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Sidar A, Voshol GP, El-Masoudi A, Vijgenboom E, Punt PJ. Streptomyces small laccase expressed in Aspergillus Niger as a new addition for the lignocellulose bioconversion toolbox. Fungal Biol Biotechnol 2024; 11:13. [PMID: 39223615 PMCID: PMC11368006 DOI: 10.1186/s40694-024-00181-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024] Open
Abstract
Laccases are multi-copper oxidases that are usually composed of three Cu-oxidase domains. Domains one and three house the copper binding sites, and the second domain is involved in forming a substrate-binding cleft. However, Streptomyces species are found to have small laccases (SLAC) that lack one of the three Cu-oxidase domains. This type of SLAC with interesting lignocellulose bioconversion activities has not been reported in Aspergillus niger. In our research, we explored the expression and engineering of the SLAC from Streptomyces leeuwenhoekii C34 in A. niger. Genes encoding two versions of the SLAC were expressed. One encoding the SLAC in its native form and a second encoding the SLAC fused to two N-terminal CBM1 domains. The latter is a configuration also known for specific yeast laccases. Both SLAC variants were functionally expressed in A. niger as shown by in vitro activity assays and proteome analysis. Laccase activity was also analyzed toward bioconversion of lignocellulosic rice straw. From this analysis it was clear that the SLAC activity improved the efficiency of saccharification of lignocellulosic biomass by cellulase enzyme cocktails.
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Affiliation(s)
- Andika Sidar
- Institute of Biology Leiden, Fungal Genetics and Biotechnology, Leiden University, 2333BE, Leiden, The Netherlands.
- Department of Food and Agricultural Product Technology, Gadjah Mada University, Yogyakarta, 55281, Indonesia.
| | - Gerben P Voshol
- Institute of Biology Leiden, Fungal Genetics and Biotechnology, Leiden University, 2333BE, Leiden, The Netherlands
- Genomescan, Leiden, 2333 BZ, The Netherlands
| | - Ahmed El-Masoudi
- Institute of Biology Leiden, Fungal Genetics and Biotechnology, Leiden University, 2333BE, Leiden, The Netherlands
| | - Erik Vijgenboom
- Institute of Biology Leiden, Fungal Genetics and Biotechnology, Leiden University, 2333BE, Leiden, The Netherlands
| | - Peter J Punt
- Institute of Biology Leiden, Fungal Genetics and Biotechnology, Leiden University, 2333BE, Leiden, The Netherlands.
- Ginkgo Bioworks NL, Zeist, 3704 HE, The Netherlands.
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Zhou H, Jia S, Gao Y, Li X, Lin Y, Yang F, Ni K. Characterization of phyllosphere endophytic lactic acid bacteria reveals a potential novel route to enhance silage fermentation quality. Commun Biol 2024; 7:117. [PMID: 38253824 PMCID: PMC10803313 DOI: 10.1038/s42003-024-05816-3] [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: 08/04/2023] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
The naturally attached phyllosphere microbiota play a crucial role in plant-derived fermentation, but the structure and function of phyllosphere endophytes remain largely unidentified. Here, we reveal the diversity, specificity, and functionality of phyllosphere endophytes in alfalfa (Medicago sativa L.) through combining typical microbial culture, high-throughput sequencing, and genomic comparative analysis. In comparison to phyllosphere bacteria (PB), the fermentation of alfalfa solely with endophytes (EN) enhances the fermentation characteristics, primarily due to the dominance of specific lactic acid bacteria (LAB) such as Lactiplantibacillus, Weissella, and Pediococcus. The inoculant with selected endophytic LAB strains also enhances the fermentation quality compared to epiphytic LAB treatment. Especially, one key endophytic LAB named Pediococcus pentosaceus EN5 shows enrichment of genes related to the mannose phosphotransferase system (Man-PTS) and carbohydrate-metabolizing enzymes and higher utilization of carbohydrates. Representing phyllosphere, endophytic LAB shows great potential of promoting ensiling and provides a novel direction for developing microbial inoculant.
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Affiliation(s)
- Hongzhang Zhou
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Shangang Jia
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yu Gao
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xiaomei Li
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yanli Lin
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Fuyu Yang
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
- College of Animal Science, Guizhou University, Guiyang, 550025, China
| | - Kuikui Ni
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China.
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Fusion of Oligopeptide to the C Terminus of α-Glucuronidase from Thermotoga maritima Improves the Catalytic Efficiency for Hemicellulose Biotransformation. Mol Biotechnol 2022; 65:741-751. [PMID: 36175749 DOI: 10.1007/s12033-022-00569-y] [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: 09/23/2021] [Accepted: 09/15/2022] [Indexed: 10/14/2022]
Abstract
Fusion protein combined the oligopeptide (HQAFFHA) with the C terminus of α-glucuronidase from Thermotoga maritima was produced in E. coli and purified for characterization and applications of glucuronic and glucaric acid production. The fusion protein with oligopeptide exhibited a 2.97-fold higher specific activity than individual protein. Their catalytic efficiency kcat/Km and kcat increased from 469.3 ± 2.6 s-1 (g mL-1)-1 and 62.4 ± 0.9 s-1 to 2209.5 ± 26.3 s-1 (g mL-1)-1 and 293.9 ± 4.9 s-1, respectively. Fusion protein had similar temperature and pH profiles to those without oligopeptide, but the thermal stability decreases and the pH stability shifts to alkaline. Using beech xylan hydrolysate as a substrate, the glucuronic acid yield of fusion enzyme increased by 9.94% compared with its parent at 65 °C pH 8.5 for 10 h, and can hydrolyze corn cob xylan with xylanase to obtain glucuronic acid, and can be combined with uronate dehydrogenase to obtain high-added value glucaric acid. Homologous modeling analysis revealed the factors contributing to the high catalytic efficiency of fusion enzyme. These results show that the peptide fusion strategy described here may be useful for improving the catalytic efficiency and stability of other industrial enzymes, and has great potential for producing high value-added products from agricultural waste.
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Carbohydrate-binding module of cycloisomaltooligosaccharide glucanotransferase from Thermoanaerobacter thermocopriae improves its cyclodextran production. Enzyme Microb Technol 2022; 157:110023. [DOI: 10.1016/j.enzmictec.2022.110023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/03/2022] [Accepted: 02/24/2022] [Indexed: 11/23/2022]
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Hu Y, Li H, Ran Q, Liu J, Zhou S, Qiao Q, Song H, Peng F, Jiang Z. Effect of carbohydrate binding modules alterations on catalytic activity of glycoside hydrolase family 6 exoglucanase from Chaetomium thermophilum to cellulose. Int J Biol Macromol 2021; 191:222-229. [PMID: 34508724 DOI: 10.1016/j.ijbiomac.2021.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 09/01/2021] [Accepted: 09/01/2021] [Indexed: 12/31/2022]
Abstract
Exoglucanase (CBH) is the rate limiting enzyme in the process of cellulose degradation. The carbohydrate binding module (CBM) can improve the accessibility of cellulase to substrate, thereby promoting the enzymatic hydrolysis of cellulase. In this study, the influence of CBM on the properties of GH6 exoglucanase from Chaetomium thermophilum (CtCBH) is systematically explored from three perspectives: the fusion of exogenous CBM, the exogenous CBM replacement of its own CBM, and the deletion of its own CBM. The parental and reconstructed CtCBH presented the same optimum pH (6.0) and temperature (60 °C) for maximum activity. Fusion of exogenous CBM increased the binding capacity of CtCBH to Avicel by 8% and 9%, respectively, but it had no significant effect on its catalytic activity. The exogenous CBM replacement of its own CBM resulted in a 12% reduction in the binding ability of CtCBH to Avicel, and a 26% reduction in the catalytic activity of Avicel. The deletion of its own CBM significantly reduced the binding ability of CtCBH to Avicel by approximately 53%, but its catalytic activity was not obviously reduced. These observations suggest that binding ability of CBM is not necessary for the catalysis of CtCBH.
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Affiliation(s)
- Yanmei Hu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan 430062, PR China; Hubei Key Laboratory of Industrial Biotechnology, School of Life Science, Hubei University, Wuhan 430062, PR China
| | - Huanan Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan 430062, PR China; Hubei Key Laboratory of Industrial Biotechnology, School of Life Science, Hubei University, Wuhan 430062, PR China
| | - Qiuping Ran
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan 430062, PR China; Hubei Key Laboratory of Industrial Biotechnology, School of Life Science, Hubei University, Wuhan 430062, PR China
| | - Jiashu Liu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan 430062, PR China; Hubei Key Laboratory of Industrial Biotechnology, School of Life Science, Hubei University, Wuhan 430062, PR China
| | - Shanna Zhou
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan 430062, PR China; Hubei Key Laboratory of Industrial Biotechnology, School of Life Science, Hubei University, Wuhan 430062, PR China
| | - Qiming Qiao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan 430062, PR China; Hubei Key Laboratory of Industrial Biotechnology, School of Life Science, Hubei University, Wuhan 430062, PR China
| | - Huiting Song
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan 430062, PR China; Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Science, Hubei University, Wuhan 430062, PR China
| | - Fang Peng
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan 430062, PR China; Hubei Key Laboratory of Regional Development and Environmental Response, Faculty of Resources and Environmental Science, Hubei University, Wuhan 430062, PR China
| | - Zhengbing Jiang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei University, Wuhan 430062, PR China; Hubei Key Laboratory of Industrial Biotechnology, School of Life Science, Hubei University, Wuhan 430062, PR China.
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Liu T, Zhang Y, Lu X, Wang P, Zhang X, Tian J, Wang Q, Song J, Jin Y, Xiao H. Binding affinity of family 4 carbohydrate binding module on cellulose films of nanocrystals and nanofibrils. Carbohydr Polym 2021; 251:116725. [PMID: 33142548 DOI: 10.1016/j.carbpol.2020.116725] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 06/28/2020] [Accepted: 06/30/2020] [Indexed: 11/26/2022]
Abstract
The binding affinity and thermodynamics of family 4 carbohydrate-binding module (CBM4), belonging to type B CBM, on model surfaces of cellulose nanocrystals (CNC) and nanofibrils (CNF) were investigated by quartz crystal microbalance with dissipation monitoring (QCM-D) technology in real-time at different temperatures. The thermodynamic parameters associated with the interaction, such as Gibbs free energy, enthalpy change, entropy change and heat capacity were obtained using the van't Hoff analysis via a nonlinear parameter estimation. The results demonstrated CBM4 binds preferentially to both CNF and CNC, whereas the driving forces behind them were very different. The former was related to the hydrogen bonds formed in the CBM4 clefts, resulting in a favorable enthalpy but compensated by unfavorable entropy change; on the contrary, the latter was mainly driven by favorable entropy but compensated by unfavorable enthalpic change due to water rearrangement.
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Affiliation(s)
- Tian Liu
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources and Joint International Research Lab of Lignocellulosic Functional Materials, Nanjing Forestry University, Nanjing, 210037, China
| | - Yu Zhang
- Dinano Tech Co., Ltd., Nanjing Branch, Nanjing, 210046, China
| | - Xiaomin Lu
- Department of Forest Biomaterials, North Carolina State University, Campus Box 8005, Raleigh, NC, 27695-8005, United States
| | - Peipei Wang
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources and Joint International Research Lab of Lignocellulosic Functional Materials, Nanjing Forestry University, Nanjing, 210037, China
| | - Xinyu Zhang
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources and Joint International Research Lab of Lignocellulosic Functional Materials, Nanjing Forestry University, Nanjing, 210037, China
| | - Jing Tian
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources and Joint International Research Lab of Lignocellulosic Functional Materials, Nanjing Forestry University, Nanjing, 210037, China
| | - Qingcheng Wang
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources and Joint International Research Lab of Lignocellulosic Functional Materials, Nanjing Forestry University, Nanjing, 210037, China
| | - Junlong Song
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources and Joint International Research Lab of Lignocellulosic Functional Materials, Nanjing Forestry University, Nanjing, 210037, China.
| | - Yongcan Jin
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources and Joint International Research Lab of Lignocellulosic Functional Materials, Nanjing Forestry University, Nanjing, 210037, China
| | - Huining Xiao
- Department of Chemical Engineering, University of New Brunswick, Fredericton, NB, E3B 5A3, Canada
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Enhanced Thermostability and Enzymatic Activity of Cel6A Variants from Thermobifida fusca by Empirical Domain Engineering (Short Title: Domain Engineering of Cel6A). BIOLOGY 2020; 9:biology9080214. [PMID: 32784797 PMCID: PMC7464639 DOI: 10.3390/biology9080214] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 07/29/2020] [Accepted: 08/02/2020] [Indexed: 02/07/2023]
Abstract
Cellulases are a set of lignocellulolytic enzymes, capable of producing eco-friendly low-cost renewable bioethanol. However, low stability and hydrolytic activity limit their wide-scale applicability at the industrial scale. In this work, we report the domain engineering of endoglucanase (Cel6A) of Thermobifida fusca to improve their catalytic activity and thermal stability. Later, enzymatic activity and thermostability of the most efficient variant named as Cel6A.CBC was analyzed by molecular dynamics simulations. This variant demonstrated profound activity against soluble and insoluble cellulosic substrates like filter paper, alkali-treated bagasse, regenerated amorphous cellulose (RAC), and bacterial microcrystalline cellulose. The variant Cel6A.CBC showed the highest catalysis of carboxymethyl cellulose (CMC) and other related insoluble substrates at a pH of 6.0 and a temperature of 60 °C. Furthermore, a sound rationale was observed between experimental findings and molecular modeling of Cel6A.CBC which revealed thermostability of Cel6A.CBC at 26.85, 60.85, and 74.85 °C as well as structural flexibility at 126.85 °C. Therefore, a thermostable derivative of Cel6A engineered in the present work has enhanced biological performance and can be a useful construct for the mass production of bioethanol from plant biomass.
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Nath P, Dhillon A, Kumar K, Sharma K, Jamaldheen SB, Moholkar VS, Goyal A. Development of bi-functional chimeric enzyme (CtGH1-L1-CtGH5-F194A) from endoglucanase (CtGH5) mutant F194A and β-1,4-glucosidase (CtGH1) from Clostridium thermocellum with enhanced activity and structural integrity. BIORESOURCE TECHNOLOGY 2019; 282:494-501. [PMID: 30897487 DOI: 10.1016/j.biortech.2019.03.051] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/08/2019] [Accepted: 03/09/2019] [Indexed: 06/09/2023]
Abstract
Site-directed mutagenesis of β-1,4-endoglucanase from family 5 glycoside hydrolase (CtGH5) from Clostridium thermocellum was performed to develop a mutant CtGH5-F194A that gave 40 U/mg specific activity against carboxymethyl cellulose, resulting 2-fold higher activity than wild-type CtGH5. CtGH5-F194A was fused with a β-1,4-glucosidase, CtGH1 from Clostridium thermocellum to develop a chimeric enzyme. The chimera (CtGH1-L1-CtGH5-F194A) expressed as a soluble protein using E. coli BL-21cells displaying 3- to 5-fold higher catalytic efficiency for endoglucanase and β-glucosidase activities. TLC analysis of hydrolysed product of CMC by chimera 1 revealed glucose as final product confirming both β-1,4-endoglucanase and β-1,4-glucosidase activities, while the products of CtGH5-F194A were cellobiose and cello-oligosaccharides. Protein melting studies of CtGH5-F194A showed melting temperature (Tm), 68 °C and of CtGH1, 79 °C, whereas, chimera showed 78 °C. The improved structural integrity, thermostability and enhanced bi-functional enzyme activities of chimera makes it potentially useful for industrial application in converting biomass to glucose and thus bioethanol.
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Affiliation(s)
- Priyanka Nath
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India; DBT PAN-IIT Center for Bioenergy, Indian Institute of Technology Guwahati, India
| | - Arun Dhillon
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Krishan Kumar
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Kedar Sharma
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Sumitha Banu Jamaldheen
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India; Centre for Energy, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Vijayanand Suryakant Moholkar
- Centre for Energy, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India; Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India; DBT PAN-IIT Center for Bioenergy, Indian Institute of Technology Guwahati, India; Centre for Energy, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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Zhou T, Xue Y, Zhang Z, Dong Y, Gao R, Li Y. Improvement of the Characteristics of Steamed Bread by Supplementation of Recombinant alpha-L-arabinofuranosidase Containing xylan-binding domain. FOOD BIOTECHNOL 2019. [DOI: 10.1080/08905436.2018.1553048] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Tao Zhou
- Department of Food Science and Nutrition, GinLing College, Nanjing Normal University, Nanjing, PR China
| | - Yemin Xue
- Department of Food Science and Nutrition, GinLing College, Nanjing Normal University, Nanjing, PR China
| | - Zonghui Zhang
- Department of Food Science and Nutrition, GinLing College, Nanjing Normal University, Nanjing, PR China
| | - Yuanyuan Dong
- Department of Food Science and Nutrition, GinLing College, Nanjing Normal University, Nanjing, PR China
| | - Rui Gao
- Department of Food Science and Nutrition, GinLing College, Nanjing Normal University, Nanjing, PR China
| | - Yaxian Li
- Department of Food Science and Nutrition, GinLing College, Nanjing Normal University, Nanjing, PR China
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de Araújo EA, de Oliveira Neto M, Polikarpov I. Biochemical characterization and low-resolution SAXS structure of two-domain endoglucanase BlCel9 from Bacillus licheniformis. Appl Microbiol Biotechnol 2018; 103:1275-1287. [PMID: 30547217 DOI: 10.1007/s00253-018-9508-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 10/03/2018] [Accepted: 11/07/2018] [Indexed: 12/16/2022]
Abstract
Lignocellulose feedstock constitutes the most abundant carbon source in the biosphere; however, its recalcitrance remains a challenge for microbial conversion into biofuel and bioproducts. Bacillus licheniformis is a microbial mesophilic bacterium capable of secreting a large number of glycoside hydrolase (GH) enzymes, including a glycoside hydrolase from GH family 9 (BlCel9). Here, we conducted biochemical and biophysical studies of recombinant BlCel9, and its low-resolution molecular shape was retrieved from small angle X-ray scattering (SAXS) data. BlCel9 is an endoglucanase exhibiting maximum catalytic efficiency at pH 7.0 and 60 °C. Furthermore, it retains 80% of catalytic activity within a broad range of pH values (5.5-8.5) and temperatures (up to 50 °C) for extended periods of time (over 48 h). It exhibits the highest hydrolytic activity against phosphoric acid swollen cellulose (PASC), followed by bacterial cellulose (BC), filter paper (FP), and to a lesser extent carboxymethylcellulose (CMC). The HPAEC-PAD analysis of the hydrolytic products demonstrated that the end product of the enzymatic hydrolysis is primarily cellobiose, and also small amounts of glucose, cellotriose, and cellotetraose are produced. SAXS data analysis revealed that the enzyme adopts a monomeric state in solution and has a molecular mass of 65.8 kDa as estimated from SAXS data. The BlCel9 has an elongated shape composed of an N-terminal family 3 carbohydrate-binding module (CBM3c) and a C-terminal GH9 catalytic domain joined together by 20 amino acid residue long linker peptides. The domains are closely juxtaposed in an extended conformation and form a relatively rigid structure in solution, indicating that the interactions between the CBM3c and GH9 catalytic domains might play a key role in cooperative cellulose biomass recognition and hydrolysis.
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Affiliation(s)
- Evandro Ares de Araújo
- Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador Saocarlense 400, São Carlos, SP, 13560-970, Brazil
| | - Mário de Oliveira Neto
- Departmento de Física e Biofísica, Universidade Estadual Paulista "Júlio de Mesquita Filho", R. Prof. Dr. Antonio Celso Wagner Zanin 689, Jardim Sao Jose, Botucatu, SP, 18618-970, Brazil
| | - Igor Polikarpov
- Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador Saocarlense 400, São Carlos, SP, 13560-970, Brazil.
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Maharjan A, Alkotaini B, Kim BS. Fusion of Carbohydrate Binding Modules to Bifunctional Cellulase to Enhance Binding Affinity and Cellulolytic Activity. BIOTECHNOL BIOPROC E 2018. [DOI: 10.1007/s12257-018-0011-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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12
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Thermostability enhancement of chitosanase CsnA by fusion a family 5 carbohydrate-binding module. Biotechnol Lett 2017; 39:1895-1901. [PMID: 28748352 DOI: 10.1007/s10529-017-2406-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 07/20/2017] [Indexed: 10/19/2022]
Abstract
OBJECTIVE To determine the effects of carbohydrate-binding modules (CBMs) on the thermostability and catalytic efficiency of chitosanase CsnA. RESULTS Three CBMs (BgCBM5, PfCBM32-2 and AoCBM35) were engineered at the C-terminus of chitosanase CsnA to create hybrid enzymes CsnA-CBM5, CsnA-CBM32 and CsnA-CBM35. K m values of all the hybrid enzymes were lower than that of the wild type (WT) enzyme; however, only CsnA-CBM5 had an elevated specific activity and catalytic efficiency. The fusion of BgCBM5 enhanced the thermostability of the enzyme, which exhibited a 8.9 °C higher T50 and a 2.9 °C higher Tm than the WT. Secondary structural analysis indicated that appending BgCBM5 at the C-terminus considerably changed the secondary structure content. CONCLUSIONS The fusion of BgCBM5 improved the thermal stability of CsnA, and the obtained hybrid enzyme (CsnA-CBM5) is a useful candidate for industrial application.
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Impact of Module-X2 and Carbohydrate Binding Module-3 on the catalytic activity of associated glycoside hydrolases towards plant biomass. Sci Rep 2017. [PMID: 28623337 PMCID: PMC5473887 DOI: 10.1038/s41598-017-03927-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Cellulolytic enzymes capable of hydrolyzing plant biomass are secreted by microbial cells specifically in response to the carbon substrate present in the environment. These enzymes consist of a catalytic domain, generally appended to one or more non-catalytic Carbohydrate Binding Module (CBM), which enhances their activity towards recalcitrant biomass. In the present study, the genome of a cellulolytic microbe Paenibacillus polymyxa A18 was annotated for the presence of CBMs and analyzed their expression in response to the plant biomass and model polysaccharides Avicel, CMC and xylan using quantitative PCR. A gene that encodes X2-CBM3 was found to be maximally induced in response to the biomass and crystalline substrate Avicel. Association of X2-CBM3 with xyloglucanase and endoglucanase led to up to 4.6-fold increase in activity towards insoluble substrates. In the substrate binding study, module X2 showed a higher affinity towards biomass and phosphoric acid swollen cellulose, whereas CBM3 showed a higher affinity towards Avicel. Further structural modeling of X2 also indicated its potential role in substrate binding. Our findings highlighted the role of module X2 along with CBM3 in assisting the enzyme catalysis of agricultural residue and paved the way to engineer glycoside hydrolases for superior activity.
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Walker JA, Pattathil S, Bergeman LF, Beebe ET, Deng K, Mirzai M, Northen TR, Hahn MG, Fox BG. Determination of glycoside hydrolase specificities during hydrolysis of plant cell walls using glycome profiling. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:31. [PMID: 28184246 PMCID: PMC5288845 DOI: 10.1186/s13068-017-0703-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/06/2017] [Indexed: 05/29/2023]
Abstract
BACKGROUND Glycoside hydrolases (GHs) are enzymes that hydrolyze polysaccharides into simple sugars. To better understand the specificity of enzyme hydrolysis within the complex matrix of polysaccharides found in the plant cell wall, we studied the reactions of individual enzymes using glycome profiling, where a comprehensive collection of cell wall glycan-directed monoclonal antibodies are used to detect polysaccharide epitopes remaining in the walls after enzyme treatment and quantitative nanostructure initiator mass spectrometry (oxime-NIMS) to determine soluble sugar products of their reactions. RESULTS Single, purified enzymes from the GH5_4, GH10, and GH11 families of glycoside hydrolases hydrolyzed hemicelluloses as evidenced by the loss of specific epitopes from the glycome profiles in enzyme-treated plant biomass. The glycome profiling data were further substantiated by oxime-NIMS, which identified hexose products from hydrolysis of cellulose, and pentose-only and mixed hexose-pentose products from the hydrolysis of hemicelluloses. The GH10 enzyme proved to be reactive with the broadest diversity of xylose-backbone polysaccharide epitopes, but was incapable of reacting with glucose-backbone polysaccharides. In contrast, the GH5 and GH11 enzymes studied here showed the ability to react with both glucose- and xylose-backbone polysaccharides. CONCLUSIONS The identification of enzyme specificity for a wide diversity of polysaccharide structures provided by glycome profiling, and the correlated identification of soluble oligosaccharide hydrolysis products provided by oxime-NIMS, offers a unique combination to understand the hydrolytic capabilities and constraints of individual enzymes as they interact with plant biomass.
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Affiliation(s)
- Johnnie A. Walker
- US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Sivakumar Pattathil
- US Department of Energy Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA
| | - Lai F. Bergeman
- US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Emily T. Beebe
- US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Kai Deng
- US Department of Energy Joint Bioenergy Institute, Emeryville, CA 94608 USA
- Sandia National Laboratories, Livermore, CA 94551 USA
| | - Maryam Mirzai
- US Department of Energy Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA
| | - Trent R. Northen
- US Department of Energy Joint Bioenergy Institute, Emeryville, CA 94608 USA
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Michael G. Hahn
- US Department of Energy Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602 USA
| | - Brian G. Fox
- US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
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15
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Liu S, Ding S. Replacement of carbohydrate binding modules improves acetyl xylan esterase activity and its synergistic hydrolysis of different substrates with xylanase. BMC Biotechnol 2016; 16:73. [PMID: 27770795 PMCID: PMC5075172 DOI: 10.1186/s12896-016-0305-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 10/13/2016] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Acetylation of the xylan backbone was a major obstacle to enzymatic decomposition. Removal of acetyl groups by acetyl xylan esterases (AXEs) is essential for completely enzymatic hydrolysis of xylan. Appended carbohydrate binding modules (CBMs) can promote the enzymatic deconstruction of plant cell walls by targeting and proximity effects. Fungal acetyl xylan esterases are strictly appended to cellulose-specific CBM1. It is still unclear whether xylan-specific CBMs have a greater advantage than CBM1 in potentiating the activity of fungal deacetylating enzymes and its synergistic hydrolysis of different substrates with xylanase. RESULTS Three recombinant AXE1s fused with different xylan-specific CBMs, together with wild-type AXE1 with CBM1 and CBM1-deleted mutant AXE1dC, were constructed in this study. The optimal temperature and pH of recombinant AXE1s was 50 °C and 8.0 (except AXE1dC-CBM6), respectively. Cellulose-specific CBM1 in AXE1 obviously contributed to its catalytic action against substrates compared with AXE1dC. However, replacement of CBM1 with xylan-specific CBM4-2 significantly enhanced AXE1 thermostability and catalytic activity against soluble substrate 4-methylumbelliferyl acetate. Whereas replacements with xylan-specific CBM6 and CBM22-2 were more effective in enzymatic release of acetic acid from destarched wheat bran, NaClO2-treated wheat straw, and water-insoluble wheat arabinoxylan compared to AXE1. Moreover, replacement with CBM6 and CBM22-2 also resulted in higher degree releases of reducing sugar and acetic acid from different substrates when simultaneous hydrolysis with xylanase. A good linear relationship exists between the acetic acid and reducing sugar release. CONCLUSIONS Our findings suggested that the replacement with CBM6 and CBM22-2 not only significantly improved the catalysis efficiency of AXE1, but also increased its synergistic hydrolysis of different substrates with xylanase, indicating the significance of targeting effect in AXE1 catalysis mediated by xylan-specific CBMs.
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Affiliation(s)
- Shiping Liu
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Shaojun Ding
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China.
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16
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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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17
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Xylan-specific carbohydrate-binding module belonging to family 6 enhances the catalytic performance of a GH11 endo-xylanase. N Biotechnol 2016; 33:467-72. [DOI: 10.1016/j.nbt.2016.02.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 01/18/2016] [Accepted: 02/16/2016] [Indexed: 01/09/2023]
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18
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Park SH, Ong RG, Sticklen M. Strategies for the production of cell wall-deconstructing enzymes in lignocellulosic biomass and their utilization for biofuel production. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1329-44. [PMID: 26627868 PMCID: PMC5063159 DOI: 10.1111/pbi.12505] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 10/23/2015] [Accepted: 11/02/2015] [Indexed: 05/18/2023]
Abstract
Microbial cell wall-deconstructing enzymes are widely used in the food, wine, pulp and paper, textile, and detergent industries and will be heavily utilized by cellulosic biorefineries in the production of fuels and chemicals. Due to their ability to use freely available solar energy, genetically engineered bioenergy crops provide an attractive alternative to microbial bioreactors for the production of cell wall-deconstructing enzymes. This review article summarizes the efforts made within the last decade on the production of cell wall-deconstructing enzymes in planta for use in the deconstruction of lignocellulosic biomass. A number of strategies have been employed to increase enzyme yields and limit negative impacts on plant growth and development including targeting heterologous enzymes into specific subcellular compartments using signal peptides, using tissue-specific or inducible promoters to limit the expression of enzymes to certain portions of the plant or certain times, and fusion of amplification sequences upstream of the coding region to enhance expression. We also summarize methods that have been used to access and maintain activity of plant-generated enzymes when used in conjunction with thermochemical pretreatments for the production of lignocellulosic biofuels.
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Affiliation(s)
- Sang-Hyuck Park
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Rebecca Garlock Ong
- Department of Chemical Engineering and Materials Science, DOE Great Lakes Bioenergy Research Center, Michigan State University, Lansing, MI, USA
- Department of Chemical Engineering, Michigan Technological University, Houghton, MI, USA
| | - Mariam Sticklen
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
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19
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Zhou SH, Liu Y, Zhao YJ, Chi Z, Chi ZM, Liu GL. Enhanced exo-inulinase activity and stability by fusion of an inulin-binding module. Appl Microbiol Biotechnol 2016; 100:8063-74. [DOI: 10.1007/s00253-016-7587-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 04/24/2016] [Accepted: 04/28/2016] [Indexed: 01/14/2023]
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20
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Zhang Q, Li H, Zhu X, Lai F, Zhai Z, Wang Y. Exploration of the key functional proteins from an efficient cellulolytic microbial consortium using dilution-to-extinction approach. J Environ Sci (China) 2016; 43:199-207. [PMID: 27155425 DOI: 10.1016/j.jes.2015.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/21/2015] [Accepted: 09/23/2015] [Indexed: 06/05/2023]
Abstract
In the present study, the cellulose binding proteins (CBPs) secreted by a putative cellulolytic microbial consortium were isolated and purified by affinity digestion. The purified CBPs were subsequently separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Using mass spectrometric analyses, eight CBPs were identified and annotated to be similar to known proteins secreted by Clostridium clariflavum DSM 19732 and Paenibacillus sp. W-61. In addition, in combination with dilution-to-extinction approach and zymogram analysis technique, CBPs 6 (97kDa) and 12 (52kDa) were confirmed to be the key functional proteins that influence cellulolytic activities. Moreover, structural domain analyses and enzymatic activity detection indicated that CBPs 6 and 12 contained glycoside hydrolase families (GH) 9 and 48 catalytic modules, which both revealed endoglucandase and xylanase activities. It was suggested that the coexistence of GH9 and GH48 catalytic domains present in these two proteins could synergistically promote the efficient degradation of cellulose.
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Affiliation(s)
- Qinghua Zhang
- College of Bioscience and Engineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China.
| | - Hanguang Li
- College of Bioscience and Engineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China.
| | - Xiangdong Zhu
- College of Bioscience and Engineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Fenju Lai
- College of Bioscience and Engineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Zhijun Zhai
- College of Bioscience and Engineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yuanxiu Wang
- College of Bioscience and Engineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
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21
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Mai-Gisondi G, Turunen O, Pastinen O, Pahimanolis N, Master ER. Enhancement of acetyl xylan esterase activity on cellulose acetate through fusion to a family 3 cellulose binding module. Enzyme Microb Technol 2015; 79-80:27-33. [DOI: 10.1016/j.enzmictec.2015.07.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 06/30/2015] [Accepted: 07/02/2015] [Indexed: 10/23/2022]
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22
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Petkun S, Rozman Grinberg I, Lamed R, Jindou S, Burstein T, Yaniv O, Shoham Y, Shimon LJ, Bayer EA, Frolow F. Reassembly and co-crystallization of a family 9 processive endoglucanase from its component parts: structural and functional significance of the intermodular linker. PeerJ 2015; 3:e1126. [PMID: 26401442 PMCID: PMC4579020 DOI: 10.7717/peerj.1126] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 07/04/2015] [Indexed: 11/22/2022] Open
Abstract
Non-cellulosomal processive endoglucanase 9I (Cel9I) from Clostridium thermocellum is a modular protein, consisting of a family-9 glycoside hydrolase (GH9) catalytic module and two family-3 carbohydrate-binding modules (CBM3c and CBM3b), separated by linker regions. GH9 does not show cellulase activity when expressed without CBM3c and CBM3b and the presence of the CBM3c was previously shown to be essential for endoglucanase activity. Physical reassociation of independently expressed GH9 and CBM3c modules (containing linker sequences) restored 60-70% of the intact Cel9I endocellulase activity. However, the mechanism responsible for recovery of activity remained unclear. In this work we independently expressed recombinant GH9 and CBM3c with and without their interconnecting linker in Escherichia coli. We crystallized and determined the molecular structure of the GH9/linker-CBM3c heterodimer at a resolution of 1.68 Å to understand the functional and structural importance of the mutual spatial orientation of the modules and the role of the interconnecting linker during their re-association. Enzyme activity assays and isothermal titration calorimetry were performed to study and compare the effect of the linker on the re-association. The results indicated that reassembly of the modules could also occur without the linker, albeit with only very low recovery of endoglucanase activity. We propose that the linker regions in the GH9/CBM3c endoglucanases are important for spatial organization and fixation of the modules into functional enzymes.
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Affiliation(s)
- Svetlana Petkun
- Department of Molecular Microbiology and Biotechnology, The Daniella Rich Institute for Structural Biology, Tel Aviv University, Ramat Aviv, Israel
| | - Inna Rozman Grinberg
- Department of Molecular Microbiology and Biotechnology, The Daniella Rich Institute for Structural Biology, Tel Aviv University, Ramat Aviv, Israel
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, The Daniella Rich Institute for Structural Biology, Tel Aviv University, Ramat Aviv, Israel
| | - Sadanari Jindou
- Department of Life Sciences, Meijo University, Nagoya, Japan
| | - Tal Burstein
- Department of Molecular Microbiology and Biotechnology, The Daniella Rich Institute for Structural Biology, Tel Aviv University, Ramat Aviv, Israel
| | - Oren Yaniv
- Department of Molecular Microbiology and Biotechnology, The Daniella Rich Institute for Structural Biology, Tel Aviv University, Ramat Aviv, Israel
| | - Yuval Shoham
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Linda J.W. Shimon
- Department of Chemical Research Support, The Weizmann Institute of Science, Rehovot, Israel
| | - Edward A. Bayer
- Department of Biological Chemistry, The Weizmann Institute of Science, Rehovot, Israel
| | - Felix Frolow
- Department of Molecular Microbiology and Biotechnology, The Daniella Rich Institute for Structural Biology, Tel Aviv University, Ramat Aviv, Israel
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23
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Foumani M, Vuong TV, MacCormick B, Master ER. Enhanced Polysaccharide Binding and Activity on Linear β-Glucans through Addition of Carbohydrate-Binding Modules to Either Terminus of a Glucooligosaccharide Oxidase. PLoS One 2015; 10:e0125398. [PMID: 25932926 PMCID: PMC4416756 DOI: 10.1371/journal.pone.0125398] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 03/23/2015] [Indexed: 02/07/2023] Open
Abstract
The gluco-oligosaccharide oxidase from Sarocladium strictum CBS 346.70 (GOOX) is a single domain flavoenzyme that favourably oxidizes gluco- and xylo- oligosaccharides. In the present study, GOOX was shown to also oxidize plant polysaccharides, including cellulose, glucomannan, β-(1→3,1→4)-glucan, and xyloglucan, albeit to a lesser extent than oligomeric substrates. To improve GOOX activity on polymeric substrates, three carbohydrate binding modules (CBMs) from Clostridium thermocellum, namely CtCBM3 (type A), CtCBM11 (type B), and CtCBM44 (type B), were separately appended to the amino and carboxy termini of the enzyme, generating six fusion proteins. With the exception of GOOX-CtCBM3 and GOOX-CtCBM44, fusion of the selected CBMs increased the catalytic activity of the enzyme (kcat) on cellotetraose by up to 50%. All CBM fusions selectively enhanced GOOX binding to soluble and insoluble polysaccharides, and the immobilized enzyme on a solid cellulose surface remained stable and active. In addition, the CBM fusions increased the activity of GOOX on soluble glucomannan by up to 30 % and on insoluble crystalline as well as amorphous cellulose by over 50 %.
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Affiliation(s)
- Maryam Foumani
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada
| | - Thu V. Vuong
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada
| | - Benjamin MacCormick
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada
| | - Emma R. Master
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada
- * E-mail:
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24
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Walker JA, Takasuka TE, Deng K, Bianchetti CM, Udell HS, Prom BM, Kim H, Adams PD, Northen TR, Fox BG. Multifunctional cellulase catalysis targeted by fusion to different carbohydrate-binding modules. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:220. [PMID: 26697109 PMCID: PMC4687162 DOI: 10.1186/s13068-015-0402-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 11/30/2015] [Indexed: 05/11/2023]
Abstract
BACKGROUND Carbohydrate binding modules (CBMs) bind polysaccharides and help target glycoside hydrolases catalytic domains to their appropriate carbohydrate substrates. To better understand how CBMs can improve cellulolytic enzyme reactivity, representatives from each of the 18 families of CBM found in Ruminoclostridium thermocellum were fused to the multifunctional GH5 catalytic domain of CelE (Cthe_0797, CelEcc), which can hydrolyze numerous types of polysaccharides including cellulose, mannan, and xylan. Since CelE is a cellulosomal enzyme, none of these fusions to a CBM previously existed. RESULTS CelEcc_CBM fusions were assayed for their ability to hydrolyze cellulose, lichenan, xylan, and mannan. Several CelEcc_CBM fusions showed enhanced hydrolytic activity with different substrates relative to the fusion to CBM3a from the cellulosome scaffoldin, which has high affinity for binding to crystalline cellulose. Additional binding studies and quantitative catalysis studies using nanostructure-initiator mass spectrometry (NIMS) were carried out with the CBM3a, CBM6, CBM30, and CBM44 fusion enzymes. In general, and consistent with observations of others, enhanced enzyme reactivity was correlated with moderate binding affinity of the CBM. Numerical analysis of reaction time courses showed that CelEcc_CBM44, a combination of a multifunctional enzyme domain with a CBM having broad binding specificity, gave the fastest rates for hydrolysis of both the hexose and pentose fractions of ionic-liquid pretreated switchgrass. CONCLUSION We have shown that fusions of different CBMs to a single multifunctional GH5 catalytic domain can increase its rate of reaction with different pure polysaccharides and with pretreated biomass. This fusion approach, incorporating domains with broad specificity for binding and catalysis, provides a new avenue to improve reactivity of simple combinations of enzymes within the complexity of plant biomass.
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Affiliation(s)
- Johnnie A. Walker
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- />Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Taichi E. Takasuka
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- />Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
- />Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan
| | - Kai Deng
- />US Department of Energy Joint BioEnergy Institute, Emeryville, CA 94608 USA
- />Sandia National Laboratories, Livermore, CA 94551 USA
| | - Christopher M. Bianchetti
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- />Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
- />Department of Chemistry, University of Wisconsin-Oshkosh, Oshkosh, WI 54901 USA
| | - Hannah S. Udell
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Ben M. Prom
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Hyunkee Kim
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Paul D. Adams
- />US Department of Energy Joint BioEnergy Institute, Emeryville, CA 94608 USA
- />Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- />Department of Bioengineering, University of California, Berkeley, CA 94720 USA
| | - Trent R. Northen
- />US Department of Energy Joint BioEnergy Institute, Emeryville, CA 94608 USA
- />Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Brian G. Fox
- />US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706 USA
- />Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
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25
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Ghatge SS, Telke AA, Waghmode TR, Lee Y, Lee KW, Oh DB, Shin HD, Kim SW. Multifunctional cellulolytic auxiliary activity protein HcAA10-2 from Hahella chejuensis enhances enzymatic hydrolysis of crystalline cellulose. Appl Microbiol Biotechnol 2014; 99:3041-55. [DOI: 10.1007/s00253-014-6116-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 09/16/2014] [Accepted: 09/19/2014] [Indexed: 12/14/2022]
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26
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Fusion of a xylan-binding module to gluco-oligosaccharide oxidase increases activity and promotes stable immobilization. PLoS One 2014; 9:e95170. [PMID: 24736604 PMCID: PMC3988151 DOI: 10.1371/journal.pone.0095170] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 03/24/2014] [Indexed: 11/19/2022] Open
Abstract
The xylan-binding module Clostridium thermocellum CBM22A was successfully fused to a gluco-oligosaccharide oxidase, GOOX-VN, from Sarocladium strictum via a short TP linker, allowing the fused protein to effectively bind different xylans. The presence of the CtCBM22A at the N-terminal of GOOX-VN increased catalytic activity on mono- and oligo-saccharides by 2-3 fold while not affecting binding affinity to these substrates. Notably, both GOOX-VN and its CBM fusion also showed oxidation of xylo-oligosaccharides with degrees of polymerization greater than six. Whereas fusion to CtCBM22A did not alter the thermostability of GOOX-VN or reduce substrate inhibition, CtCBM22A_GOOX-VN could be immobilized to insoluble oat spelt xylan while retaining wild-type activity. QCM-D analysis showed that the fused enzyme remained bound during oxidation. These features could be harnessed to generate hemicellulose-based biosensors that detect and quantify the presence of different oligosaccharides.
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Kurniasih SD, Alfi A, Natalia D, Radjasa OK, Nurachman Z. Construction of individual, fused, and co-expressed proteins of endoglucanase and β-glucosidase for hydrolyzing sugarcane bagasse. Microbiol Res 2014; 169:725-32. [PMID: 24598011 DOI: 10.1016/j.micres.2014.02.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Revised: 01/20/2014] [Accepted: 02/01/2014] [Indexed: 11/30/2022]
Abstract
At least a combination of endoglucanase (EglII) and β-glucosidase (BglZ) is required for hydrolyzing crystalline cellulose. To understand the catalytic efficiency of combination enzymes for converting biomass to sugars, EglII and BglZ were constructed in the form of individual, fused as well as co-expression proteins, and their activities for hydrolyzing sugarcane bagasse were evaluated. The genes, eglII isolated from Bacillus amyloliquefaciens PSM3.1 earlier and bglZ from B. amyloliquefaciens ABBD, were expressed extracellularly in Bacillus megaterium MS941. EglII exhibited both exoglucanase and endoglucanase activities, and BglZ belonging to the glycoside hydrolase 1 family (GH 1) showed β-glucosidase activity. A combination of EglII and BglZ showed activity on substrates Avicel, CMC and sugarcane bagasse. Specifically for hydrolyzing sugarcane bagasse, fused protein (fus-EglII+BglZ), co-expression protein (coex-BglZ+EglII), and mixed-individual protein (mix-EglII+BglZ) produced cellobiose as the main product, along with a small amount of glucose. The amount of reducing sugars released from the hydrolyzing bleached sugarcane bagasse (BSB) using fus-EglII+BglZ and mix-EglII+BglZ was 2.7- and 4.2-fold higher, respectively, than steamed sugarcane bagasse (SSB), indicating the synergetic enzymes worked better on treated sugarcane bagasse. Compared with fus-EglII+BglZ and mix-EglII+BglZ, coex-BglZ+EglII released more mol reducing sugars from SSB, indicating the enzymes were potential for biomass conversion. Additionally, coex-BglZ+EglII acted on BSB 2.5-fold faster than fus-EglII+BglZ. Thus, coex-bglZ+eglII expression system was the best choice to produce enzymes for hydrolyzing sugarcane baggase.
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Affiliation(s)
- Sari Dewi Kurniasih
- Biochemistry Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung 40132, Indonesia
| | - Almasul Alfi
- Biochemistry Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung 40132, Indonesia
| | - Dessy Natalia
- Biochemistry Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung 40132, Indonesia
| | - Ocky Karna Radjasa
- Research Center for Tropical Marine Biotechnology, Diponegoro University, Jl. Soedarto SH No. 1, Semarang 50275, Indonesia
| | - Zeily Nurachman
- Biochemistry Division, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Jl. Ganesha 10, Bandung 40132, Indonesia.
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Ghatge SS, Telke AA, Kang SH, Arulalapperumal V, Lee KW, Govindwar SP, Um Y, Oh DB, Shin HD, Kim SW. Characterization of modular bifunctional processive endoglucanase Cel5 from Hahella chejuensis KCTC 2396. Appl Microbiol Biotechnol 2013; 98:4421-35. [PMID: 24343767 DOI: 10.1007/s00253-013-5446-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 11/28/2013] [Accepted: 11/28/2013] [Indexed: 11/29/2022]
Abstract
Cel5 from marine Hahella chejuensis is composed of glycoside hydrolase family-5 (GH5) catalytic domain (CD) and two carbohydrate binding modules (CBM6-2). The enzyme was expressed in Escherichia coli and purified to homogeneity. The optimum endoglucanase and xylanase activities of recombinant Cel5 were observed at 65 °C, pH 6.5 and 55 °C, pH 5.5, respectively. It exhibited K m of 1.8 and 7.1 mg/ml for carboxymethyl cellulose and birchwood xylan, respectively. The addition of Ca(2+) greatly improved thermostability and endoglucanase activity of Cel5. The Cel5 retained 90 % of its endoglucanase activity after 24 h incubation in presence of 5 M concentration of NaCl. Recombinant Cel5 showed production of cellobiose after hydrolysis of cellulosic substrates (soluble/insoluble) and methylglucuronic acid substituted xylooligosaccharides after hydrolysis of glucuronoxylans by endo-wise cleavage. These results indicated that Cel5 as bifunctional enzyme having both processive endoglucanase and xylanase activities. The multidomain structure of Cel5 is clearly distinguished from the GH5 bifunctional glycoside hydrolases characterized to date, which are single domain enzymes. Sequence analysis and homology modeling suggested presence of two conserved binding sites with different substrate specificities in CBM6-2 and a single catalytic site in CD. Residues Glu132 and Glu219 were identified as key catalytic amino acids by sequence alignment and further verified by using site directed mutagenesis. CBM6-2 plays vital role in catalytic activity and thermostability of Cel5. The bifunctional activities and multiple substrate specificities of Cel5 can be utilized for efficient hydrolysis of cellulose and hemicellulose into soluble sugars.
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Affiliation(s)
- Sunil Subhash Ghatge
- Division of Applied Life Sciences (BK21), PMBBRC, Gyeongsang National University, Jinju, Gyeongnam, Republic of Korea
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Martín M, Wayllace NZ, Valdez HA, Gomez-Casati DF, Busi MV. Improving the glycosyltransferase activity of Agrobacterium tumefaciens glycogen synthase by fusion of N-terminal starch binding domains (SBDs). Biochimie 2013; 95:1865-70. [DOI: 10.1016/j.biochi.2013.06.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Accepted: 06/13/2013] [Indexed: 11/17/2022]
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Kim HD, Choi SL, Kim H, Sohn JH, Lee SG. Enzyme-linked assay of cellulose-binding domain functions from Cellulomonas fimi on multi-well microtiter plate. BIOTECHNOL BIOPROC E 2013. [DOI: 10.1007/s12257-013-0242-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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31
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Telke AA, Zhuang N, Ghatge SS, Lee SH, Ali Shah A, Khan H, Um Y, Shin HD, Chung YR, Lee KH, Kim SW. Engineering of family-5 glycoside hydrolase (Cel5A) from an uncultured bacterium for efficient hydrolysis of cellulosic substrates. PLoS One 2013; 8:e65727. [PMID: 23785445 PMCID: PMC3681849 DOI: 10.1371/journal.pone.0065727] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 04/27/2013] [Indexed: 01/29/2023] Open
Abstract
Cel5A, an endoglucanase, was derived from the metagenomic library of vermicompost. The deduced amino acid sequence of Cel5A shows high sequence homology with family-5 glycoside hydrolases, which contain a single catalytic domain but no distinct cellulose-binding domain. Random mutagenesis and cellulose-binding module (CBM) fusion approaches were successfully applied to obtain properties required for cellulose hydrolysis. After two rounds of error-prone PCR and screening of 3,000 mutants, amino acid substitutions were identified at various positions in thermotolerant mutants. The most heat-tolerant mutant, Cel5A_2R2, showed a 7-fold increase in thermostability. To enhance the affinity and hydrolytic activity of Cel5A on cellulose substrates, the family-6 CBM from Saccharophagus degradans was fused to the C-terminus of the Cel5A_2R2 mutant using overlap PCR. The Cel5A_2R2-CBM6 fusion protein showed 7-fold higher activity than the native Cel5A on Avicel and filter paper. Cellobiose was a major product obtained from the hydrolysis of cellulosic substrates by the fusion enzyme, which was identified by using thin layer chromatography analysis.
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Affiliation(s)
- Amar A. Telke
- Division of Applied Life Sciences (BK21), PMBBRC, Gyeongsang National University, Jinju, Republic of Korea
| | - Ningning Zhuang
- Division of Applied Life Sciences (BK21), PMBBRC, Gyeongsang National University, Jinju, Republic of Korea
| | - Sunil S. Ghatge
- Division of Applied Life Sciences (BK21), PMBBRC, Gyeongsang National University, Jinju, Republic of Korea
| | - Sook-Hee Lee
- Division of Applied Life Sciences (BK21), PMBBRC, Gyeongsang National University, Jinju, Republic of Korea
| | - Asad Ali Shah
- Division of Applied Life Sciences (BK21), PMBBRC, Gyeongsang National University, Jinju, Republic of Korea
| | - Haji Khan
- Division of Applied Life Sciences (BK21), PMBBRC, Gyeongsang National University, Jinju, Republic of Korea
| | - Youngsoon Um
- Center for Environmental Technology Research, KIST, Seoul, Republic of Korea
| | - Hyun-Dong Shin
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Young Ryun Chung
- Division of Applied Life Sciences (BK21), PMBBRC, Gyeongsang National University, Jinju, Republic of Korea
| | - Kon Ho Lee
- Division of Applied Life Sciences (BK21), PMBBRC, Gyeongsang National University, Jinju, Republic of Korea
- Department of Microbiology, School of Medicine, Gyeongsang National University, Jinju, Republic of Korea
- * E-mail: (SWK); (KHL)
| | - Seon-Won Kim
- Division of Applied Life Sciences (BK21), PMBBRC, Gyeongsang National University, Jinju, Republic of Korea
- * E-mail: (SWK); (KHL)
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