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Liu G, Song L, Li J, Song X, Mei X, Zhang Y, Fan C, Chang Y, Xue C. Identification and characterization of a chondroitinase ABC with a novel carbohydrate-binding module. Int J Biol Macromol 2024; 271:132518. [PMID: 38777025 DOI: 10.1016/j.ijbiomac.2024.132518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
Chondroitinases play important roles in structural and functional studies of chondroitin sulfates. Carbohydrate-binding module (CBM) is generally considered as an accessory module in carbohydrate-active enzymes, which promotes the association of the appended enzyme with the substrate and potentiates the catalytic activity. However, the role of natural CBM in chondroitinases has not been investigated. Herein, a novel chondroitinase ChABC29So containing an unknown domain with a predicted β-sandwich fold was discovered from Segatella oris. Recombinant ChABC29So showed enzyme activity towards chondroitin sulfates and hyaluronic acid and acted in a random endo-acting manner. The unknown domain exhibited a chondroitin sulfate-binding capacity and was identified as a CBM. Biochemical characterization of ChABC29So and the CBM-truncated enzyme revealed that the CBM enhances the catalytic activity, thermostability, and disaccharide proportion in the final enzymatic products of ChABC29So. These findings demonstrate the role of the natural CBM in a chondroitinase and will guide future modification of chondroitinases.
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Affiliation(s)
- Guanchen Liu
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Lin Song
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Jiajing Li
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Xiao Song
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Xuanwei Mei
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Yuying Zhang
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Chuan Fan
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Yaoguang Chang
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China.
| | - Changhu Xue
- College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
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2
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Takahashi M, Yano S, Horaguchi Y, Otsuka Y, Suyotha W, Makabe K, Konno H, Kokeguchi S. α-1,3-Glucanase from the gram-negative bacterium Flavobacterium sp. EK-14 hydrolyzes fungal cell wall α-1,3-glucan. Sci Rep 2023; 13:21420. [PMID: 38049513 PMCID: PMC10696023 DOI: 10.1038/s41598-023-48627-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/28/2023] [Indexed: 12/06/2023] Open
Abstract
The glycoside hydrolase (GH) 87 α-1,3-glucanase (Agl-EK14) gene was cloned from the genomic DNA of the gram-negative bacterium Flavobacterium sp. EK14. The gene consisted of 2940 nucleotides and encoded 980 amino acid residues. The deduced amino acid sequence of Agl-EK14 included a signal peptide, a catalytic domain, a first immunoglobulin-like domain, a second immunoglobulin-like domain, a ricin B-like lectin domain, and a carboxyl-terminal domain (CTD) involved in extracellular secretion. Phylogenetic analysis of the catalytic domain of GH87 enzymes suggested that Agl-EK14 is distinct from known clusters, such as clusters composed of α-1,3-glucanases from bacilli and mycodextranases from actinomycetes. Agl-EK14 without the signal peptide and CTD hydrolyzed α-1,3-glucan, and the reaction residues from 1 and 2% substrates were almost negligible after 1440 min reaction. Agl-EK14 hydrolyzed the cell wall preparation of Aspergillus oryzae and released glucose, nigerose, and nigero-triose from the cell wall preparation. After treatment of A. oryzae live mycelia with Agl-EK14 (at least 0.5 nmol/ml), mycelia were no longer stained by red fluorescent protein-fused α-1,3-glucan binding domains of α-1,3-glucanase Agl-KA from Bacillus circulans KA-304. Results suggested that Agl-EK14 can be applied to a fungal cell wall lytic enzyme.
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Affiliation(s)
- Masaki Takahashi
- Graduate School of Sciences and Engineering, Yamagata University, Jonan, Yonezawa, Yamagata, 992-8510, Japan
| | - Shigekazu Yano
- Graduate School of Sciences and Engineering, Yamagata University, Jonan, Yonezawa, Yamagata, 992-8510, Japan.
| | - Yui Horaguchi
- Graduate School of Sciences and Engineering, Yamagata University, Jonan, Yonezawa, Yamagata, 992-8510, Japan
| | - Yuitsu Otsuka
- Graduate School of Sciences and Engineering, Yamagata University, Jonan, Yonezawa, Yamagata, 992-8510, Japan
| | - Wasana Suyotha
- Enzyme Technology Laboratory, Faculty of Agro-Industry, Prince of Songkla University, Hat Yai, 90112, Thailand
| | - Koki Makabe
- Graduate School of Sciences and Engineering, Yamagata University, Jonan, Yonezawa, Yamagata, 992-8510, Japan
| | - Hiroyuki Konno
- Graduate School of Sciences and Engineering, Yamagata University, Jonan, Yonezawa, Yamagata, 992-8510, Japan
| | - Susumu Kokeguchi
- Department of Oral Microbiology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8525, Japan
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Yao T, Deemer DG, Chen MH, Reuhs BL, Hamaker BR, Lindemann SR. Differences in fine arabinoxylan structures govern microbial selection and competition among human gut microbiota. Carbohydr Polym 2023; 316:121039. [PMID: 37321733 DOI: 10.1016/j.carbpol.2023.121039] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/27/2023] [Accepted: 05/18/2023] [Indexed: 06/17/2023]
Abstract
Dietary fibers are known to modulate microbiome composition, but it is unclear to what extent minor fiber structural differences impact community assembly, microbial division of labor, and organismal metabolic responses. To test the hypothesis that fine linkage variations afford different ecological niches for distinct communities and metabolism, we employed a 7-day in vitro sequential batch fecal fermentation with four fecal inocula and measured responses using an integrated multi-omics approach. Two sorghum arabinoxylans (SAXs) were fermented, with one (RSAX) having slightly more complex branch linkages than the other (WSAX). Although there were minor glycoysl linkage differences, consortia on RSAX retained much higher species diversity (42 members) than on WSAX (18-23 members) with distinct species-level genomes and metabolic outcomes (e.g., higher short chain fatty acid production from RSAX and more lactic acid produced from WSAX). The major SAX-selected members were from genera of Bacteroides and Bifidobacterium and family Lachnospiraceae. Carbohydrate active enzyme (CAZyme) genes in metagenomes revealed broad AX-related hydrolytic potentials among key members; however, CAZyme genes enriched in different consortia displayed various catabolic domain fusions with diverse accessory motifs that differ among the two SAX types. These results suggest that fine polysaccharide structure exerts deterministic selection effect for distinct fermenting consortia.
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Affiliation(s)
- Tianming Yao
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907, USA
| | - Dane G Deemer
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907, USA
| | - Ming-Hsu Chen
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907, USA; Institute of Food Science and Technology of National Taiwan University. No. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Bradley L Reuhs
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907, USA
| | - Bruce R Hamaker
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907, USA
| | - Stephen R Lindemann
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907, USA.
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Wang M, Zhang C, Xu Y, Ma M, Yao T, Sui Z. Impact of Six Extraction Methods on Molecular Composition and Antioxidant Activity of Polysaccharides from Young Hulless Barley Leaves. Foods 2023; 12:3381. [PMID: 37761090 PMCID: PMC10527962 DOI: 10.3390/foods12183381] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/02/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Young hulless barley leaves are gaining recognition for potential health benefits, and the method of extracting polysaccharides from them is critical for potential food industry applications. This study delves into a comparative analysis of six distinct fiber extraction techniques: hot water extraction; high-pressure steam extraction; alkaline extraction; xylanase extraction; cellulase extraction; and combined xylanase and cellulase extraction. This analysis included a thorough comparison of polysaccharide-monosaccharide composition, structural properties, antioxidant activities (DPPH, ABTS, and FRAP), and rheological properties among fibers extracted using these methods. The results underscore that the combined enzymatic extraction method yielded the highest extraction yield (22.63%), while the rest of the methods yielded reasonable yields (~20%), except for hot water extraction (4.11%). Monosaccharide composition exhibited divergence across methods; alkaline extraction yielded a high abundance of xylose residues, whereas the three enzymatic methods demonstrated elevated galactose components. The extracted crude polysaccharides exhibited relatively low molecular weights, ranging from 5.919 × 104 Da to 3.773 × 105 Da across different extraction methods. Regarding antioxidant activities, alkaline extraction yielded the highest value in the ABTS assay, whereas enzymatically extracted polysaccharides, despite higher yield, demonstrated lower antioxidant capacity. In addition, enzymatically extracted polysaccharides exerted stronger shear thinning behavior and higher initial viscosity.
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Affiliation(s)
- Mingming Wang
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (M.W.); (C.Z.); (Y.X.); (M.M.)
| | - Chuangchuang Zhang
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (M.W.); (C.Z.); (Y.X.); (M.M.)
| | - Yuting Xu
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (M.W.); (C.Z.); (Y.X.); (M.M.)
| | - Mengting Ma
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (M.W.); (C.Z.); (Y.X.); (M.M.)
| | - Tianming Yao
- Department of Food Science, Whistler Center for Carbohydrate Research, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907, USA
| | - Zhongquan Sui
- Department of Food Science & Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (M.W.); (C.Z.); (Y.X.); (M.M.)
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Xing M, Wang Y, Zhao Y, Chi Z, Chi Z, Liu G. C-Terminal Bacterial Immunoglobulin-like Domain of κ-Carrageenase Serves as a Multifunctional Module to Promote κ-Carrageenan Hydrolysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:1212-1222. [PMID: 35057622 DOI: 10.1021/acs.jafc.1c07233] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
κ-Carrageenase is an important component for κ-carrageenan oligosaccharide production. Generally, noncatalytic domains are appended to carbohydrate-active domains and potentiate catalytic activity. However, studies devoted to κ-carrageenase are relatively few. Here, a C-terminal bacterial immunoglobulin-like domain (Big_2) was identified in κ-carrageenase (PpCgk) from Pseudoalteromonas porphyrae. Biochemical characterization of native PpCgk and its two truncations, PpCgkCD (catalytic domain) and PpBig_2 (Big_2 domain), revealed that the specific activity, catalytic efficiency (kcat/Km(app)), specific κ-carrageenan-binding capacity, and thermostability of PpCgk were significantly higher than those of PpCgkCD, suggesting that the noncatalytic PpBig_2 domain is a multifunctional module and essential for maintaining the activity and thermostability of PpCgk. Furthermore, it was found that the mode of action of PpCgk was more processive on both the dissolved and gelled substrates than that of PpCgkCD, indicating that PpBig_2 contributes to the processivity of PpCgk. Interestingly, PpBig_2 can be used as an independent module to enhance the hydrolysis of κ-carrageenan through its disruptive function. In addition, sequence analysis suggests that Big_2 domains are highly conserved in bacterial κ-carrageenases, implying the universality of their noncatalytic functions. These findings reveal the multifunctional role of the noncatalytic PpBig_2 and will guide future functional analyses and biotechnology applications of Big_2 domains.
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Affiliation(s)
- Mengdan Xing
- College of Marine Life Science, Ocean University of China, Qingdao 266003, China
| | - Yan Wang
- College of Marine Life Science, Ocean University of China, Qingdao 266003, China
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Yujuan Zhao
- College of Marine Life Science, Ocean University of China, Qingdao 266003, China
| | - Zhe Chi
- College of Marine Life Science, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266003, China
| | - Zhenming Chi
- College of Marine Life Science, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266003, China
| | - Guanglei Liu
- College of Marine Life Science, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266003, China
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6
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Mishra S, Wang W, de Oliveira IP, Atapattu AJ, Xia SW, Grillo R, Lescano CH, Yang X. Interaction mechanism of plant-based nanoarchitectured materials with digestive enzymes of termites as target for pest control: Evidence from molecular docking simulation and in vitro studies. JOURNAL OF HAZARDOUS MATERIALS 2021; 403:123840. [PMID: 33264921 DOI: 10.1016/j.jhazmat.2020.123840] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/15/2020] [Accepted: 08/26/2020] [Indexed: 06/12/2023]
Abstract
The integration of nanotechnology for efficient pest management is gaining momentum to overcome the challenges and drawbacks of traditional approaches. However, studies pertaining to termite pest control using biosynthesized nanoparticles are seldom. The present study aims to highlight the following key points: a) green synthesis of AgNPs using Glochidion eriocarpum and their activity against wood-feeding termites, b) testing the hypothesis that AgNPs diminish digestive enzymes in termite gut through in silico analysis. The green synthesis route generated spherical PsAgNPs in the size range of 4-44.5 nm exhibiting higher thermal stability with minimal weight loss at 700 °C. The choice and no-choice bioassays confirmed strong repellent (80.97%) and antifeedant activity of PsAgNPs. Moreover, PsAgNPs exposure caused visible morphological changes in termites. Molecular docking simulation indicated possible attenuation of endoglucanase and bacteria-origin xylanase, digestive enzymes from termite gut, through partial blocking of the catalytic site by AgNPs. Altogether, our preliminary study suggests promising potentials of PsAgNPs for pest management in forestry and agriculture sectors to prevent damages to living trees, wood, crops, etc. As sustainable pest management practices demand low risk to the environment and biodiversity therefore, we recommend that more extensive studies should be performed to elucidate the environmental compatibility of PsAgNPs.
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Affiliation(s)
- Sandhya Mishra
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Xishuangbanna, China.
| | - Wenting Wang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Xishuangbanna, China
| | - Ivan Pires de Oliveira
- Department of Pharmacology, Institute of Biomedical Sciences, University of São Paulo - USP, São Paulo, 05508-900, Brazil
| | - Anjana J Atapattu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Xishuangbanna, China
| | - Shang-Wen Xia
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Xishuangbanna, China
| | - Renato Grillo
- São Paulo State University (UNESP), Department of Physics and Chemistry, School of Engineering, 15385-000, Ilha Solteira, SP, Brazil
| | - Caroline Honaiser Lescano
- Department of Pharmacology, School of Medical Science, University of Campinas - UNICAMP, Campinas, São Paulo, 13083-887, Brazil
| | - Xiaodong Yang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan, 666303, China; Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Xishuangbanna, China.
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Wang J, Liang J, Li Y, Tian L, Wei Y. Characterization of efficient xylanases from industrial-scale pulp and paper wastewater treatment microbiota. AMB Express 2021; 11:19. [PMID: 33464408 PMCID: PMC7815853 DOI: 10.1186/s13568-020-01178-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 12/31/2020] [Indexed: 02/08/2023] Open
Abstract
Xylanases are widely used enzymes in the food, textile, and paper industries. Most efficient xylanases have been identified from lignocellulose-degrading microbiota, such as the microbiota of the cow rumen and the termite hindgut. Xylanase genes from efficient pulp and paper wastewater treatment (PPWT) microbiota have been previously recovered by metagenomics, assigning most of the xylanase genes to the GH10 family. In this study, a total of 40 GH10 family xylanase genes derived from a certain PPWT microbiota were cloned and expressed in Escherichia coli BL21 (DE3). Among these xylanase genes, 14 showed xylanase activity on beechwood substrate. Two of these, PW-xyl9 and PW-xyl37, showed high activities, and were purified to evaluate their xylanase properties. Values of optimal pH and temperature for PW-xyl9 were pH 7 and 60 ℃, respectively, while those for PW-xyl37 were pH 7 and 55 ℃, respectively; their specific xylanase activities under optimal conditions were 470.1 U/mg protein and 113.7 U/mg protein, respectively. Furthermore, the Km values of PW-xyl9 and PW-xyl37 were determined as 8.02 and 18.8 g/L, respectively. The characterization of these two xylanases paves the way for potential application in future pulp and paper production and other industries, indicating that PPWT microbiota has been an undiscovered reservoir of efficient lignocellulase genes. This study demonstrates that a metagenomic approach has the potential to screen efficient xylanases of uncultured microorganisms from lignocellulose-degrading microbiota. In a similar way, other efficient lignocellulase genes might be identified from PPWT treatment microbiota in the future.
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Adegboye MF, Ojuederie OB, Talia PM, Babalola OO. Bioprospecting of microbial strains for biofuel production: metabolic engineering, applications, and challenges. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:5. [PMID: 33407786 PMCID: PMC7788794 DOI: 10.1186/s13068-020-01853-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 12/09/2020] [Indexed: 05/17/2023]
Abstract
The issues of global warming, coupled with fossil fuel depletion, have undoubtedly led to renewed interest in other sources of commercial fuels. The search for renewable fuels has motivated research into the biological degradation of lignocellulosic biomass feedstock to produce biofuels such as bioethanol, biodiesel, and biohydrogen. The model strain for biofuel production needs the capability to utilize a high amount of substrate, transportation of sugar through fast and deregulated pathways, ability to tolerate inhibitory compounds and end products, and increased metabolic fluxes to produce an improved fermentation product. Engineering microbes might be a great approach to produce biofuel from lignocellulosic biomass by exploiting metabolic pathways economically. Metabolic engineering is an advanced technology for the construction of highly effective microbial cell factories and a key component for the next-generation bioeconomy. It has been extensively used to redirect the biosynthetic pathway to produce desired products in several native or engineered hosts. A wide range of novel compounds has been manufactured through engineering metabolic pathways or endogenous metabolism optimizations by metabolic engineers. This review is focused on the potential utilization of engineered strains to produce biofuel and gives prospects for improvement in metabolic engineering for new strain development using advanced technologies.
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Affiliation(s)
- Mobolaji Felicia Adegboye
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, Private Bag X2046, 2735, South Africa
| | - Omena Bernard Ojuederie
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, Private Bag X2046, 2735, South Africa
- Department of Biological Sciences, Faculty of Science, Kings University, Ode-Omu, PMB 555, Osun State, Nigeria
| | - Paola M Talia
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA CICVyA, CNIA, INTA Castelar, Dr. N. Repetto y Los Reseros s/n, (1686) Hurlingham, 1686) Hurlingham, Provincia de Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas Y Tecnológicas (CONICET), Buenos Aires, Provincia de Buenos Aires, Argentina
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, Private Bag X2046, 2735, South Africa.
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Pullulan biosynthesis and its regulation in Aureobasidium spp. Carbohydr Polym 2021; 251:117076. [DOI: 10.1016/j.carbpol.2020.117076] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/06/2020] [Accepted: 09/07/2020] [Indexed: 02/06/2023]
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10
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Qi CY, Jia SL, Wei X, Yang G, Chi Z, Liu GL, Hu Z, Chi ZM. The differences between fungal α-glucan synthase determining pullulan synthesis and that controlling cell wall α-1,3 glucan synthesis. Int J Biol Macromol 2020; 162:436-444. [DOI: 10.1016/j.ijbiomac.2020.06.147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 06/16/2020] [Indexed: 11/30/2022]
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Neotropical termite microbiomes as sources of novel plant cell wall degrading enzymes. Sci Rep 2020; 10:3864. [PMID: 32123275 PMCID: PMC7052144 DOI: 10.1038/s41598-020-60850-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 12/24/2019] [Indexed: 11/08/2022] Open
Abstract
In this study, we used shotgun metagenomic sequencing to characterise the microbial metabolic potential for lignocellulose transformation in the gut of two colonies of Argentine higher termite species with different feeding habits, Cortaritermes fulviceps and Nasutitermes aquilinus. Our goal was to assess the microbial community compositions and metabolic capacity, and to identify genes involved in lignocellulose degradation. Individuals from both termite species contained the same five dominant bacterial phyla (Spirochaetes, Firmicutes, Proteobacteria, Fibrobacteres and Bacteroidetes) although with different relative abundances. However, detected functional capacity varied, with C. fulviceps (a grass-wood-feeder) gut microbiome samples containing more genes related to amino acid metabolism, whereas N. aquilinus (a wood-feeder) gut microbiome samples were enriched in genes involved in carbohydrate metabolism and cellulose degradation. The C. fulviceps gut microbiome was enriched specifically in genes coding for debranching- and oligosaccharide-degrading enzymes. These findings suggest an association between the primary food source and the predicted categories of the enzymes present in the gut microbiomes of each species. To further investigate the termite microbiomes as sources of biotechnologically relevant glycosyl hydrolases, a putative GH10 endo-β-1,4-xylanase, Xyl10E, was cloned and expressed in Escherichia coli. Functional analysis of the recombinant metagenome-derived enzyme showed high specificity towards beechwood xylan (288.1 IU/mg), with the optimum activity at 50 °C and a pH-activity range from 5 to 10. These characteristics suggest that Xy110E may be a promising candidate for further development in lignocellulose deconstruction applications.
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12
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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: 74] [Impact Index Per Article: 14.8] [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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13
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Pazhang M, Younesi FS, Mehrnejad F, Najavand S, Tarinejad A, Haghi M, Rashno F, Khajeh K. Ig-like Domain in Endoglucanase Cel9A from Alicyclobacillus acidocaldarius Makes Dependent the Enzyme Stability on Calcium. Mol Biotechnol 2018; 60:698-711. [PMID: 30062637 DOI: 10.1007/s12033-018-0105-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Endoglucanase Cel9A from Alicyclobacillus acidocaldarius (AaCel9A) has an Ig-like domain and the enzyme stability is dependent to calcium. In this study the effect of calcium on the structure and stability of the wild-type enzyme and the truncated form (the wild-type enzyme without Ig-like domain, AaCel9AΔN) was investigated. Fluorescence quenching results indicated that calcium increased and decreased the rigidity of the wild-type and truncated enzymes, respectively. RMSF results indicated that AaCel9A has two flexible regions (regions A and B) and deleting the Ig-like domain increased the truncated enzyme stability by decreasing the flexibility of region B probably through increasing the hydrogen bonds. Calcium contact map analysis showed that deleting the Ig-like domain decreased the calcium contacting residues and their calcium binding affinities, especially, in region B which has a role in calcium binding site in AaCel9A. Metal depletion and activity recovering as well as stability results showed that the structure and stability of the wild-type and truncated enzymes are completely dependent on and independent of calcium, respectively. Finally, one can conclude that the deletion of Ig-like domain makes AaCel9AΔN independent of calcium via decreasing the flexibility of region B through increasing the hydrogen bonds. This suggests a new role for the Ig-like domain which makes AaCel9A structure dependent on calcium.
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Affiliation(s)
- Mohammad Pazhang
- Department of Cellular and Molecular Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran.
| | - Fereshteh S Younesi
- Department of Cellular and Molecular Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Faramarz Mehrnejad
- Department of Life Science Engineering, Faculty of New Sciences & Technologies, University of Tehran, Tehran, Iran
| | - Saeed Najavand
- Department of Cellular and Molecular Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Alireza Tarinejad
- Department of Biotechnology, Faculty of Agriculture, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Mehrnaz Haghi
- Department of Cellular and Molecular Biology, Faculty of Science, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Fatemeh Rashno
- Department of Biochemistry, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran
| | - Khosro Khajeh
- Department of Biochemistry, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran
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14
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Liu C, Zou G, Yan X, Zhou X. Screening of multimeric β-xylosidases from the gut microbiome of a higher termite, Globitermes brachycerastes. Int J Biol Sci 2018; 14:608-615. [PMID: 29904275 PMCID: PMC6001650 DOI: 10.7150/ijbs.22763] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 01/03/2018] [Indexed: 11/24/2022] Open
Abstract
Termite gut microbiome is a rich reservoir for glycoside hydrolases, a suite of enzymes critical for the degradation of lignocellulosic biomass. To search for hemicellulases, we screened 12,000 clones from a fosmid gut library of a higher termite, Globitermes brachycerastes. As a common Southeastern Asian genus, Globitermes distributes predominantly in tropical rain forests and relies on the lignocellulases from themselves and bacterial symbionts to digest wood. In total, 22 positive clones with β-xylosidase activity were isolated, in which 11 representing different restriction fragment length polymorphism (RFLP) patterns were pooled and subjected to 454 pyrosequencing. As a result, eight putative β-xylosidases were cloned and heterologously expressed in Escherichia coli BL21 competent cells. After purification using Ni-NTA affinity chromatography, recombinant G. brachycerastes symbiotic β-xylosidases were characterized enzymatically, including their pH and temperature optimum. In addition to β-xylosidase activity, four of them also exhibited either β-glucosidase or α-arabinosidases activities, suggesting the existence of bifunctional hemicellulases in the gut microbiome of G. brachycerastes. In comparison to multimeric protein engineering, the involvement of naturally occurring multifunctional biocatalysts streamlines the genetic modification procedures and simplifies the overall production processes. Alternatively, these multimeric enzymes could serve as the substitutes for β-glucosidase, β-xylosidase and α-arabinosidase to facilitate a wide range of industrial applications, including food processing, animal feed, environment and waste management, and biomass conversion.
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Affiliation(s)
- Chunyan Liu
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, China
| | - Gen Zou
- Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xing Yan
- Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xuguo Zhou
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, China.,Department of Entomology, University of Kentucky, Lexington, KY, 40546-0091, USA
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15
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Deleting the Ig-Like Domain of Alicyclobacillus acidocaldarius Endoglucanase Cel9A Causes a Simultaneous Increase in the Activity and Stability. Mol Biotechnol 2016; 58:12-21. [PMID: 26537871 DOI: 10.1007/s12033-015-9900-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Endoglucanase Cel9A from Alicyclobacillus acidocaldarius (AaCel9A) is a monomeric enzyme with 537 residues. This enzyme has an Ig-like domain in the N-terminus of the catalytic domain. In this study, the role of the Ig-like domain on the activity, stability, and structural rigidity of AaCel9A and the effect of calcium on enzyme activity and stability were examined by comparing a truncated enzyme with deletion of the Ig-like domain (AaCel9AΔN) to the wild-type enzyme. Our results showed that the deletion of the Ig-like domain increased the catalytic efficiency of the truncated enzyme up to threefold without any significant changes in the K m of the enzyme. Furthermore, pH and temperature optimum for activity were shifted from 6.5 to 7.5 and from 65 to 60 °C, respectively, by deletion of the Ig-like domain. The thermal stability and fluorescence quenching results indicated that the stability and rigidity of the truncated enzyme have been more than that of the wild-type enzyme. Calcium similarly increased the catalytic efficiency of the enzymes (up to 40 %) and remarkably raised the stability of the AaCel9A compared to the AaCel9AΔN. This shows that Ig-like domain has a role in the increase of the enzyme stability by calcium in the wild-type enzyme.
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16
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Valk V, Lammerts van Bueren A, Kaaij RM, Dijkhuizen L. Carbohydrate‐binding module 74 is a novel starch‐binding domain associated with large and multidomain α‐amylase enzymes. FEBS J 2016; 283:2354-68. [DOI: 10.1111/febs.13745] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 03/01/2016] [Accepted: 04/20/2016] [Indexed: 01/02/2023]
Affiliation(s)
- Vincent Valk
- Microbial Physiology Groningen Biomolecular Sciences and Biotechnology Institute (GBB) The Netherlands
| | | | - Rachel M. Kaaij
- Microbial Physiology Groningen Biomolecular Sciences and Biotechnology Institute (GBB) The Netherlands
| | - Lubbert Dijkhuizen
- Microbial Physiology Groningen Biomolecular Sciences and Biotechnology Institute (GBB) The Netherlands
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17
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Classification, mode of action and production strategy of xylanase and its application for biofuel production from water hyacinth. Int J Biol Macromol 2016; 82:1041-54. [DOI: 10.1016/j.ijbiomac.2015.10.086] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 10/26/2015] [Accepted: 10/27/2015] [Indexed: 01/07/2023]
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18
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Wang M, Lai GL, Nie Y, Geng S, Liu L, Zhu B, Shi Z, Wu XL. Synergistic function of four novel thermostable glycoside hydrolases from a long-term enriched thermophilic methanogenic digester. Front Microbiol 2015; 6:509. [PMID: 26052323 PMCID: PMC4441150 DOI: 10.3389/fmicb.2015.00509] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 05/08/2015] [Indexed: 12/25/2022] Open
Abstract
In biofuel production from lignocellulose, low thermostability and product inhibition strongly restrict the enzyme activities and production process. Application of multiple thermostable glycoside hydrolases, forming an enzyme "cocktail", can result in a synergistic action and therefore improve production efficiency and reduce operational costs. Therefore, increasing enzyme thermostabilities and compatibility are important for the biofuel industry. In this study, we reported the screening, cloning and biochemical characterization of four novel thermostable lignocellulose hydrolases from a metagenomic library of a long-term dry thermophilic methanogenic digester community, which were highly compatible with optimal conditions and specific activities. The optimal temperatures of the four enzymes, β-xylosidase, xylanase, β-glucosidase, and cellulase ranged from 60 to 75°C, and over 80% residual activities were observed after 2 h incubation at 50°C. Mixtures of these hydrolases retained high residual synergistic activities after incubation with cellulose, xylan, and steam-exploded corncob at 50°C for 72 h. In addition, about 55% dry weight of steam-exploded corncob was hydrolyzed to glucose and xylose by the synergistic action of the four enzymes at 50°C for 48 h. This work suggested that since different enzymes from a same ecosystem could be more compatible, screening enzymes from a long-term enriching community could be a favorable strategy.
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Affiliation(s)
- Meng Wang
- School of Biotechnology, Jiangnan University Wuxi, China ; Department of Energy and Resources Engineering, College of Engineering, Peking University Beijing, China
| | - Guo-Li Lai
- Department of Energy and Resources Engineering, College of Engineering, Peking University Beijing, China ; Institute of Engineering (Baotou), College of Engineering, Peking University Baotou, China
| | - Yong Nie
- Department of Energy and Resources Engineering, College of Engineering, Peking University Beijing, China ; Institute of Engineering (Baotou), College of Engineering, Peking University Baotou, China
| | - Shuang Geng
- Department of Energy and Resources Engineering, College of Engineering, Peking University Beijing, China
| | - Liming Liu
- School of Biotechnology, Jiangnan University Wuxi, China
| | - Baoli Zhu
- Institute of Microbiology, Chinese Academy of Sciences Beijing, China
| | - Zhongping Shi
- School of Biotechnology, Jiangnan University Wuxi, China
| | - Xiao-Lei Wu
- Department of Energy and Resources Engineering, College of Engineering, Peking University Beijing, China ; Institute of Engineering (Baotou), College of Engineering, Peking University Baotou, China
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19
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Abstract
Termites have many unique evolutionary adaptations associated with their eusocial lifestyles. Recent omics research has created a wealth of new information in numerous areas of termite biology (e.g., caste polyphenism, lignocellulose digestion, and microbial symbiosis) with wide-ranging applications in diverse biotechnological niches. Termite biotechnology falls into two categories: (a) termite-targeted biotechnology for pest management purposes, and (b) termite-modeled biotechnology for use in various industrial applications. The first category includes several candidate termiticidal modes of action such as RNA interference, digestive inhibition, pathogen enhancement, antimicrobials, endocrine disruption, and primer pheromone mimicry. In the second category, termite digestomes are deep resources for host and symbiont lignocellulases and other enzymes with applications in a variety of biomass, industrial, and processing applications. Moving forward, one of the most important approaches for accelerating advances in both termite-targeted and termite-modeled biotechnology will be to consider host and symbiont together as a single functional unit.
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Affiliation(s)
- Michael E Scharf
- Department of Entomology, Purdue University, West Lafayette, Indiana 47907;
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