which individual clones are isolated, based on specific activities of interest. Sequence data are required for complete characterization of such clones, but the sequencing of a large set of clones requires individual barcode-based sample preparation; this can become costly, as the cost of clone barcoding scales linearly with the number of clones processed, and thus sequencing a large number of metagenomic clones often remains cost-prohibitive. We investigated a hybrid Sanger/Illumina pooled sequencing strategy that omits barcoding altogether, and we evaluated this strategy by comparing the pooled sequencing results to reference sequence data obtained from traditional barcode-based sequencing of the same set of clones. Using identity and coverage metrics in our evaluation, we show that pooled sequencing can generate high-quality sequence data, without producing problematic chimeras. Though caveats of a pooled strategy exist and further optimization of the method is required to improve recovery of complete clone sequences and to avoid circumstances that generate unrecoverable clone sequences, our results demonstrate that pooled sequencing represents an effective and low-cost alternative for sequencing large sets of metagenomic clones.
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Bergmann JC, Costa OYA, Gladden JM, Singer S, Heins R, D'haeseleer P, Simmons BA, Quirino BF. Discovery of two novel β-glucosidases from an Amazon soil metagenomic library. FEMS Microbiol Lett 2013; 351:147-55. [PMID: 24236615 DOI: 10.1111/1574-6968.12332] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 11/07/2013] [Accepted: 11/07/2013] [Indexed: 11/30/2022] Open
Abstract
An Amazon soil microbial community metagenomic fosmid library was functionally screened for β-glucosidase activity. Contig analysis of positive clones revealed the presence of two ORFs encoding novel β-glucosidases, AmBGL17 and AmBGL18, from the GH3 and GH1 families, respectively. Both AmBGL17 and AmBGL18 were functionally identified as β-glucosidases. The enzymatic activity of AmBGL17 was further characterized. AmBGL17 was tested with different substrates and showed highest activity on pNPβG substrate with an optimum temperature of 45 °C and an optimum pH of 6. AmBGL17 showed a Vmax of 116 mM s(-1) and Km of 0.30 ± 0.017 mM. This is the first report of β-glucosidases from an Amazon soil microbial community using a metagenomic approach.
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Affiliation(s)
- Jessica C Bergmann
- Genomic Sciences and Biotechnology Program, Universidade Católica de Brasília, Brasília, Brazil
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Park DJ, Lee YS, Choi YL. Characterization of a Cold-Active β-Glucosidase from Paenibacillus xylanilyticus KJ-03 Capable of Hydrolyzing Isoflavones Daidzin and Genistin. Protein J 2013; 32:579-84. [DOI: 10.1007/s10930-013-9520-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Fungal Beta-glucosidases: a bottleneck in industrial use of lignocellulosic materials. Biomolecules 2013; 3:612-31. [PMID: 24970184 PMCID: PMC4030957 DOI: 10.3390/biom3030612] [Citation(s) in RCA: 161] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 08/17/2013] [Accepted: 08/20/2013] [Indexed: 12/16/2022] Open
Abstract
Profitable biomass conversion processes are highly dependent on the use of efficient enzymes for lignocellulose degradation. Among the cellulose degrading enzymes, beta-glucosidases are essential for efficient hydrolysis of cellulosic biomass as they relieve the inhibition of the cellobiohydrolases and endoglucanases by reducing cellobiose accumulation. In this review, we discuss the important role beta-glucosidases play in complex biomass hydrolysis and how they create a bottleneck in industrial use of lignocellulosic materials. An efficient beta-glucosidase facilitates hydrolysis at specified process conditions, and key points to consider in this respect are hydrolysis rate, inhibitors, and stability. Product inhibition impairing yields, thermal inactivation of enzymes, and the high cost of enzyme production are the main obstacles to commercial cellulose hydrolysis. Therefore, this sets the stage in the search for better alternatives to the currently available enzyme preparations either by improving known or screening for new beta-glucosidases.
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Lu J, Du L, Wei Y, Hu Y, Huang R. Expression and characterization of a novel highly glucose-tolerant β-glucosidase from a soil metagenome. Acta Biochim Biophys Sin (Shanghai) 2013; 45:664-73. [PMID: 23752618 DOI: 10.1093/abbs/gmt061] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A β-glucosidase gene unbgl1A was isolated by the function-based screening of a metagenomic library and the enzyme protein was expressed in Escherichia coli, purified, and biochemically characterized. The enzyme Unbgl1A had a Km value of 2.09 ± 0.31 mM, and a Vmax value of 183.90 ± 9.61 μmol min(-1) mg(-1) under the optimal reaction conditions, which were pH 6.0 at 50°C. Unbgl1A can be activated by a variety of monosaccharides, disaccharides, and NaCl, and exhibits a high level of stability at high concentration of NaCl. Two prominent features for this enzyme are: (i) high glucose tolerance. It can be tolerant to glucose as high as 2000 mM, with Ki = 1500 mM; (ii) high NaCl tolerance. Its activity is not affected by 600 mM NaCl. The enzyme showed transglucosylation activities resulting in the formation of cellotriose from cellobiose. These properties of Unbgl1A should have important practical implication in its potential applications for better industrial production of glucose or bioethanol started from lignocellulosic biomass.
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Affiliation(s)
- Jian Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530005, China
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Wang Q, Qian C, Zhang XZ, Liu N, Yan X, Zhou Z. Characterization of a novel thermostable β-glucosidase from a metagenomic library of termite gut. Enzyme Microb Technol 2012; 51:319-24. [DOI: 10.1016/j.enzmictec.2012.07.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 07/13/2012] [Accepted: 07/17/2012] [Indexed: 10/28/2022]
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Xing MN, Zhang XZ, Huang H. Application of metagenomic techniques in mining enzymes from microbial communities for biofuel synthesis. Biotechnol Adv 2012; 30:920-9. [DOI: 10.1016/j.biotechadv.2012.01.021] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Bao L, Huang Q, Chang L, Sun Q, Zhou J, Lu H. Cloning and Characterization of Two β-Glucosidase/Xylosidase Enzymes from Yak Rumen Metagenome. Appl Biochem Biotechnol 2011; 166:72-86. [PMID: 22020745 DOI: 10.1007/s12010-011-9405-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Accepted: 10/04/2011] [Indexed: 10/16/2022]
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23
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Jiang C, Li SX, Luo FF, Jin K, Wang Q, Hao ZY, Wu LL, Zhao GC, Ma GF, Shen PH, Tang XL, Wu B. Biochemical characterization of two novel β-glucosidase genes by metagenome expression cloning. BIORESOURCE TECHNOLOGY 2011; 102:3272-3278. [PMID: 20971635 DOI: 10.1016/j.biortech.2010.09.114] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Revised: 09/28/2010] [Accepted: 09/28/2010] [Indexed: 05/30/2023]
Abstract
Two novel β-glucosidase genes designated as bgl1D and bgl1E, which encode 172- and 151-aa peptides, respectively, were cloned by function-based screening of a metagenomic library from uncultured soil microorganisms. Sequence analyses indicated that Bgl1D and Bgl1E exhibited lower similarities with some putative β-glucosidases. Functional characterization through high-performance liquid chromatography demonstrated that purified recombinant Bgl1D and Bgl1E proteins hydrolyzed D-glucosyl-β-(1-4)-D-glucose to glucose. Using p-nitrophenyl-β-D-glucoside as substrate, K(m) was 0.54 and 2.11 mM, and k(cat)/K(m) was 1489 and 787 mM(-1) min(-1) for Bgl1D and Bgl1E, respectively. The optimum pH and temperature for Bgl1D was pH 10.0 and 30°C, while the optimum values for Bgl1E were pH 10.0 and 25°C. Bgl1D exhibited habitat-specific characteristics, including higher activity in lower temperature and at high concentrations of AlCl(3) and LiCl. Bgl1D also displayed remarkable activity across a broad pH range (5.5-10.5), making it a potential candidate for industrial applications.
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Affiliation(s)
- Chengjian Jiang
- Guangxi Key Laboratory of Subtropical Bioresources Conservation and Utilization, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, People's Republic of China
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Xu H, Xiong AS, Zhao W, Tian YS, Peng RH, Chen JM, Yao QH. Characterization of a Glucose-, Xylose-, Sucrose-, and d-Galactose-Stimulated β-Glucosidase from the Alkalophilic Bacterium Bacillus halodurans C-125. Curr Microbiol 2010; 62:833-9. [DOI: 10.1007/s00284-010-9766-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Accepted: 09/08/2010] [Indexed: 09/29/2022]
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Duan CJ, Feng JX. Mining metagenomes for novel cellulase genes. Biotechnol Lett 2010; 32:1765-75. [PMID: 20640872 DOI: 10.1007/s10529-010-0356-z] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Accepted: 07/09/2010] [Indexed: 11/26/2022]
Abstract
Cellulases hydrolyze the β-1,4 linkages of cellulose and are widely used in food, brewing and wine, animal feed, textiles and laundry, and pulp and paper industries, especially for hydrolyzing cellulosic materials into sugars, which can be fermented to produce useful products such as ethanol. Metagenomics has become an alternative approach to conventional culture-dependent methods as it allows exhaustive mining of microbial genomes in their natural environments. This review covers the current state of research and challenges in mining novel cellulase genes from the metagenomes of various environments, and discusses the potential biotechnological applications of metagenome-derived cellulases.
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Affiliation(s)
- Cheng-Jie Duan
- Guangxi Key Laboratory of Subtropical Bioresource Conservation and Utilization, Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, People's Republic of China
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Jiang C, Hao ZY, Jin K, Li SX, Che ZQ, Ma GF, Wu B. Identification of a metagenome-derived β-glucosidase from bioreactor contents. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.molcatb.2009.11.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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