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Nyathi M, Dhlamini Z, Ncube T. Cloning Cellulase Genes from Victoria Falls Rainforest Decaying Logs Metagenome. Pol J Microbiol 2024; 0:pjm-2024-029. [PMID: 39074063 DOI: 10.33073/pjm-2024-029] [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: 09/20/2022] [Accepted: 12/28/2022] [Indexed: 07/31/2024] Open
Abstract
The Victoria Falls rainforest is a protected site whose forest floors harbor a host of cellulolytic microorganisms involved in biomass degradation. This study collected decaying logs and soil from the rainforest for bioprospecting cellulases from their metagenomes. Metagenomic DNA was isolated from the compound sample. Degenerate cellulase primers were used to amplify cellulase genes in the metagenome. The resulting amplicons cloned into Z-competent Escherichia coli DH5α were analyzed by functional screening for the production of cellulase extracellularly. Functional screening of the clones resulted in one clone (Clone-i) testing positive for extracellular cellulase production. Submerged fermentation of Clone-i was carried out for cellulase production. The cellulases were characterized to determine their activity's optimum pH and temperature. The diversity of the cellulases produced by Clone-i was determined. Clone-i's optimum enzyme activity was observed after 72 hours of incubation at 50°C and pH 5. Clone-i produced 80% more exoglucanases as compared to endoglucanases. The cellulolytic Clone-i' isolate shows Victoria Falls rainforest's potential as an enzyme bioprospecting site, reflecting that metagenomics is a valuable tool in microbial ecology.
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Affiliation(s)
- Makhosazana Nyathi
- Department of Applied Biology and Biochemistry, National University of Science and Technology, Bulawayo, Zimbabwe
| | - Zephaniah Dhlamini
- Department of Applied Biology and Biochemistry, National University of Science and Technology, Bulawayo, Zimbabwe
| | - Thembekile Ncube
- Department of Applied Biology and Biochemistry, National University of Science and Technology, Bulawayo, Zimbabwe
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2
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Hua D, Hendriks WH, Xiong B, Pellikaan WF. Starch and Cellulose Degradation in the Rumen and Applications of Metagenomics on Ruminal Microorganisms. Animals (Basel) 2022; 12:ani12213020. [PMID: 36359144 PMCID: PMC9653558 DOI: 10.3390/ani12213020] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Simple Summary Starch and cellulose are the principal components in diets for dairy cows worldwide, providing the primary energy to the rumen microorganisms as well as the host. Starch and cellulose degradation in the rumen have always been of key importance for dairy cows to obtain high production performance. To improve the starch- and cellulose-degrading activities in the rumen, the amylolytic and cellulolytic microbes and the related enzymes need to be well understood. As the rapid development of sequencing technologies, bioinformatic tools and reference databases, the rumen metagenomics have made great progress in mining the rumen microbial community for novel enzymes, such as the carbohydrate active enzymes (CAZymes). This review will summarize the ruminal microbes and enzymes involved in starch and cellulose degradation. Recent studies with metagenomics techniques on CAZymes related to starch and cellulose degradation will be discussed. Abstract Carbohydrates (e.g., starch and cellulose) are the main energy source in the diets of dairy cows. The ruminal digestion of starch and cellulose is achieved by microorganisms and digestive enzymes. In order to improve their digestibility, the microbes and enzymes involved in starch and cellulose degradation should be identified and their role(s) and activity known. As existing and new analytical techniques are continuously being developed, our knowledge of the amylolytic and cellulolytic microbial community in the rumen of dairy cows has been evolving rapidly. Using traditional culture-based methods, the main amylolytic and cellulolytic bacteria, fungi and protozoa in the rumen of dairy cows have been isolated. These culturable microbes have been found to only account for a small fraction of the total population of microorganisms present in the rumen. A more recent application of the culture-independent approach of metagenomics has acquired a more complete genetic structure and functional composition of the rumen microbial community. Metagenomics can be divided into functional metagenomics and sequencing-based computational metagenomics. Both approaches have been applied in determining the microbial composition and function in the rumen. With these approaches, novel microbial species as well as enzymes, especially glycosyl hydrolases, have been discovered. This review summarizes the current state of knowledge regarding the major amylolytic and cellulolytic microorganisms present in the rumen of dairy cows. The ruminal amylases and cellulases are briefly discussed. The application of metagenomics technology in investigating glycosyl hydrolases is provided and the novel enzymes are compared in terms of glycosyl hydrolase families related to amylolytic and cellulolytic activities.
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Affiliation(s)
- Dengke Hua
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Animal Nutrition Group, Department of Animal Sciences, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Wouter H. Hendriks
- Animal Nutrition Group, Department of Animal Sciences, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Benhai Xiong
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence: ; Tel.: +86-(10)-62811680
| | - Wilbert F. Pellikaan
- Animal Nutrition Group, Department of Animal Sciences, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
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Isolation, identification, and characterization of lignocellulose-degrading Geobacillus thermoleovorans from Yellowstone National Park. Appl Environ Microbiol 2021; 88:e0095821. [PMID: 34669438 DOI: 10.1128/aem.00958-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The microbial degradation of lignocellulose in natural ecosystems presents numerous biotechnological opportunities, including biofuel production from agricultural waste and feedstock biomass. To explore the degradation potential of specific thermophiles, we have identified and characterized extremophilic microorganisms isolated from hot springs environments that are capable of biodegrading lignin and cellulose substrates under thermoalkaline conditions, using a combination of culturing, genomics and metabolomics techniques. Organisms that can use lignin and cellulose as a sole carbon source at 60-75°C were isolated from sediment slurry of thermoalkaline hot springs (71-81°C and pH 8-9) of Yellowstone National Park. Full-length 16S rRNA gene sequencing indicated that these isolates were closely related to Geobacillus thermoleovorans. Interestingly, most of these isolates demonstrated biofilm formation on lignin, a phenotype that is correlated with increased bioconversion. Assessment of metabolite level changes in two Geobacillus isolates from two representative springs were undertaken to characterize the metabolic responses associated with growth on glucose versus lignin carbon source as a function of pH and temperature. Overall, results from this study support that thermoalkaline springs harbor G. thermoleovorans microorganisms with lignocellulosic biomass degradation capabilities and potential downstream biotechnological applications. IMPORTANCE As lignocellulosic biomass represents a major agro-industrial waste and renewable resource, its potential to replace non-renewable petroleum-based products for energy production is considerable. Microbial ligninolytic and cellulolytic enzymes are of high interest in bio-refineries for the valorization of lignocellulosic biomass, as they can withstand the extreme conditions (e.g., high temperature, high pH) required for processing. Of high interest is the ligninolytic potential of specific Geobacillus thermoleovorans isolates to function at a broad range of pH and temperatures, as lignin is the bottleneck in the bioprocessing of lignocellulose. In this study, results obtain from G. thermolerovorans isolates originating from YNP springs are significant as very few microorganisms from alkaline thermal environments have been discovered to have lignin and cellulose biodegrading capabilities, and this work opens new avenues for the biotechnological valorization of lignocellulosic biomass at an industrial scale.
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Banu JR, Kumar G, Chattopadhyay I. Management of microbial enzymes for biofuels and biogas production by using metagenomic and genome editing approaches. 3 Biotech 2021; 11:429. [PMID: 34603908 DOI: 10.1007/s13205-021-02962-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 08/04/2021] [Indexed: 12/16/2022] Open
Abstract
Non-renewable fossil fuels such as bitumen, coal, natural gas, oil shale, and petroleum are depleting over the world owing to unrestricted consumption. Biofuels such as biodiesel, biobutanol, bioethanol, and biogas are considered an eco-friendly and cost-effective alternatives of fossil fuels. For energy sustainability, the production of advanced biofuels is required. The advancement of genetic and metabolic engineering in microbial cells played a significant contribution to biofuels overproduction. Essential approaches such as next-generation sequencing technologies and CRISPR/Cas9-mediated genome editing of microbial cells are required for the mass manufacture of biofuels globally. Advanced "omics" approaches are used to construct effective microorganisms for biofuels manufacturing. A new investigation is required to augment the production of lignocellulosic-based biofuels with minimal use of energy. Advanced areas of metabolic engineering are introduced in the manufacture of biofuels by the use of engineered microbial strains. Genetically modified microorganisms are used for the production of biofuels in large quantities at a low-cost.
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Affiliation(s)
- J Rajesh Banu
- Department of Life Sciences, Central University of Tamil Nadu, Thiruvarur, Tamilnadu India
| | - Gopalakrishnan Kumar
- Faculty of Science and Technology, Institute of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, Forus, Box 8600, 4036 Stavanger, Norway
| | - Indranil Chattopadhyay
- Department of Life Sciences, Central University of Tamil Nadu, Thiruvarur, Tamilnadu India
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Ariaeenejad S, Lanjanian H, Motamedi E, Kavousi K, Moosavi-Movahedi AA, Hosseini Salekdeh G. The Stabilizing Mechanism of Immobilized Metagenomic Xylanases on Bio-Based Hydrogels to Improve Utilization Performance: Computational and Functional Perspectives. Bioconjug Chem 2020; 31:2158-2171. [DOI: 10.1021/acs.bioconjchem.0c00361] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Shohreh Ariaeenejad
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, 31359, Iran
| | - Hossein Lanjanian
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, 13145, Iran
| | - Elaheh Motamedi
- Department of Nanotechnology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, 31359, Iran
| | - Kaveh Kavousi
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, 13145, Iran
| | | | - Ghasem Hosseini Salekdeh
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, 31359, Iran
- Department of Molecular Sciences, Macquarie University, Sydney, 2109, New South Wales, Australia
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Thermostable endoglucanase gene derived by amplification from the genomic DNA of a cellulose-enriched mixed culture from mudspring water of Mt. Makiling, Laguna, Philippines. World J Microbiol Biotechnol 2020; 36:51. [PMID: 32157408 DOI: 10.1007/s11274-020-02825-2] [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: 11/15/2019] [Accepted: 02/29/2020] [Indexed: 10/24/2022]
Abstract
Culture-independent molecular-based approaches can be used to identify genes of interest from environmental sources that have desirable properties such as thermo activity. For this study, a putative thermo stable endoglucanase gene was identified from a mixed culture resulting from the inoculation of Brock-CMcellulose (1%) broth with mudspring water from Mt. Makiling, Laguna, Philippines that had been incubated at 90 °C. Genomic DNA was extracted from the cellulose-enriched mixed culture and endo1949 forward and reverse primers were used to amplify the endoglucanase gene, which was cloned into pCR-script plasmid vector. Blastn alignment of the sequenced insert revealed 99.69% similarity to the glycosyl hydrolase, sso1354 (CelA1; Q97YG7) from Saccharolobus solfataricus. The endoglucanase gene (GenBank accession number MK984682) was determined to be 1,021 nucleotide bases in length, corresponding to 333 amino acids with a molecular mass of ~ 37 kDa. The endoglucanase gene was inserted into a pET21 vector and transformed in E. coli BL21 for expression. Partially purified recombinant Mt. Makiling endoglucanase (MM-Engl) showed a specific activity of 187.61 U/mg and demonstrated heat stability up to 80 °C. The thermo-acid stable endoglucanase can be used in a supplementary hydrolysis step to further hydrolyze the lignocellulosic materials that were previously treated under high temperature-dilute acid conditions, thereby enhancing the release of more glucose sugars for bioethanol production.
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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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8
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Barajas JF, Wehrs M, To M, Cruickshanks L, Urban R, McKee A, Gladden J, Goh EB, Brown ME, Pierotti D, Carothers JM, Mukhopadhyay A, Keasling JD, Fortman JL, Singer SW, Bailey CB. Isolation and Characterization of Bacterial Cellulase Producers for Biomass Deconstruction: A Microbiology Laboratory Course. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2019; 20:jmbe-20-34. [PMID: 31388393 PMCID: PMC6656525 DOI: 10.1128/jmbe.v20i2.1723] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 02/22/2019] [Indexed: 06/10/2023]
Abstract
The conversion of biomass to biofuels presents a solution to one of the largest global challenges of our era, climate change. A critical part of this pipeline is the process of breaking down cellulosic sugars from plant matter to be used by microbes containing biosynthetic pathways that produce biofuels or bioproducts. In this inquiry-based course, students complete a research project that isolates cellulase-producing bacteria from samples collected from the environment. After obtaining isolates, the students characterize the production of cellulases. Students then amplify and sequence the 16S rRNA genes of confirmed cellulase producers and use bioinformatic methods to identify the bacterial isolates. Throughout the course, students learn about the process of generating biofuels and bioproducts through the deconstruction of cellulosic biomass to form monosaccharides from the biopolymers in plant matter. The program relies heavily on active learning and enables students to connect microbiology with issues of sustainability. In addition, it provides exposure to basic microbiology, molecular biology, and biotechnology laboratory techniques and concepts. The described activity was initially developed for the Introductory College Level Experience in Microbiology (iCLEM) program, a research-based immersive laboratory course at the US Department of Energy Joint BioEnergy Institute. Originally designed as an accelerated program for high-potential, low-income, high school students (11th-12th grade), this curriculum could also be implemented for undergraduate coursework in a research-intensive laboratory course at a two- or four-year college or university.
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Affiliation(s)
- Jesus F. Barajas
- Agile BioFoundry, Emeryville, CA 94608
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
| | - Maren Wehrs
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Joint BioEnergy Institute, Emeryville, CA 94608
| | - Milton To
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Joint BioEnergy Institute, Emeryville, CA 94608
| | | | - Rochelle Urban
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Joint BioEnergy Institute, Emeryville, CA 94608
- University of Southern California Viterbi School of Engineering, Los Angeles, CA 90089
| | - Adrienne McKee
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Joint BioEnergy Institute, Emeryville, CA 94608
- Helix OpCo, San Carlos, CA 94070
| | - John Gladden
- Sandia National Laboratories, Livermore CA 94551
| | - Ee-Been Goh
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Joint BioEnergy Institute, Emeryville, CA 94608
- Lygos Inc., Berkeley, CA 94710
| | - Margaret E. Brown
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Joint BioEnergy Institute, Emeryville, CA 94608
- MicroByre, Berkeley, CA 94720
| | - Diane Pierotti
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Joint BioEnergy Institute, Emeryville, CA 94608
| | - James M. Carothers
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Joint BioEnergy Institute, Emeryville, CA 94608
| | - Jay D. Keasling
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Joint BioEnergy Institute, Emeryville, CA 94608
- Department of Chemical Engineering, University of Washington, Seattle, WA 98195
- QB3 Institute, University of California-Berkeley, Emeryville, CA 94608
- University of California, Berkeley, Department of Chemical & Biomolecular Engineering, Berkeley, CA 94720
- University of California, Berkeley, Department of Bioengineering, Berkeley, CA 94720
- Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, DK2970-Horsholm, Denmark
- Synthetic Biochemistry Center, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| | - Jeffrey L. Fortman
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Joint BioEnergy Institute, Emeryville, CA 94608
- Synthetic Biochemistry Center, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| | - Steven W. Singer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Joint BioEnergy Institute, Emeryville, CA 94608
| | - Constance B. Bailey
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- Joint BioEnergy Institute, Emeryville, CA 94608
- QB3 Institute, University of California-Berkeley, Emeryville, CA 94608
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9
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Sahoo JK, Navani NK, Pathania R. Retracted: Bacteria diversity overview and endoglucanase assessment from Himalayan Tapovan geothermal spring. J Basic Microbiol 2018; 58:643. [PMID: 26617413 DOI: 10.1002/jobm.201500135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 08/09/2015] [Indexed: 11/07/2022]
Abstract
The above article from the Journal of Basic Microbiology, published online on 25 August 2015 in Wiley Online Library as Early View (http://onlinelibrary.wiley.com/doi/10.1002/jobm.201500135/pdf), has been retracted by agreement between Naveen Kumar Navani and Ranjana Pathania, the Editor-in-Chief and Wiley-VCH GmbH & Co. KGaA. The retraction has been agreed because the article has been submitted and approved for publication by Jitendra Kumar Sahoo without consent in any form by the named co-authors Naveen Kumar Navani and Ranjana Pathania.
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Affiliation(s)
- Jitendra Kumar Sahoo
- Department of Biotechnology, Chemical Biology and Drug Discovery Lab, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Naveen Kumar Navani
- Department of Biotechnology, Chemical Biology and Drug Discovery Lab, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
| | - Ranjana Pathania
- Department of Biotechnology, Chemical Biology and Drug Discovery Lab, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India
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Hammerer F, Loots L, Do JL, Therien JPD, Nickels CW, Friščić T, Auclair K. Solvent-Free Enzyme Activity: Quick, High-Yielding Mechanoenzymatic Hydrolysis of Cellulose into Glucose. Angew Chem Int Ed Engl 2018; 57:2621-2624. [PMID: 29342316 DOI: 10.1002/anie.201711643] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/16/2017] [Indexed: 12/15/2022]
Abstract
Mechanochemistry enables enzymatic cleavage of cellulose into glucose without bulk solvents, acids, other aggressive reagents, or substrate pre-treatment. This clean mechanoenzymatic process (coined RAging) is also directly applicable to biomass, avoids many limitations associated with the use of cellulases, and produces glucose concentrations greater than three times that obtained by conventional methods.
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Affiliation(s)
- Fabien Hammerer
- Department of Chemistry, McGill University, Montreal, Quebec, H3A 0B8, Canada
| | - Leigh Loots
- Department of Chemistry, McGill University, Montreal, Quebec, H3A 0B8, Canada
| | - Jean-Louis Do
- Department of Chemistry, McGill University, Montreal, Quebec, H3A 0B8, Canada
| | - J P Daniel Therien
- Department of Chemistry, McGill University, Montreal, Quebec, H3A 0B8, Canada
| | | | - Tomislav Friščić
- Department of Chemistry, McGill University, Montreal, Quebec, H3A 0B8, Canada
| | - Karine Auclair
- Department of Chemistry, McGill University, Montreal, Quebec, H3A 0B8, Canada
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11
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Hammerer F, Loots L, Do JL, Therien JPD, Nickels CW, Friščić T, Auclair K. Solvent-Free Enzyme Activity: Quick, High-Yielding Mechanoenzymatic Hydrolysis of Cellulose into Glucose. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201711643] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Fabien Hammerer
- Department of Chemistry; McGill University; Montreal Quebec H3A 0B8 Canada
| | - Leigh Loots
- Department of Chemistry; McGill University; Montreal Quebec H3A 0B8 Canada
| | - Jean-Louis Do
- Department of Chemistry; McGill University; Montreal Quebec H3A 0B8 Canada
| | | | | | - Tomislav Friščić
- Department of Chemistry; McGill University; Montreal Quebec H3A 0B8 Canada
| | - Karine Auclair
- Department of Chemistry; McGill University; Montreal Quebec H3A 0B8 Canada
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12
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Yadav SK. Technological advances and applications of hydrolytic enzymes for valorization of lignocellulosic biomass. BIORESOURCE TECHNOLOGY 2017; 245:1727-1739. [PMID: 28552567 DOI: 10.1016/j.biortech.2017.05.066] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/10/2017] [Accepted: 05/11/2017] [Indexed: 06/07/2023]
Abstract
Hydrolytic enzymes are indispensable tools in the production of various foodstuffs, drugs, and consumables owing to their applications in almost every industrial process nowadays. One of the foremost areas of interest involving the use of hydrolytic enzymes is in the transformation of lignocellulosic biomass into value added products. However, limitations of the processes due to inadequate enzyme activity and stability with a narrow range of pH and temperature optima often limit their effective usage. The innovative technologies, involving manipulation of enzyme activity and stability through mutagenesis, genetic engineering and metagenomics lead to a major leap in all the fields using hydrolytic enzymes. This article provides recent advancement towards the isolation and use of microbes for lignocellulosic biomass utilisation, microbes producing the hydrolytic enzymes, the modern age technologies used to manipulate and enhance the hydrolytic enzyme activity and the applications of such enzymes in value added products development from lignocellulosic biomass.
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Affiliation(s)
- Sudesh Kumar Yadav
- Center of Innovative and Applied Bioprocessing (CIAB), Knowledge City, Sector-81, Mohali, India.
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13
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Gupta P, Mishra AK, Vakhlu J. Cloning and characterization of thermo-alkalistable and surfactant stable endoglucanase from Puga hot spring metagenome of Ladakh (J&K). Int J Biol Macromol 2017; 103:870-877. [DOI: 10.1016/j.ijbiomac.2017.05.113] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/16/2017] [Accepted: 05/18/2017] [Indexed: 11/28/2022]
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14
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Prospects of Metagenomic Cellulases for Converting Lignocellulosic Biomass into Bio-ethanol. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2017. [DOI: 10.22207/jpam.11.2.51] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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15
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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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16
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Tiwari R, Kumar K, Singh S, Nain L, Shukla P. Molecular Detection and Environment-Specific Diversity of Glycosyl Hydrolase Family 1 β-Glucosidase in Different Habitats. Front Microbiol 2016; 7:1597. [PMID: 27790196 PMCID: PMC5062022 DOI: 10.3389/fmicb.2016.01597] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 09/26/2016] [Indexed: 12/23/2022] Open
Abstract
β-glucosidase is a crucial element of the microbial cellulose multienzyme complex since it is responsible for the regulation of the entire cellulose hydrolysis process. Therefore, the aim of the present work was to explore the diversity and distribution of glycosyl hydrolase family 1 β-glucosidase genes in three different environmental niches including, Himalayan soil, cow dung and compost by metagenomic approach. Preliminary evaluation through metabolic profiling using BIOLOG based utilization patterns of carbon, nitrogen, phosphorus and sulfur revealed the environment and substrate specific nature of the indigenous microbial population. Furthermore, clonal library selection, screening and sequence analysis revealed that most of the GH1 β-glucosidase proteins had low identities with the available database. Analysis of the distribution of GH1 β-glucosidase gene fragments and β-glucosidase producing microbial community revealed the environment specific nature. The OTUs obtained from Himalayan soil and compost metagenomic libraries were grouped into 19 different genera comprising 6 groups. The cow dung sample displayed the least diversity of GH1 β-glucosidase sequences, with only 14 genera, distributed among three groups- Bacteroidetes, Firmicutes, and Actinobacteria. The metagenomic study coupled with metabolic profiling of GH1 β-glucosidase illustrated the existence of intricate relationship between the geochemical environmental factors and inherent microbial community.
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Affiliation(s)
- Rameshwar Tiwari
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand UniversityRohtak, India; Division of Microbiology, ICAR-Indian Agricultural Research InstituteNew Delhi, India
| | - Kanika Kumar
- ICAR-National Research Centre on Plant Biotechnology, LBS Centre, Indian Agricultural Research Institute New Delhi, India
| | - Surender Singh
- Division of Microbiology, ICAR-Indian Agricultural Research Institute New Delhi, India
| | - Lata Nain
- Division of Microbiology, ICAR-Indian Agricultural Research Institute New Delhi, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University Rohtak, India
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Rosnow JJ, Anderson LN, Nair RN, Baker ES, Wright AT. Profiling microbial lignocellulose degradation and utilization by emergent omics technologies. Crit Rev Biotechnol 2016; 37:626-640. [PMID: 27439855 DOI: 10.1080/07388551.2016.1209158] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The use of plant materials to generate renewable biofuels and other high-value chemicals is the sustainable and preferable option, but will require considerable improvements to increase the rate and efficiency of lignocellulose depolymerization. This review highlights novel and emerging technologies that are being developed and deployed to characterize the process of lignocellulose degradation. The review will also illustrate how microbial communities deconstruct and metabolize lignocellulose by identifying the necessary genes and enzyme activities along with the reaction products. These technologies include multi-omic measurements, cell sorting and isolation, nuclear magnetic resonance spectroscopy (NMR), activity-based protein profiling, and direct measurement of enzyme activity. The recalcitrant nature of lignocellulose necessitates the need to characterize the methods microbes employ to deconstruct lignocellulose to inform new strategies on how to greatly improve biofuel conversion processes. New technologies are yielding important insights into microbial functions and strategies employed to degrade lignocellulose, providing a mechanistic blueprint in order to advance biofuel production.
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Affiliation(s)
- Joshua J Rosnow
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Lindsey N Anderson
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Reji N Nair
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Erin S Baker
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Aaron T Wright
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
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Maruthamuthu M, Jiménez DJ, Stevens P, van Elsas JD. A multi-substrate approach for functional metagenomics-based screening for (hemi)cellulases in two wheat straw-degrading microbial consortia unveils novel thermoalkaliphilic enzymes. BMC Genomics 2016; 17:86. [PMID: 26822785 PMCID: PMC4730625 DOI: 10.1186/s12864-016-2404-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 01/18/2016] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Functional metagenomics is a promising strategy for the exploration of the biocatalytic potential of microbiomes in order to uncover novel enzymes for industrial processes (e.g. biorefining or bleaching pulp). Most current methodologies used to screen for enzymes involved in plant biomass degradation are based on the use of single substrates. Moreover, highly diverse environments are used as metagenomic sources. However, such methods suffer from low hit rates of positive clones and hence the discovery of novel enzymatic activities from metagenomes has been hampered. RESULTS Here, we constructed fosmid libraries from two wheat straw-degrading microbial consortia, denoted RWS (bred on untreated wheat straw) and TWS (bred on heat-treated wheat straw). Approximately 22,000 clones from each library were screened for (hemi)cellulose-degrading enzymes using a multi-chromogenic substrate approach. The screens yielded 71 positive clones for both libraries, giving hit rates of 1:440 and 1:1,047 for RWS and TWS, respectively. Seven clones (NT2-2, T5-5, NT18-17, T4-1, 10BT, NT18-21 and T17-2) were selected for sequence analyses. Their inserts revealed the presence of 18 genes encoding enzymes belonging to twelve different glycosyl hydrolase families (GH2, GH3, GH13, GH17, GH20, GH27, GH32, GH39, GH53, GH58, GH65 and GH109). These encompassed several carbohydrate-active gene clusters traceable mainly to Klebsiella related species. Detailed functional analyses showed that clone NT2-2 (containing a beta-galactosidase of ~116 kDa) had highest enzymatic activity at 55 °C and pH 9.0. Additionally, clone T5-5 (containing a beta-xylosidase of ~86 kDa) showed > 90% of enzymatic activity at 55 °C and pH 10.0. CONCLUSIONS This study employed a high-throughput method for rapid screening of fosmid metagenomic libraries for (hemi)cellulose-degrading enzymes. The approach, consisting of screens on multi-substrates coupled to further analyses, revealed high hit rates, as compared with recent other studies. Two clones, 10BT and T4-1, required the presence of multiple substrates for detectable activity, indicating a new avenue in library activity screening. Finally, clones NT2-2, T5-5 and NT18-17 were found to encode putative novel thermo-alkaline enzymes, which could represent a starting point for further biotechnological applications.
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Affiliation(s)
- Mukil Maruthamuthu
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands.
| | - Diego Javier Jiménez
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands.
| | - Patricia Stevens
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands.
| | - Jan Dirk van Elsas
- Department of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands.
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Zarafeta D, Kissas D, Sayer C, Gudbergsdottir SR, Ladoukakis E, Isupov MN, Chatziioannou A, Peng X, Littlechild JA, Skretas G, Kolisis FN. Discovery and Characterization of a Thermostable and Highly Halotolerant GH5 Cellulase from an Icelandic Hot Spring Isolate. PLoS One 2016; 11:e0146454. [PMID: 26741138 PMCID: PMC4704807 DOI: 10.1371/journal.pone.0146454] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 12/17/2015] [Indexed: 12/20/2022] Open
Abstract
With the ultimate goal of identifying robust cellulases for industrial biocatalytic conversions, we have isolated and characterized a new thermostable and very halotolerant GH5 cellulase. This new enzyme, termed CelDZ1, was identified by bioinformatic analysis from the genome of a polysaccharide-enrichment culture isolate, initiated from material collected from an Icelandic hot spring. Biochemical characterization of CelDZ1 revealed that it is a glycoside hydrolase with optimal activity at 70°C and pH 5.0 that exhibits good thermostability, high halotolerance at near-saturating salt concentrations, and resistance towards metal ions and other denaturing agents. X-ray crystallography of the new enzyme showed that CelDZ1 is the first reported cellulase structure that lacks the defined sugar-binding 2 subsite and revealed structural features which provide potential explanations of its biochemical characteristics.
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Affiliation(s)
- Dimitra Zarafeta
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Dimitrios Kissas
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Christopher Sayer
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | | | - Efthymios Ladoukakis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Michail N. Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Aristotelis Chatziioannou
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Xu Peng
- Danish Archaea Centre, Department of Biology, Copenhagen University, Copenhagen, Denmark
| | - Jennifer A. Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Georgios Skretas
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Fragiskos N. Kolisis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
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Zhou Y, Wang X, Wei W, Xu J, Wang W, Xie Z, Zhang Z, Jiang H, Wang Q, Wei C. A novel efficient β-glucanase from a paddy soil microbial metagenome with versatile activities. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:36. [PMID: 26877766 PMCID: PMC4752780 DOI: 10.1186/s13068-016-0449-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 01/26/2016] [Indexed: 05/07/2023]
Abstract
BACKGROUND Cellulose, an abundant and renewable polysaccharides, constitutes the largest resource for bioconversion of biofuels. Plant polysaccharides hydrolysis is catalyzed by cellulases, which include endoglucanases, exoglucanases, and β-glucosidases. Converting cellulose and hemicellulose to short chains of oligosaccharides by endo-/exoglucanases is the key step for biofuel transformation. Intriguingly, β-glucanases with transglycosylation activity not only can relieve product inhibition of glucan hydrolysis but also has potential application as biocatalysts for functional materials. RESULTS Here, a metagenomic fosmid library was constructed from a paddy soil for cellulase screening. One purified clone showing carboxymethylcellulase activity was isolated, and the complete β-glucanase gene (umcel9y-1) was cloned and overexpressed in Escherichia coli. Phylogenetic analysis indicated that β-glucanase Umcel9y-1 belonged to the theme C of glycoside hydrolase family 9. Amino acids sequence showed 58.4 % similarity between Umcel9y-1 and its closest characterized reference, cellulase Cel01. Biological characterization showed that Umcel9y-1 was an efficient endoglucanase and also exhibited high activities of exoglucanase and transglycosylation. The transglycosylation products of Umcel9y-1 including sophorose, laminaribiose, and gentiobiose, and transglycosylation was detected under all activated conditions. The order of catalytic efficiency for polysaccharides, cellooligosaccharides, and aryl-β-glycosides was p-nitrophenol-D-cellobioside, barley glucan, cellopentaose, cellotetraose, cellotriose, hydroxyethylcellulose, cellohexose, laminarin, and carboxymethylcellulose, respectively. The barley glucan was the optimal polysaccharides for Umcel9y-1 with K m and K cat/K m values of 13.700 mM and 239.152 s(-1) mM(-1), respectively. CONCLUSION Biological characterizations of recombinant Umcel9y-1 showed that the versatile β-glucanase had efficient endoglucanase activity to barley glucan and also exhibited high activities of exoglucanase and transglycosylation. The optimum conditions of recombinant Umcel9y-1 was pH 6.5-7.0 at 37 °C with predominant halotolerance and high-thermal stability. These results indicate that the novel metagenomic-derived β-glucanase may be a potent candidate for industrial applications.
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Affiliation(s)
- Yu Zhou
- />State Key Laboratory of Tea Biology and Utilization, School of Tea and Food Science Technology, Anhui Agricultural University, Hefei, 230036 China
| | - Xu Wang
- />State Key Laboratory of Tea Biology and Utilization, School of Tea and Food Science Technology, Anhui Agricultural University, Hefei, 230036 China
| | - Wei Wei
- />Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 China
| | - Jimin Xu
- />Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 China
| | - Wei Wang
- />Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 China
| | - Zhongwen Xie
- />State Key Laboratory of Tea Biology and Utilization, School of Tea and Food Science Technology, Anhui Agricultural University, Hefei, 230036 China
| | - Zhengzhu Zhang
- />State Key Laboratory of Tea Biology and Utilization, School of Tea and Food Science Technology, Anhui Agricultural University, Hefei, 230036 China
| | - Hongchen Jiang
- />State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074 China
| | - Qi Wang
- />Novus International (Shanghai) Inc, Shanghai, 200080 China
| | - Chaoling Wei
- />State Key Laboratory of Tea Biology and Utilization, School of Tea and Food Science Technology, Anhui Agricultural University, Hefei, 230036 China
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21
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Lopes LD, de Souza Lima AO, Taketani RG, Darias P, da Silva LRF, Romagnoli EM, Louvandini H, Abdalla AL, Mendes R. Exploring the sheep rumen microbiome for carbohydrate-active enzymes. Antonie van Leeuwenhoek 2015; 108:15-30. [PMID: 25900454 DOI: 10.1007/s10482-015-0459-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 04/16/2015] [Indexed: 10/23/2022]
Abstract
The rumen is a complex ecosystem enriched for microorganisms able to degrade biomass during the animal's digestion process. The recovery of new enzymes from naturally evolved biomass-degrading microbial communities is a promising strategy to overcome the inefficient enzymatic plant destruction in industrial production of biofuels. In this context, this study aimed to describe the bacterial composition and functions in the sheep rumen microbiome, focusing on carbohydrate-active enzymes (CAE). Here, we used phylogenetic profiling analysis (inventory of 16S rRNA genes) combined with metagenomics to access the rumen microbiome of four sheep and explore its potential to identify fibrolytic enzymes. The bacterial community was dominated by Bacteroidetes and Firmicutes, followed by Proteobacteria. As observed for other ruminants, Prevotella was the dominant genus in the microbiome, comprising more than 30 % of the total bacterial community. Multivariate analysis of the phylogenetic profiling data and chemical parameters showed a positive correlation between the abundance of Prevotellaceae (Bacteroidetes phylum) and organic matter degradability. A negative correlation was observed between Succinivibrionaceae (Proteobacteria phylum) and methane production. An average of 2 % of the shotgun metagenomic reads was assigned to putative CAE when considering nine protein databases. In addition, assembled contigs allowed recognition of 67 putative partial CAE (NCBI-Refseq) representing 12 glycosyl hydrolase families (Pfam database). Overall, we identified a total of 28 lignocellulases, 22 amylases and 9 other putative CAE, showing the sheep rumen microbiome as a promising source of new fibrolytic enzymes.
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Affiliation(s)
- Lucas Dantas Lopes
- Laboratory of Environmental Microbiology, Embrapa Environment, Rod. SP340 km 127.5, Jaguaríuna, SP, Zip Code 13820-000, Brazil
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22
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Backbone structures in human milk oligosaccharides: trans-glycosylation by metagenomic β-N-acetylhexosaminidases. Appl Microbiol Biotechnol 2015; 99:7997-8009. [DOI: 10.1007/s00253-015-6550-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 03/13/2015] [Accepted: 03/16/2015] [Indexed: 10/23/2022]
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Abstract
Soil microbial diversity represents the largest global reservoir of novel microorganisms and enzymes. In this study, we coupled functional metagenomics and DNA stable-isotope probing (DNA-SIP) using multiple plant-derived carbon substrates and diverse soils to characterize active soil bacterial communities and their glycoside hydrolase genes, which have value for industrial applications. We incubated samples from three disparate Canadian soils (tundra, temperate rainforest, and agricultural) with five native carbon (12C) or stable-isotope-labeled (13C) carbohydrates (glucose, cellobiose, xylose, arabinose, and cellulose). Indicator species analysis revealed high specificity and fidelity for many uncultured and unclassified bacterial taxa in the heavy DNA for all soils and substrates. Among characterized taxa, Actinomycetales (Salinibacterium), Rhizobiales (Devosia), Rhodospirillales (Telmatospirillum), and Caulobacterales (Phenylobacterium and Asticcacaulis) were bacterial indicator species for the heavy substrates and soils tested. Both Actinomycetales and Caulobacterales (Phenylobacterium) were associated with metabolism of cellulose, and Alphaproteobacteria were associated with the metabolism of arabinose; members of the order Rhizobiales were strongly associated with the metabolism of xylose. Annotated metagenomic data suggested diverse glycoside hydrolase gene representation within the pooled heavy DNA. By screening 2,876 cloned fragments derived from the 13C-labeled DNA isolated from soils incubated with cellulose, we demonstrate the power of combining DNA-SIP, multiple-displacement amplification (MDA), and functional metagenomics by efficiently isolating multiple clones with activity on carboxymethyl cellulose and fluorogenic proxy substrates for carbohydrate-active enzymes. The ability to identify genes based on function, instead of sequence homology, allows the discovery of genes that would not be identified through sequence alone. This is arguably the most powerful application of metagenomics for the recovery of novel genes and a natural partner of the stable-isotope-probing approach for targeting active-yet-uncultured microorganisms. We expanded on previous efforts to combine stable-isotope probing and metagenomics, enriching microorganisms from multiple soils that were active in degrading plant-derived carbohydrates, followed by construction of a cellulose-based metagenomic library and recovery of glycoside hydrolases through functional metagenomics. The major advance of our study was the discovery of active-yet-uncultivated soil microorganisms and enrichment of their glycoside hydrolases. We recovered positive cosmid clones in a higher frequency than would be expected with direct metagenomic analysis of soil DNA. This study has generated an invaluable metagenomic resource that future research will exploit for genetic and enzymatic potential.
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24
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Sae-Lee R, Boonmee A. Newly derived GH43 gene from compost metagenome showing dual xylanase and cellulase activities. Folia Microbiol (Praha) 2014; 59:409-17. [PMID: 24737296 DOI: 10.1007/s12223-014-0313-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 03/05/2014] [Indexed: 10/25/2022]
Abstract
A metagenomic fosmid library was constructed from compost microbial communities that were collected from various farms throughout the Khon Kaen province, Thailand. The library was enriched in carboxymethylcellulose (CM-cellulose)--containing media prior to the screening of clones capable of degrading cellulosic materials. Two clones were selected for further subcloning and sequencing based on different patterns from restriction analysis. Deduced amino acid analysis of possible ORFs revealed one novel gene encoding an enzyme belonging to glycosyl hydrolase family 43 (GH43), which is a GH family rarely found in metagenomic studies. The most notable finding is that this enzyme, designated as Biof1_09, shows dual activities, namely endocellulase and endoxylanase activities. Biof1_09 showed greater than 50% of its activity under acidic conditions ranging from pH 3.5 to 5.5 with a pH optimum of 4.5. The optimum temperature of this enzyme was between 45 and 55 °C with an optimum of 50 °C. The properties of Biof1_09 make this enzyme an attractive candidate for large-scale expression for use in lignocellulose degradation for various bioprocess applications, including bioethanol fermentation.
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Affiliation(s)
- Ritthironk Sae-Lee
- Department of Microbiology, Faculty of Science, Khon Kaen University, Khon Kaen, 40002, Thailand
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25
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Jacquiod S, Demanèche S, Franqueville L, Ausec L, Xu Z, Delmont TO, Dunon V, Cagnon C, Mandic-Mulec I, Vogel TM, Simonet P. Characterization of new bacterial catabolic genes and mobile genetic elements by high throughput genetic screening of a soil metagenomic library. J Biotechnol 2014; 190:18-29. [PMID: 24721211 DOI: 10.1016/j.jbiotec.2014.03.036] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Revised: 03/24/2014] [Accepted: 03/28/2014] [Indexed: 11/27/2022]
Abstract
A mix of oligonucleotide probes was used to hybridize soil metagenomic DNA from a fosmid clone library spotted on high density membranes. The pooled radio-labeled probes were designed to target genes encoding glycoside hydrolases GH18, dehalogenases, bacterial laccases and mobile genetic elements (integrases from integrons and insertion sequences). Positive hybridizing spots were affiliated to the corresponding clones in the library and the metagenomic inserts were sequenced. After assembly and annotation, new coding DNA sequences related to genes of interest were identified with low protein similarity against the closest hits in databases. This work highlights the sensitivity of DNA/DNA hybridization techniques as an effective and complementary way to recover novel genes from large metagenomic clone libraries. This study also supports that some of the identified catabolic genes might be associated with horizontal transfer events.
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Affiliation(s)
- Samuel Jacquiod
- Environmental Microbial Genomics Group, Laboratoire Ampère, CNRS, École Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France.
| | - Sandrine Demanèche
- Environmental Microbial Genomics Group, Laboratoire Ampère, CNRS, École Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France
| | - Laure Franqueville
- Environmental Microbial Genomics Group, Laboratoire Ampère, CNRS, École Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France
| | - Luka Ausec
- Department for Food Science and Technology Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Zhuofei Xu
- Molecular Microbial Ecology Group, Section of Microbiology, København Universitet, København, Denmark
| | - Tom O Delmont
- Environmental Microbial Genomics Group, Laboratoire Ampère, CNRS, École Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France
| | - Vincent Dunon
- Division of Soil and Water Management, Department of Earth and Environmental Sciences, University of Leuven, Kasteelpark Arenberg 20, B-3001 Heverlee, Belgium
| | - Christine Cagnon
- Équipe Environnement et Microbiologie, IBEAS - UFR Sciences et Techniques, Université de Pau et des Pays de l'Adour, 64013 Pau, France
| | - Ines Mandic-Mulec
- Department for Food Science and Technology Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Timothy M Vogel
- Environmental Microbial Genomics Group, Laboratoire Ampère, CNRS, École Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France
| | - Pascal Simonet
- Environmental Microbial Genomics Group, Laboratoire Ampère, CNRS, École Centrale de Lyon, Université de Lyon, 36 Avenue Guy de Collongue, 69134 Ecully, France.
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26
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Enhanced production of cellulose degrading CMCase by newly isolated strain of Aspergillus versicolor. Carbohydr Polym 2014; 104:199-203. [DOI: 10.1016/j.carbpol.2014.01.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 12/21/2013] [Accepted: 01/03/2014] [Indexed: 11/16/2022]
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Portillo MDC, Saadeddin A. Recent trends in ionic liquid (IL) tolerant enzymes and microorganisms for biomass conversion. Crit Rev Biotechnol 2014; 35:294-301. [DOI: 10.3109/07388551.2013.843069] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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28
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Konietzny SGA, Pope PB, Weimann A, McHardy AC. Inference of phenotype-defining functional modules of protein families for microbial plant biomass degraders. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:124. [PMID: 25342967 PMCID: PMC4189754 DOI: 10.1186/s13068-014-0124-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Accepted: 08/05/2014] [Indexed: 05/14/2023]
Abstract
BACKGROUND Efficient industrial processes for converting plant lignocellulosic materials into biofuels are a key to global efforts to come up with alternative energy sources to fossil fuels. Novel cellulolytic enzymes have been discovered in microbial genomes and metagenomes of microbial communities. However, the identification of relevant genes without known homologs, and the elucidation of the lignocellulolytic pathways and protein complexes for different microorganisms remain challenging. RESULTS We describe a new computational method for the targeted discovery of functional modules of plant biomass-degrading protein families, based on their co-occurrence patterns across genomes and metagenome datasets, and the strength of association of these modules with the genomes of known degraders. From approximately 6.4 million family annotations for 2,884 microbial genomes, and 332 taxonomic bins from 18 metagenomes, we identified 5 functional modules that are distinctive for plant biomass degraders, which we term "plant biomass degradation modules" (PDMs). These modules incorporate protein families involved in the degradation of cellulose, hemicelluloses, and pectins, structural components of the cellulosome, and additional families with potential functions in plant biomass degradation. The PDMs were linked to 81 gene clusters in genomes of known lignocellulose degraders, including previously described clusters of lignocellulolytic genes. On average, 70% of the families of each PDM were found to map to gene clusters in known degraders, which served as an additional confirmation of their functional relationships. The presence of a PDM in a genome or taxonomic metagenome bin furthermore allowed us to accurately predict the ability of any particular organism to degrade plant biomass. For 15 draft genomes of a cow rumen metagenome, we used cross-referencing to confirmed cellulolytic enzymes to validate that the PDMs identified plant biomass degraders within a complex microbial community. CONCLUSIONS Functional modules of protein families that are involved in different aspects of plant cell wall degradation can be inferred from co-occurrence patterns across (meta-)genomes with a probabilistic topic model. PDMs represent a new resource of protein families and candidate genes implicated in microbial plant biomass degradation. They can also be used to predict the plant biomass degradation ability for a genome or taxonomic bin. The method is also suitable for characterizing other microbial phenotypes.
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Affiliation(s)
- Sebastian GA Konietzny
- />Max-Planck Research Group for Computational Genomics and Epidemiology, Max-Planck Institute for Informatics, University Campus E1 4, Saarbrücken, 66123 Germany
- />Department of Algorithmic Bioinformatics, Heinrich Heine University Düsseldorf, Düsseldorf, 40225 Germany
| | - Phillip B Pope
- />Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Post Office Box 5003, 1432 Ås, Norway
| | - Aaron Weimann
- />Department of Algorithmic Bioinformatics, Heinrich Heine University Düsseldorf, Düsseldorf, 40225 Germany
| | - Alice C McHardy
- />Max-Planck Research Group for Computational Genomics and Epidemiology, Max-Planck Institute for Informatics, University Campus E1 4, Saarbrücken, 66123 Germany
- />Department of Algorithmic Bioinformatics, Heinrich Heine University Düsseldorf, Düsseldorf, 40225 Germany
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Alvarez TM, Goldbeck R, dos Santos CR, Paixão DAA, Gonçalves TA, Franco Cairo JPL, Almeida RF, de Oliveira Pereira I, Jackson G, Cota J, Büchli F, Citadini AP, Ruller R, Polo CC, de Oliveira Neto M, Murakami MT, Squina FM. Development and biotechnological application of a novel endoxylanase family GH10 identified from sugarcane soil metagenome. PLoS One 2013; 8:e70014. [PMID: 23922891 PMCID: PMC3726488 DOI: 10.1371/journal.pone.0070014] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 06/13/2013] [Indexed: 01/26/2023] Open
Abstract
Metagenomics has been widely employed for discovery of new enzymes and pathways to conversion of lignocellulosic biomass to fuels and chemicals. In this context, the present study reports the isolation, recombinant expression, biochemical and structural characterization of a novel endoxylanase family GH10 (SCXyl) identified from sugarcane soil metagenome. The recombinant SCXyl was highly active against xylan from beechwood and showed optimal enzyme activity at pH 6,0 and 45°C. The crystal structure was solved at 2.75 Å resolution, revealing the classical (β/α)8-barrel fold with a conserved active-site pocket and an inherent flexibility of the Trp281-Arg291 loop that can adopt distinct conformational states depending on substrate binding. The capillary electrophoresis analysis of degradation products evidenced that the enzyme displays unusual capacity to degrade small xylooligosaccharides, such as xylotriose, which is consistent to the hydrophobic contacts at the +1 subsite and low-binding energies of subsites that are distant from the site of hydrolysis. The main reaction products from xylan polymers and phosphoric acid-pretreated sugarcane bagasse (PASB) were xylooligosaccharides, but, after a longer incubation time, xylobiose and xylose were also formed. Moreover, the use of SCXyl as pre-treatment step of PASB, prior to the addition of commercial cellulolytic cocktail, significantly enhanced the saccharification process. All these characteristics demonstrate the advantageous application of this enzyme in several biotechnological processes in food and feed industry and also in the enzymatic pretreatment of biomass for feedstock and ethanol production.
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Affiliation(s)
- Thabata M. Alvarez
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brasil
- Departamento de Bioquímica, Instituto de Biologia (IB), Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brasil
| | - Rosana Goldbeck
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brasil
| | - Camila Ramos dos Santos
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brasil
| | - Douglas A. A. Paixão
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brasil
| | - Thiago A. Gonçalves
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brasil
- Departamento de Bioquímica, Instituto de Biologia (IB), Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brasil
| | - João Paulo L. Franco Cairo
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brasil
- Departamento de Bioquímica, Instituto de Biologia (IB), Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brasil
| | - Rodrigo Ferreira Almeida
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brasil
| | - Isabela de Oliveira Pereira
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brasil
| | - George Jackson
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brasil
| | - Junio Cota
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brasil
| | - Fernanda Büchli
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brasil
- Departamento de Bioquímica, Instituto de Biologia (IB), Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brasil
| | - Ana Paula Citadini
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brasil
| | - Roberto Ruller
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brasil
| | - Carla Cristina Polo
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brasil
| | - Mario de Oliveira Neto
- Departamento de Física e Biofísica, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, São Paulo, Brasil
| | - Mário T. Murakami
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brasil
- * E-mail: (FMS); (MTM)
| | - Fabio M. Squina
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, São Paulo, Brasil
- * E-mail: (FMS); (MTM)
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Qi H, Bai F, Liu A. Purification and characteristics of xyloglucanase and five other cellulolytic enzymes from Trichoderma reesei QM9414. BIOCHEMISTRY (MOSCOW) 2013; 78:424-30. [DOI: 10.1134/s0006297913040123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Rashamuse KJ, Visser DF, Hennessy F, Kemp J, Roux-van der Merwe MP, Badenhorst J, Ronneburg T, Francis-Pope R, Brady D. Characterisation of Two Bifunctional Cellulase–Xylanase Enzymes Isolated from a Bovine Rumen Metagenome Library. Curr Microbiol 2012; 66:145-51. [DOI: 10.1007/s00284-012-0251-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Accepted: 09/28/2012] [Indexed: 10/27/2022]
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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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Kim MK, Barman DN, Kang TH, Kim JH, Kim H, Yun HD. Cloning and Characterization of Cellulase Gene (cel5C) from Cow Rumen Metagenomic Library. ACTA ACUST UNITED AC 2012. [DOI: 10.5352/jls.2012.22.4.437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Abstract
Meat and milk produced by ruminants are important agricultural products and are major sources of protein for humans. Ruminant production is of considerable economic value and underpins food security in many regions of the world. However, the sector faces major challenges because of diminishing natural resources and ensuing increases in production costs, and also because of the increased awareness of the environmental impact of farming ruminants. The digestion of feed and the production of enteric methane are key functions that could be manipulated by having a thorough understanding of the rumen microbiome. Advances in DNA sequencing technologies and bioinformatics are transforming our understanding of complex microbial ecosystems, including the gastrointestinal tract of mammals. The application of these techniques to the rumen ecosystem has allowed the study of the microbial diversity under different dietary and production conditions. Furthermore, the sequencing of genomes from several cultured rumen bacterial and archaeal species is providing detailed information about their physiology. More recently, metagenomics, mainly aimed at understanding the enzymatic machinery involved in the degradation of plant structural polysaccharides, is starting to produce new insights by allowing access to the total community and sidestepping the limitations imposed by cultivation. These advances highlight the promise of these approaches for characterising the rumen microbial community structure and linking this with the functions of the rumen microbiota. Initial results using high-throughput culture-independent technologies have also shown that the rumen microbiome is far more complex and diverse than the human caecum. Therefore, cataloguing its genes will require a considerable sequencing and bioinformatic effort. Nevertheless, the construction of a rumen microbial gene catalogue through metagenomics and genomic sequencing of key populations is an attainable goal. A rumen microbial gene catalogue is necessary to understand the function of the microbiome and its interaction with the host animal and feeds, and it will provide a basis for integrative microbiome-host models and inform strategies promoting less-polluting, more robust and efficient ruminants.
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Park IH, Chang J, Lee YS, Fang SJ, Choi YL. Gene Cloning of Endoglucanase Cel5A from Cellulose-Degrading Paenibacillus xylanilyticus KJ-03 and Purification and Characterization of the Recombinant Enzyme. Protein J 2012; 31:238-45. [DOI: 10.1007/s10930-012-9396-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Identification and Characterization of a Cellulase-Encoding Gene from the Buffalo Rumen Metagenomic Library. Biosci Biotechnol Biochem 2012; 76:1075-84. [DOI: 10.1271/bbb.110786] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Abstract
Most of the microorganisms responsible for nutrient cycling in the environment have yet to be cultivated, and this could include those species responsible for the degradation of cellulose. Known cellulases are well defined at the protein sequence level, but gene variants are difficult to amplify from environmental DNA. The identification of novel cellulase genes independent of DNA amplification is made possible by adopting a direct metagenome sequencing approach to provide genes that can be cloned, expressed, and characterized prior to potential exploitation, all in the absence of any information on the species from which they originated. In this chapter, emerging strategies and methods that will enable the identification of novel cellulase genes and provide an unbiased perspective on gene expression in situ are presented.
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Affiliation(s)
- David J Rooks
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
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Nacke H, Engelhaupt M, Brady S, Fischer C, Tautzt J, Daniel R. Identification and characterization of novel cellulolytic and hemicellulolytic genes and enzymes derived from German grassland soil metagenomes. Biotechnol Lett 2011; 34:663-75. [PMID: 22187078 PMCID: PMC3298741 DOI: 10.1007/s10529-011-0830-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Accepted: 12/08/2011] [Indexed: 11/07/2022]
Abstract
Soil metagenomes represent an unlimited resource for the discovery of novel biocatalysts from soil microorganisms. Three large-inserts metagenomic DNA libraries were constructed from different grassland soil samples and screened for genes conferring cellulase or xylanase activity. Function-driven screening identified a novel cellulase-encoding gene (cel01) and two xylanase-encoding genes (xyn01 and xyn02). From sequence and protein domain analyses, Cel01 (831 amino acids) belongs to glycoside hydrolase family 9 whereas Xyn01 (170 amino acids) and Xyn02 (255 amino acids) are members of glycoside hydrolase family 11. Cel01 harbors a family 9 carbohydrate-binding module, previously found only in xylanases. Both Xyn01 and Xyn02 were most active at 60°C with high activities from 4 to 10 and optimal at pH 7 (Xyn01) and pH 6 (Xyn02). The cellulase gene, cel01, was expressed in E. coli BL21 and the recombinant enzyme (91.9 kDa) was purified. Cel01 exhibited high activity with soluble cellulose substrates containing β-1,4-linkages. Activity with microcrystalline cellulose was not detected. These data, together with the analysis of the degradation profiles of carboxymethyl cellulose and barley glucan indicated that Cel01 is an endo 1,4-β-glucanase. Cel01 showed optimal activity at 50°C and pH 7 being highly active from pH range 5 to 9 and possesses remarkable halotolerance.
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Affiliation(s)
- Heiko Nacke
- Department of Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University Göttingen, Grisebachstr. 8, 37077, Göttingen, Germany
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Cheng CL, Chang JS. Hydrolysis of lignocellulosic feedstock by novel cellulases originating from Pseudomonas sp. CL3 for fermentative hydrogen production. BIORESOURCE TECHNOLOGY 2011; 102:8628-34. [PMID: 21481585 DOI: 10.1016/j.biortech.2011.03.053] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 03/16/2011] [Accepted: 03/17/2011] [Indexed: 05/12/2023]
Abstract
A newly isolated indigenous bacterium Pseudomonas sp. CL3 was able to produce novel cellulases consisting of endo-β-1,4-d-glucanase (80 and 100 kDa), exo-β-1,4-d-glucanase (55 kDa) and β-1,4-d-glucosidase (65 kDa) characterized by enzyme assay and zymography analysis. In addition, the CL3 strain also produced xylanase with a molecular weight of 20 kDa. The optimal temperature for enzyme activity was 50, 45, 45 and 55 °C for endo-β-1,4-d-glucanase, exo-β-1,4-d-glucanase, β-1,4-d-glucosidase and xylanase, respectively. All the enzymes displayed optimal activity at pH 6.0. The cellulases/xylanase could hydrolyze cellulosic materials very effectively and were thus used to hydrolyze natural agricultural waste (i.e., bagasse) for clean energy (H2) production by Clostridium pasteurianum CH4 using separate hydrolysis and fermentation process. The maximum hydrogen production rate and cumulative hydrogen production were 35 ml/L/h and 1420 ml/L, respectively, with a hydrogen yield of around 0.96 mol H2/mol glucose.
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Affiliation(s)
- Chieh-Lun Cheng
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan
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40
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Glycoside hydrolase activities of thermophilic bacterial consortia adapted to switchgrass. Appl Environ Microbiol 2011; 77:5804-12. [PMID: 21724886 DOI: 10.1128/aem.00032-11] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Industrial-scale biofuel production requires robust enzymatic cocktails to produce fermentable sugars from lignocellulosic biomass. Thermophilic bacterial consortia are a potential source of cellulases and hemicellulases adapted to harsher reaction conditions than commercial fungal enzymes. Compost-derived microbial consortia were adapted to switchgrass at 60°C to develop thermophilic biomass-degrading consortia for detailed studies. Microbial community analysis using small-subunit rRNA gene amplicon pyrosequencing and short-read metagenomic sequencing demonstrated that thermophilic adaptation to switchgrass resulted in low-diversity bacterial consortia with a high abundance of bacteria related to thermophilic paenibacilli, Rhodothermus marinus, and Thermus thermophilus. At lower abundance, thermophilic Chloroflexi and an uncultivated lineage of the Gemmatimonadetes phylum were observed. Supernatants isolated from these consortia had high levels of xylanase and endoglucanase activities. Compared to commercial enzyme preparations, the endoglucanase enzymes had a higher thermotolerance and were more stable in the presence of 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]), an ionic liquid used for biomass pretreatment. The supernatants were used to saccharify [C2mim][OAc]-pretreated switchgrass at elevated temperatures (up to 80°C), demonstrating that these consortia are an excellent source of enzymes for the development of enzymatic cocktails tailored to more extreme reaction conditions.
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Fujii K, Kuwahara A, Nakamura K, Yamashita Y. Development of a simple cultivation method for isolating hitherto-uncultured cellulase-producing microbes. Appl Microbiol Biotechnol 2011; 91:1183-92. [DOI: 10.1007/s00253-011-3376-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Revised: 05/02/2011] [Accepted: 05/03/2011] [Indexed: 11/30/2022]
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Hess M, Sczyrba A, Egan R, Kim TW, Chokhawala H, Schroth G, Luo S, Clark DS, Chen F, Zhang T, Mackie RI, Pennacchio LA, Tringe SG, Visel A, Woyke T, Wang Z, Rubin EM. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 2011; 331:463-7. [PMID: 21273488 DOI: 10.1126/science.1200387] [Citation(s) in RCA: 819] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The paucity of enzymes that efficiently deconstruct plant polysaccharides represents a major bottleneck for industrial-scale conversion of cellulosic biomass into biofuels. Cow rumen microbes specialize in degradation of cellulosic plant material, but most members of this complex community resist cultivation. To characterize biomass-degrading genes and genomes, we sequenced and analyzed 268 gigabases of metagenomic DNA from microbes adherent to plant fiber incubated in cow rumen. From these data, we identified 27,755 putative carbohydrate-active genes and expressed 90 candidate proteins, of which 57% were enzymatically active against cellulosic substrates. We also assembled 15 uncultured microbial genomes, which were validated by complementary methods including single-cell genome sequencing. These data sets provide a substantially expanded catalog of genes and genomes participating in the deconstruction of cellulosic biomass.
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Affiliation(s)
- Matthias Hess
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
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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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Tuffin M, Anderson D, Heath C, Cowan DA. Metagenomic gene discovery: how far have we moved into novel sequence space? Biotechnol J 2010; 4:1671-83. [PMID: 19946882 DOI: 10.1002/biot.200900235] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Metagenomics emerged in the late 1990s as a tool for accessing and studying the collective microbial genetic material in the environment. The advent of the technology generated great excitement, as it has provided new opportunities and technologies for studying the wealth of microbial genetic diversity in the environment. Metagenomics has been widely predicted to access new dimensions of protein sequence space. A decade on, we review how far we have actually moved into new sequence space (and other aspects of protein space) using metagenomic tools. While several novel enzyme activities and protein structures have been identified through metagenomic strategies, the greatest advancement has been made in the isolation of novel protein sequences, some of which have no close relatives, form deeply branched lineages and even represent novel families. This is particularly true for glycosyl hydrolases and lipase/esterases, despite the fact that these activities are frequently screened for in metagenomic studies. However, there is much room for improvement in the methods employed and they will need to be addressed so that access to novel biocatalytic activities can be widened.
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Affiliation(s)
- Marla Tuffin
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of Western Cape, Cape town, South Africa
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