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Guo H, Zhao Y, Chang JS, Lee DJ. Enzymes and enzymatic mechanisms in enzymatic degradation of lignocellulosic biomass: A mini-review. BIORESOURCE TECHNOLOGY 2023; 367:128252. [PMID: 36334864 DOI: 10.1016/j.biortech.2022.128252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/26/2022] [Accepted: 10/28/2022] [Indexed: 06/16/2023]
Abstract
Enzymatic hydrolysis is the key step limiting the efficiency of the biorefinery of lignocellulosic biomass. Enzymes involved in enzymatic hydrolysis and their interactions with biomass should be comprehended to form the basis for looking for strategies to improve process efficiency. This article updates the contemporary research on the properties of key enzymes in the lignocellulose biorefinery and their interactions with biomass, adsorption, and hydrolysis. The advanced analytical techniques to track the interactions for exploiting mechanisms are discussed. The challenges and prospects for future research are outlined.
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Affiliation(s)
- Hongliang Guo
- College of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Ying Zhao
- College of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Jo-Shu Chang
- Research Center for Smart Sustainable Circular Economy, Tunghai University, Taichung 407, Taiwan; Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan; Department of Chemical and Materials Engineering, Tunghai University, Taichung 407, Taiwan
| | - Duu-Jong Lee
- Department of Mechanical Engineering, City University of Hong Kong, Kowloon Tong, Hong Kong; Department of Chemical Engineering and Materials Science, Yuan Ze University, Chung-li 32003, Taiwan.
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2
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High Sugar Production from Hydrolysate of Pineapple Residues via Integrated Enzyme‐Membrane System. Chem Eng Technol 2022. [DOI: 10.1002/ceat.202100646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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3
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Arora J, Kinjo Y, Šobotník J, Buček A, Clitheroe C, Stiblik P, Roisin Y, Žifčáková L, Park YC, Kim KY, Sillam-Dussès D, Hervé V, Lo N, Tokuda G, Brune A, Bourguignon T. The functional evolution of termite gut microbiota. MICROBIOME 2022; 10:78. [PMID: 35624491 PMCID: PMC9137090 DOI: 10.1186/s40168-022-01258-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 03/16/2022] [Indexed: 05/11/2023]
Abstract
BACKGROUND Termites primarily feed on lignocellulose or soil in association with specific gut microbes. The functioning of the termite gut microbiota is partly understood in a handful of wood-feeding pest species but remains largely unknown in other taxa. We intend to fill this gap and provide a global understanding of the functional evolution of termite gut microbiota. RESULTS We sequenced the gut metagenomes of 145 samples representative of the termite diversity. We show that the prokaryotic fraction of the gut microbiota of all termites possesses similar genes for carbohydrate and nitrogen metabolisms, in proportions varying with termite phylogenetic position and diet. The presence of a conserved set of gut prokaryotic genes implies that essential nutritional functions were present in the ancestor of modern termites. Furthermore, the abundance of these genes largely correlated with the host phylogeny. Finally, we found that the adaptation to a diet of soil by some termite lineages was accompanied by a change in the stoichiometry of genes involved in important nutritional functions rather than by the acquisition of new genes and pathways. CONCLUSIONS Our results reveal that the composition and function of termite gut prokaryotic communities have been remarkably conserved since termites first appeared ~ 150 million years ago. Therefore, the "world's smallest bioreactor" has been operating as a multipartite symbiosis composed of termites, archaea, bacteria, and cellulolytic flagellates since its inception. Video Abstract.
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Affiliation(s)
- Jigyasa Arora
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan.
| | - Yukihiro Kinjo
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - Jan Šobotník
- Faculty of Tropical AgriSciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Aleš Buček
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - Crystal Clitheroe
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - Petr Stiblik
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Yves Roisin
- Evolutionary Biology and Ecology, Université Libre de Bruxelles, Brussels, Belgium
| | - Lucia Žifčáková
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan
| | - Yung Chul Park
- Division of Forest Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Ki Yoon Kim
- Division of Forest Science, Kangwon National University, Chuncheon, Republic of Korea
| | - David Sillam-Dussès
- Faculty of Tropical AgriSciences, Czech University of Life Sciences, Prague, Czech Republic
- University Sorbonne Paris Nord, Laboratory of Experimental and Comparative Ethology, LEEC, UR 4443, Villetaneuse, France
| | - Vincent Hervé
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Gaku Tokuda
- Tropical Biosphere Research Center, Center of Molecular Biosciences, University of the Ryukyus, Nishihara, Okinawa, 903-0213, Japan
| | - Andreas Brune
- Research Group Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Thomas Bourguignon
- Okinawa Institute of Science & Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, 904-0495, Japan.
- Faculty of Tropical AgriSciences, Czech University of Life Sciences, Prague, Czech Republic.
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Zafar A, Hamid A, Peng L, Wang Y, Aftab MN. Enzymatic hydrolysis of lignocellulosic biomass using a novel, thermotolerant recombinant xylosidase enzyme from Clostridium clariflavum: a potential addition for biofuel industry. RSC Adv 2022; 12:14917-14931. [PMID: 35702232 PMCID: PMC9115876 DOI: 10.1039/d2ra00304j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 04/13/2022] [Indexed: 11/28/2022] Open
Abstract
The present study describes the cloning, expression, purification and characterization of the xylosidase gene (1650 bp) from a thermophilic bacterium Clostridium clariflavum into E. coli BL21 (DE3) using the expression vector pET-21a(+) for utilization in biofuel production. The recombinant xylosidase enzyme was purified to homogeneity by heat treatment and immobilized metal ion affinity chromatography. SDS-PAGE determined that the molecular weight of purified xylosidase was 60 kDa. This purified recombinant xylosidase showed its maximum activity at a temperature of 37 °C and pH 6.0. The purified recombinant xylosidase enzyme remains stable up to 90 °C for 4 h and retained 54.6% relative activity as compared to the control. The presence of metal ions such as Ca2+ and Mg2+ showed a positive impact on xylosidase enzyme activity whereas Cu2+ and Hg2+ inhibit its activity. Organic solvents did not considerably affect the stability of the purified xylosidase enzyme while DMSO and SDS cause the inhibition of enzyme activity. Pretreatment experiments were run in triplicate for 72 h at 30 °C using 10% NaOH. Saccharification experiment was performed by using 1% substrate (pretreated plant biomass) in citrate phosphate buffer of pH 6.5 loaded with 150 U mL−1 of purified recombinant xylosidase enzyme along with ampicillin (10 μg mL−1). Subsequent incubation was carried out at 50 °C and 100 rpm in a shaking incubator for 24 h. Saccharification potential of the recombinant xylosidase enzyme was calculated against both pretreated and untreated sugarcane bagasse and wheat straw as 9.63% and 8.91% respectively. All these characteristics of the recombinant thermotolerant xylosidase enzyme recommended it as a potential candidate for biofuel industry. The present study describes the cloning, expression, purification and characterization of a xylosidase gene from Clostridium clariflavum into E. coli BL21 (DE3) using the expression vector pET-21a(+) for utilization in biofuel production.![]()
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Affiliation(s)
- Asma Zafar
- Faculty of Life Sciences, University of Central Punjab Lahore Pakistan
| | - Attia Hamid
- Institute of Industrial Biotechnology, Government College University Lahore 54000 Pakistan +92 99213341 +92 3444704190
| | - Liangcai Peng
- Biomass and Bioenergy Research Center, Huazhong Agriculture University Wuhan China
| | - Yanting Wang
- Biomass and Bioenergy Research Center, Huazhong Agriculture University Wuhan China
| | - Muhammad Nauman Aftab
- Institute of Industrial Biotechnology, Government College University Lahore 54000 Pakistan +92 99213341 +92 3444704190
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Klaus T, Ninck S, Albersmeier A, Busche T, Wibberg D, Jiang J, Elcheninov AG, Zayulina KS, Kaschani F, Bräsen C, Overkleeft HS, Kalinowski J, Kublanov IV, Kaiser M, Siebers B. Activity-Based Protein Profiling for the Identification of Novel Carbohydrate-Active Enzymes Involved in Xylan Degradation in the Hyperthermophilic Euryarchaeon Thermococcus sp. Strain 2319x1E. Front Microbiol 2022; 12:734039. [PMID: 35095781 PMCID: PMC8790579 DOI: 10.3389/fmicb.2021.734039] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 11/22/2021] [Indexed: 12/02/2022] Open
Abstract
Activity-based protein profiling (ABPP) has so far scarcely been applied in Archaea in general and, especially, in extremophilic organisms. We herein isolated a novel Thermococcus strain designated sp. strain 2319x1E derived from the same enrichment culture as the recently reported Thermococcus sp. strain 2319x1. Both strains are able to grow with xylan as the sole carbon and energy source, and for Thermococcus sp. strain 2319x1E (optimal growth at 85°C, pH 6–7), the induction of xylanolytic activity in the presence of xylan was demonstrated. Since the solely sequence-based identification of xylanolytic enzymes is hardly possible, we established a complementary approach by conducting comparative full proteome analysis in combination with ABPP using α- or β-glycosidase selective probes and subsequent mass spectrometry (MS)-based analysis. This complementary proteomics approach in combination with recombinant protein expression and classical enzyme characterization enabled the identification of a novel bifunctional maltose-forming α-amylase and deacetylase (EGDIFPOO_00674) belonging to the GH57 family and a promiscuous β-glycosidase (EGIDFPOO_00532) with β-xylosidase activity. We thereby further substantiated the general applicability of ABPP in archaea and expanded the ABPP repertoire for the identification of glycoside hydrolases in hyperthermophiles.
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Affiliation(s)
- Thomas Klaus
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Faculty of Chemistry, Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Essen, Germany
| | - Sabrina Ninck
- Department of Chemical Biology, Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Andreas Albersmeier
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Jianbing Jiang
- Section of Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Alexander G Elcheninov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Kseniya S Zayulina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Farnusch Kaschani
- Department of Chemical Biology, Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Christopher Bräsen
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Faculty of Chemistry, Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Essen, Germany
| | - Herman S Overkleeft
- Section of Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, Leiden, Netherlands
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Ilya V Kublanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Markus Kaiser
- Department of Chemical Biology, Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Faculty of Chemistry, Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Essen, Germany
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Ndata K, Nevondo W, Cekuse B, van Zyl LJ, Trindade M. Characterization of a highly xylose tolerant β-xylosidase isolated from high temperature horse manure compost. BMC Biotechnol 2021; 21:61. [PMID: 34689773 PMCID: PMC8543862 DOI: 10.1186/s12896-021-00722-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 10/07/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There is a continued need for improved enzymes for industry. β-xylosidases are enzymes employed in a variety of industries and although many wild-type and engineered variants have been described, enzymes that are highly tolerant of the products produced by catalysis are not readily available and the fundamental mechanisms of tolerance are not well understood. RESULTS Screening of a metagenomic library constructed of mDNA isolated from horse manure compost for β-xylosidase activity identified 26 positive hits. The fosmid clones were sequenced and bioinformatic analysis performed to identity putative β-xylosidases. Based on the novelty of its amino acid sequence and potential thermostability one enzyme (XylP81) was selected for expression and further characterization. XylP81 belongs to the family 39 β-xylosidases, a comparatively rarely found and characterized GH family. The enzyme displayed biochemical characteristics (KM-5.3 mM; Vmax-122 U/mg; kcat-107; Topt-50 °C; pHopt-6) comparable to previously characterized glycoside hydrolase family 39 (GH39) β-xylosidases and despite nucleotide identity to thermophilic species, the enzyme displayed only moderate thermostability with a half-life of 32 min at 60 °C. Apart from acting on substrates predicted for β-xylosidase (xylobiose and 4-nitrophenyl-β-D-xylopyranoside) the enzyme also displayed measurable α-L-arabainofuranosidase, β-galactosidase and β-glucosidase activity. A remarkable feature of this enzyme is its ability to tolerate high concentrations of xylose with a Ki of 1.33 M, a feature that is highly desirable for commercial applications. CONCLUSIONS Here we describe a novel β-xylosidase from a poorly studied glycosyl hydrolase family (GH39) which despite having overall kinetic properties similar to other bacterial GH39 β-xylosidases, displays unusually high product tolerance. This trait is shared with only one other member of the GH39 family, the recently described β-xylosidases from Dictyoglomus thermophilum. This feature should allow its use as starting material for engineering of an enzyme that may prove useful to industry and should assist in the fundamental understanding of the mechanism by which glycosyl hydrolases evolve product tolerance.
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Affiliation(s)
- Kanyisa Ndata
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Walter Nevondo
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, Bellville, South Africa.,Division of Medical Virology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Bongi Cekuse
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Leonardo Joaquim van Zyl
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, Bellville, South Africa.
| | - Marla Trindade
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, Bellville, South Africa
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Xu S, Qi X, Gao S, Zhang Y, Wang H, Shao Y, Yang Y, An Y. Modification of DNA regions with metagenomic DNA fragments (MDRMDF): A convenient strategy for efficient protein engineering. Biochimie 2021; 187:75-81. [PMID: 34051307 DOI: 10.1016/j.biochi.2021.05.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 10/25/2022]
Abstract
In this study, we have established a convenient and efficient approach named Modification of DNA Regions with Metagenomic DNA Fragments (MDRMDF) for protein engineering. Degenerate primers were designed corresponding to conserved regions of the gene of interest which were used for amplification of fragments with template of the metagenomic DNA. The resulting PCR products were used to replace the corresponding regions of the gene of interest to introduce modified gene for function-based screening. Therefore, this method can make full use of the metagenomic DNA sequences with unknown metagenomic gene information for efficient protein engineering. The β-xylosidase BH3683 was used to construct a MDRMDF library which was screened with a newly designed p-NPX-M9 medium-based strategy. As a result, a mutant protein Xyl-M56 showing high activity, improved pH stability and higher tolerance to organic solvents was obtained which may have potential for industrial application. The MDRMDF method may find wide application in enzyme engineering, metabolic engineering and other fields, especially offering a new methodological option for the directed evolution of proteins.
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Affiliation(s)
- Shumin Xu
- College of Food Science, Shenyang Agricultural University, Shenyang, China; College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Xianghui Qi
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Song Gao
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Yifeng Zhang
- College of Food Science, Shenyang Agricultural University, Shenyang, China; College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Hongling Wang
- College of Food Science, Shenyang Agricultural University, Shenyang, China; College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Yilun Shao
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Yao Yang
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Yingfeng An
- College of Food Science, Shenyang Agricultural University, Shenyang, China; College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China.
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Verma D, Satyanarayana T. Xylanolytic Extremozymes Retrieved From Environmental Metagenomes: Characteristics, Genetic Engineering, and Applications. Front Microbiol 2020; 11:551109. [PMID: 33042057 PMCID: PMC7527525 DOI: 10.3389/fmicb.2020.551109] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 08/21/2020] [Indexed: 01/29/2023] Open
Abstract
Xylanolytic enzymes have extensive applications in paper, food, and feed, pharmaceutical, and biofuel industries. These industries demand xylanases that are functional under extreme conditions, such as high temperature, acidic/alkaline pH, and others, which are prevailing in bioprocessing industries. Despite the availability of several xylan-hydrolyzing enzymes from cultured microbes, there is a huge gap between what is available and what industries require. DNA manipulations as well as protein-engineering techniques are also not quite satisfactory in generating xylan-hydrolyzing extremozymes. With a compound annual growth rate of 6.6% of xylan-hydrolyzing enzymes in the global market, there is a need for xylanolytic extremozymes. Therefore, metagenomic approaches have been employed to uncover hidden xylanolytic genes that were earlier inaccessible in culture-dependent approaches. Appreciable success has been achieved in retrieving several unusual xylanolytic enzymes with novel and desirable characteristics from different extreme environments using functional and sequence-based metagenomic approaches. Moreover, the Carbohydrate Active Enzymes database includes approximately 400 GH-10 and GH-11 unclassified xylanases. This review discusses sources, characteristics, and applications of xylanolytic enzymes obtained through metagenomic approaches and their amelioration by genetic engineering techniques.
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Affiliation(s)
- Digvijay Verma
- Department of Microbiology, Babasaheb Bhimrao Ambedkar (Central) University, Lucknow, India
| | - Tulasi Satyanarayana
- Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, India
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Bioprospection of Enzymes and Microorganisms in Insects to Improve Second-Generation Ethanol Production. Ind Biotechnol (New Rochelle N Y) 2019. [DOI: 10.1089/ind.2019.0019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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10
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Xu B, Dai L, Zhang W, Yang Y, Wu Q, Li J, Tang X, Zhou J, Ding J, Han N, Huang Z. Characterization of a novel salt-, xylose- and alkali-tolerant GH43 bifunctional β-xylosidase/α-l-arabinofuranosidase from the gut bacterial genome. J Biosci Bioeng 2019; 128:429-437. [PMID: 31109875 DOI: 10.1016/j.jbiosc.2019.03.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 02/13/2019] [Accepted: 03/30/2019] [Indexed: 10/26/2022]
Abstract
A GH43 bifunctional β-xylosidase encoding gene (XylRBM26) was cloned from Massilia sp. RBM26 and successfully expressed in Escherichia coli. Recombinant XylRBM26 exhibited β-xylosidase and α-l-arabinofuranosidase activities. When 4-nitrophenyl-β-d-xylopyranoside was used as a substrate, the enzyme reached optimal activity at pH 6.5 and 50°C and remained stable at pH 5.0-10.0. Purified XylRBM26 presented good salt tolerance and retained 96.6% activity in 3.5 M NaCl and 77.9% initial activity even in 4.0 M NaCl. In addition, it exhibited high tolerance to xylose with Ki value of 500 mM. This study was the first to identify and characterize NaCl-tolerant β-xylosidase/α-l-arabinofuranosidase from the gut microbiota. The enzyme's salt, xylose, and alkali stability and resistance to various chemicals make it a potential biocatalyst for the saccharification of lignocellulose, the food industry, and industrial processes conducted in sea water.
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Affiliation(s)
- Bo Xu
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming 650500, People's Republic of China; Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming 650500, People's Republic of China; School of Life Science, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Liming Dai
- School of Life Science, Yunnan Normal University, Kunming 650500, People's Republic of China; Yunnan Institute of Tropical Crops, Jinghong 666100, People's Republic of China
| | - Wenhong Zhang
- School of Life Science, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Yunjuan Yang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming 650500, People's Republic of China; Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming 650500, People's Republic of China; School of Life Science, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Qian Wu
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming 650500, People's Republic of China; Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming 650500, People's Republic of China; School of Life Science, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Junjun Li
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming 650500, People's Republic of China; Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming 650500, People's Republic of China; School of Life Science, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Xianghua Tang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming 650500, People's Republic of China; Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming 650500, People's Republic of China; School of Life Science, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Junpei Zhou
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming 650500, People's Republic of China; Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming 650500, People's Republic of China; School of Life Science, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Junmei Ding
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming 650500, People's Republic of China; Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming 650500, People's Republic of China; School of Life Science, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Nanyu Han
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming 650500, People's Republic of China; Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming 650500, People's Republic of China; School of Life Science, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Zunxi Huang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming 650500, People's Republic of China; Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming 650500, People's Republic of China; School of Life Science, Yunnan Normal University, Kunming 650500, People's Republic of China.
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Liu N, Li H, Chevrette MG, Zhang L, Cao L, Zhou H, Zhou X, Zhou Z, Pope PB, Currie CR, Huang Y, Wang Q. Functional metagenomics reveals abundant polysaccharide-degrading gene clusters and cellobiose utilization pathways within gut microbiota of a wood-feeding higher termite. THE ISME JOURNAL 2019; 13:104-117. [PMID: 30116044 PMCID: PMC6298952 DOI: 10.1038/s41396-018-0255-1] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 07/16/2018] [Accepted: 07/20/2018] [Indexed: 12/27/2022]
Abstract
Plant cell-wall polysaccharides constitute the most abundant but recalcitrant organic carbon source in nature. Microbes residing in the digestive tract of herbivorous bilaterians are particularly efficient at depolymerizing polysaccharides into fermentable sugars and play a significant support role towards their host's lifestyle. Here, we combine large-scale functional screening of fosmid libraries, shotgun sequencing, and biochemical assays to interrogate the gut microbiota of the wood-feeding "higher" termite Globitermes brachycerastes. A number of putative polysaccharide utilization gene clusters were identified with multiple fibrolytic genes. Our large-scale functional screening of 50,000 fosmid clones resulted in 464 clones demonstrating plant polysaccharide-degrading activities, including 267 endoglucanase-, 24 exoglucanase-, 72 β-glucosidase-, and 101 endoxylanase-positive clones. We sequenced 173 functionally active clones and identified ~219 genes encoding putative carbohydrate-active enzymes (CAZymes) targeting cellulose, hemicellulose and pectin. Further analyses revealed that 68 of 154 contigs encode one or more CAZyme, which includes 35 examples of putative saccharolytic operons, suggesting that clustering of CAZymes is common in termite gut microbial inhabitants. Biochemical characterization of a representative xylanase cluster demonstrated that constituent enzymes exhibited complementary physicochemical properties and saccharolytic capabilities. Furthermore, diverse cellobiose-metabolizing enzymes include β-glucosidases, cellobiose phosphorylases, and phopho-6-β-glucosidases were identified and functionally verified, indicating that the termite gut micro-ecosystem utilizes diverse metabolic pathways to interconnect hydrolysis and central metabolism. Collectively, these results provide an in-depth view of the adaptation and digestive strategies employed by gut microbiota within this tiny-yet-efficient host-associated ecosystem.
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Affiliation(s)
- Ning Liu
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hongjie Li
- Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, USA
- Department Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Marc G Chevrette
- Department Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Lei Zhang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lin Cao
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Haokui Zhou
- Institute for Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky, Lexington, USA
| | - Zhihua Zhou
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Phillip B Pope
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Cameron R Currie
- Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, USA
- Department Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Yongping Huang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Qian Wang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China.
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