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Li N, Han J, Zhou Y, Zhang H, Xu X, He B, Liu M, Wang J, Wang Q. A rumen-derived bifunctional glucanase/mannanase uncanonically releases oligosaccharides with a high degree of polymerization preferentially from branched substrates. Carbohydr Polym 2024; 330:121828. [PMID: 38368107 DOI: 10.1016/j.carbpol.2024.121828] [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: 09/06/2023] [Revised: 01/07/2024] [Accepted: 01/12/2024] [Indexed: 02/19/2024]
Abstract
Glycoside hydrolases (GHs) are known to depolymerize polysaccharides into oligo-/mono-saccharides, they are extensively used as additives for both animals feed and our food. Here we reported the characterization of IDSGH5-14(CD), a weakly-acidic mesophilic bifunctional mannanase/glucanase of GH5, originally isolated from sheep rumen microbes. Biochemical characterization studies revealed that IDSGH5-14(CD) exhibited preferential hydrolysis of mannan-like and glucan-like substrates. Interestingly, the enzyme exhibited significantly robust catalytic activity towards branched-substrates compared to linear polysaccharides (P < 0.05). Substrate hydrolysis pattern indicated that IDSGH5-14(CD) predominantly liberated oligosaccharides with a degree of polymerization (DP) of 3-7 as the end products, dramatically distinct from canonical endo-acting enzymes. Comparative modeling revealed that IDSGH5-14(CD) was mainly comprised of a (β/α)8-barrel-like structure with a spacious catalytic cleft on surface, facilitating the enzyme to target high-DP or branched oligosaccharides. Molecular dynamics (MD) simulations further suggested that the branched-ligand, 64-α-D-galactosyl-mannohexose, was steadily accommodated within the catalytic pocket via a two-sided clamp formed by the aromatic residues. This study first reports a bifunctional GH5 enzyme that predominantly generates high-DP oligosaccharides, preferentially from branched-substrates. This provides novel insights into the catalytic mechanism and molecular underpinnings of polysaccharide depolymerization, with potential implications for feed additive development and high-DP oligosaccharides preparation.
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Affiliation(s)
- Nuo Li
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou 310058, China
| | - Junyan Han
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou 310058, China; College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, China
| | - Yebo Zhou
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, China
| | - Huien Zhang
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, China
| | - Xiaofeng Xu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou 310058, China; College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, China
| | - Bo He
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mingqi Liu
- Key Laboratory of Specialty Agri-product Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Jiakun Wang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou 310058, China
| | - Qian Wang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou 310058, China.
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Wu X, Zhao S, Tian Z, Han C, Jiang X, Wang L. Dynamics of loops surrounding the active site architecture in GH5_2 subfamily TfCel5A for cellulose degradation. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:154. [PMID: 37853500 PMCID: PMC10583438 DOI: 10.1186/s13068-023-02411-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 10/12/2023] [Indexed: 10/20/2023]
Abstract
BACKGROUND Lignocellulose is the most abundant natural biomass resource for the production of biofuels and other chemicals. The efficient degradation of cellulose by cellulases is a critical step for the lignocellulose bioconversion. Understanding the structure-catalysis relationship is vital for rational design of more stable and highly active enzymes. Glycoside hydrolase (GH) family 5 is the largest and most functionally diverse group of cellulases, with a conserved TIM barrel structure. The important roles of the various loop regions of GH5 enzymes in catalysis, however, remain poorly understood. RESULTS In the present study, we investigated the relationship between the loops surrounding active site architecture and its catalytic efficiency, taking TfCel5A, an enzyme from GH5_2 subfamily of Thermobifida fusca, as an example. Large-scale computational simulations and site-directed mutagenesis experiments revealed that three loops (loop 8, 3, and 7) around active cleft played diverse roles in substrate binding, intermediate formation, and product release, respectively. The highly flexible and charged residue triad of loop 8 was responsible for capturing the ligand into the active cleft. Severe fluctuation of loop 3 led to the distortion of sugar conformation at the - 1 subsite. The wobble of loop 7 might facilitate product release, and the enzyme activity of the mutant Y361W in loop 7 was increased by approximately 40%. CONCLUSION This study unraveled the vital roles of loops in active site architecture and provided new insights into the catalytic mechanism of the GH5_2 cellulases.
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Affiliation(s)
- Xiuyun Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Sha Zhao
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Zhennan Tian
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Chao Han
- Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural University, Tai'an, 271018, China
| | - Xukai Jiang
- National Glycoengineering Research Center, Shandong University, Qingdao, 266237, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China.
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Dementiev A, Lillington SP, Jin S, Kim Y, Jedrzejczak R, Michalska K, Joachimiak A, O'Malley MA. Structure and enzymatic characterization of CelD endoglucanase from the anaerobic fungus Piromyces finnis. Appl Microbiol Biotechnol 2023; 107:5999-6011. [PMID: 37548665 PMCID: PMC10485095 DOI: 10.1007/s00253-023-12684-0] [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: 05/02/2023] [Revised: 06/24/2023] [Accepted: 06/29/2023] [Indexed: 08/08/2023]
Abstract
Anaerobic fungi found in the guts of large herbivores are prolific biomass degraders whose genomes harbor a wealth of carbohydrate-active enzymes (CAZymes), of which only a handful are structurally or biochemically characterized. Here, we report the structure and kinetic rate parameters for a glycoside hydrolase (GH) family 5 subfamily 4 enzyme (CelD) from Piromyces finnis, a modular, cellulosome-incorporated endoglucanase that possesses three GH5 domains followed by two C-terminal fungal dockerin domains (double dockerin). We present the crystal structures of an apo wild-type CelD GH5 catalytic domain and its inactive E154A mutant in complex with cellotriose at 2.5 and 1.8 Å resolution, respectively, finding the CelD GH5 catalytic domain adopts the (β/α)8-barrel fold common to many GH5 enzymes. Structural superimposition of the apo wild-type structure with the E154A mutant-cellotriose complex supports a catalytic mechanism in which the E154 carboxylate side chain acts as an acid/base and E278 acts as a complementary nucleophile. Further analysis of the cellotriose binding pocket highlights a binding groove lined with conserved aromatic amino acids that when docked with larger cellulose oligomers is capable of binding seven glucose units and accommodating branched glucan substrates. Activity analyses confirm P. finnis CelD can hydrolyze mixed linkage glucan and xyloglucan, as well as carboxymethylcellulose (CMC). Measured kinetic parameters show the P. finnis CelD GH5 catalytic domain has CMC endoglucanase activity comparable to other fungal endoglucanases with kcat = 6.0 ± 0.6 s-1 and Km = 7.6 ± 2.1 g/L CMC. Enzyme kinetics were unperturbed by the addition or removal of the native C-terminal dockerin domains as well as the addition of a non-native N-terminal dockerin, suggesting strict modularity among the domains of CelD. KEY POINTS: • Anaerobic fungi host a wealth of industrially useful enzymes but are understudied. • P. finnis CelD has endoglucanase activity and structure common to GH5_4 enzymes. • CelD's kinetics do not change with domain fusion, exhibiting high modularity.
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Affiliation(s)
- Alexey Dementiev
- Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Stephen P Lillington
- Department of Chemical Engineering, University of California, Santa Barbara, CA, USA
| | - Shiyan Jin
- Department of Chemical Engineering, University of California, Santa Barbara, CA, USA
| | - Youngchang Kim
- Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Robert Jedrzejczak
- Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Karolina Michalska
- Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Andrzej Joachimiak
- Structural Biology Center, X-Ray Science Division, Argonne National Laboratory, Lemont, IL, 60439, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Michelle A O'Malley
- Department of Chemical Engineering, University of California, Santa Barbara, CA, USA.
- Biological Engineering Program, University of California, Santa Barbara, CA, USA.
- Joint BioEnergy Institute (JBEI), Emeryville, CA, 94608, USA.
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Ha NS, Onley JR, Deng K, Andeer P, Bowen BP, Gupta K, Kim PW, Kuch N, Kutschke M, Parker A, Song F, Fox B, Adams PD, de Raad M, Northen TR. A combinatorial droplet microfluidic device integrated with mass spectrometry for enzyme screening. LAB ON A CHIP 2023; 23:3361-3369. [PMID: 37401915 PMCID: PMC10484474 DOI: 10.1039/d2lc00980c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
Mass spectrometry (MS) enables detection of different chemical species with a very high specificity; however, it can be limited by its throughput. Integrating MS with microfluidics has a tremendous potential to improve throughput and accelerate biochemical research. In this work, we introduce Drop-NIMS, a combination of a passive droplet loading microfluidic device and a matrix-free MS laser desorption ionization technique called nanostructure-initiator mass spectrometry (NIMS). This platform combines different droplets at random to generate a combinatorial library of enzymatic reactions that are deposited directly on the NIMS surface without requiring additional sample handling. The enzyme reaction products are then detected with MS. Drop-NIMS was used to rapidly screen enzymatic reactions containing low (on the order of nL) volumes of glycoside reactants and glycoside hydrolase enzymes per reaction. MS "barcodes" (small compounds with unique masses) were added to the droplets to identify different combinations of substrates and enzymes created by the device. We assigned xylanase activities to several putative glycoside hydrolases, making them relevant to food and biofuel industrial applications. Overall, Drop-NIMS is simple to fabricate, assemble, and operate and it has potential to be used with many other small molecule metabolites.
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Affiliation(s)
- Noel S Ha
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jenny R Onley
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Sandia National Laboratories, Livermore, California, USA
| | - Kai Deng
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Sandia National Laboratories, Livermore, California, USA
| | - Peter Andeer
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Kshitiz Gupta
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Peter W Kim
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Sandia National Laboratories, Livermore, California, USA
| | - Nathaniel Kuch
- University of Wisconsin - Madison, Madison, WI, USA
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, WI, USA
| | | | - Alex Parker
- University of Wisconsin - Madison, Madison, WI, USA
| | - Fangchao Song
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Brian Fox
- University of Wisconsin - Madison, Madison, WI, USA
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, WI, USA
| | - Paul D Adams
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- University of California, Berkeley, CA, USA
| | - Markus de Raad
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Trent R Northen
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Kuch NJ, Kutschke ME, Parker A, Bingman CA, Fox BG. Contribution of calcium ligands in substrate binding and product release in the Acetovibrio thermocellus glycoside hydrolase family 9 cellulase CelR. J Biol Chem 2023; 299:104655. [PMID: 36990218 PMCID: PMC10149213 DOI: 10.1016/j.jbc.2023.104655] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 03/16/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023] Open
Abstract
Enzymatic deconstruction of lignocellulosic biomass is crucial to establishment of the renewable biofuel and bioproduct economy. Better understanding of these enzymes, including their catalytic and binding domains, and other features offer potential avenues for improvement. Glycoside hydrolase family 9 (GH9) enzymes are attractive targets because they have members that exhibit exo- and endo-cellulolytic activity, processivity of reaction, and thermostability. This study examines a GH9 from Acetovibrio thermocellus ATCC 27405, AtCelR containing a catalytic domain and a carbohydrate binding module (CBM3c). Crystal structures of the enzyme without substrate, bound to cellohexaose (substrate) or cellobiose (product), show the positioning of ligands to calcium and adjacent residues in the catalytic domain that may contribute to substrate binding and facilitate product release. We also investigated the properties of the enzyme engineered to contain an additional carbohydrate binding module (CBM3a). Relative to the catalytic domain alone, CBM3a gave improved binding for Avicel (a crystalline form of cellulose), and catalytic efficiency (kcat/KM) was improved 40× with both CBM3c and CBM3a present. However, because of the molecular weight added by CBM3a, the specific activity of the engineered enzyme was not increased relative to the native construct consisting of only the catalytic and CBM3c domains. This work provides new insight into a potential role of the conserved calcium in the catalytic domain and identifies contributions and limitations of domain engineering for AtCelR and perhaps other GH9 enzymes.
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Affiliation(s)
- Nathaniel J Kuch
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Mark E Kutschke
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Alex Parker
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA; Dane County Youth Apprenticeship Program, Dane County School Consortium, Monona, Wisconsin, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA; Collaborative Crystallography Core, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Brian G Fox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA.
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Eljonaid MY, Tomita H, Okazaki F, Tamaru Y. Enzymatic Characterization of Unused Biomass Degradation Using the Clostridium cellulovorans Cellulosome. Microorganisms 2022; 10:microorganisms10122514. [PMID: 36557767 PMCID: PMC9784398 DOI: 10.3390/microorganisms10122514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/13/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
The cellulolytic system of Clostridium cellulovorans mainly consisting of a cellulosome that synergistically collaborates with non-complexed enzymes was investigated using cellulosic biomass. The cellulosomes were isolated from the culture supernatants with shredded paper, rice straw and sugarcane bagasse using crystalline cellulose. Enzyme solutions, including the cellulosome fractions, were analyzed by SDS-PAGE and Western blot using an anti-CbpA antibody. As a result, C. cellulovorans was able to completely degrade shredded paper for 9 days and to be continuously cultivated by the addition of new culture medium containing shredded paper, indicating, through TLC analysis, that its degradative products were glucose and cellobiose. Regarding the rice straw and sugarcane bagasse, while the degradative activity of rice straw was most active using the cellulosome in the culture supernatant of rice straw medium, that of sugarcane bagasse was most active using the cellulosome from the supernatant of cellobiose medium. Based on these results, no alcohols were found when C. acetobutylicum was cultivated in the absence of C. cellulovorans as it cannot degrade the cellulose. While 1.5 mM of ethanol was produced with C. cellulovorans cultivation, both n-butanol (1.67 mM) and ethanol (1.89 mM) were detected with the cocultivation of C. cellulovorans and C. acetobutylicum. Regarding the enzymatic activity evaluation against rice straw and sugarcane bagasse, the rice straw cellulosome fraction was the most active when compared against rice straw. Furthermore, since we attempted to choose reaction conditions more efficiently for the degradation of sugarcane bagasse, a wet jet milling device together with L-cysteine as a reducing agent was used. As a result, we found that the degradation activity was almost twice as high with 10 mM L-cysteine compared with without it. These results will provide new insights for biomass utilization.
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Affiliation(s)
- Mohamed Yahia Eljonaid
- Department of Life Sciences, Graduate School of Bioresources, Mie University, 1577 Kurimamachiya, Tsu 514-8507, Japan
| | - Hisao Tomita
- Department of Life Sciences, Graduate School of Bioresources, Mie University, 1577 Kurimamachiya, Tsu 514-8507, Japan
| | - Fumiyoshi Okazaki
- Department of Life Sciences, Graduate School of Bioresources, Mie University, 1577 Kurimamachiya, Tsu 514-8507, Japan
- Department of Bioinfomatics, Mie University Advanced Science Research Center, Mie University, 1577 Kurimamachiya, Tsu 514-8507, Japan
- Smart Cell Innovation Research Center, Mie University, 1577 Kurimamachiya, Tsu 514-8507, Japan
| | - Yutaka Tamaru
- Department of Life Sciences, Graduate School of Bioresources, Mie University, 1577 Kurimamachiya, Tsu 514-8507, Japan
- Department of Bioinfomatics, Mie University Advanced Science Research Center, Mie University, 1577 Kurimamachiya, Tsu 514-8507, Japan
- Smart Cell Innovation Research Center, Mie University, 1577 Kurimamachiya, Tsu 514-8507, Japan
- Correspondence: ; Tel.: +81-59-231-9560
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Multifunctionality and mechanism of processivity of family GH5 endoglucanase, RfGH5_4 from Ruminococcus flavefaciens on lignocellulosic polymers. Int J Biol Macromol 2022; 224:1395-1411. [DOI: 10.1016/j.ijbiomac.2022.10.227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/15/2022] [Accepted: 10/24/2022] [Indexed: 11/05/2022]
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Zhan M, Wang A, Yao Y, Zhou Y, Zhang S, Fu X, Zhou J, Pei E, Wang L. An amateur gut microbial configuration formed in giant panda for striving to digest cellulose in bamboo: Systematic evidence from intestinal digestive enzymes, functional genes and microbial structures. Front Microbiol 2022; 13:926515. [PMID: 35958139 PMCID: PMC9363027 DOI: 10.3389/fmicb.2022.926515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/04/2022] [Indexed: 11/14/2022] Open
Abstract
The giant panda has been considered to maximize nutritional intake including protein and soluble carbohydrates in bamboo, but it has spent almost entire life with the high-cellulose diet. Whether giant panda is still helpless about digesting bamboo cellulose or not is always contentious among many researchers around the world. The work has systematically clarified this issue from the perspectives of digestive enzymes, functional genes, and microbial structures in giant panda gut. The intestinal cellulase activities of panda increase with bamboo consumption, performing that the endoglucanase activity of adults reaches 10-fold that of pandas first consuming bamboo. More abundance and types of microbial endoglucanase genes occur in bamboo-diet giant panda gut, and the corresponding GH5 gene cluster is still efficiently transcribed. Gut microbes possessing cellulose-degrading genes, belong to the phylum Firmicutes and some Bacteroidetes, but their structural and functional configurations are insufficient to completely degrade cellulose. Therefore, giant panda is striving to digest cellulose in bamboo, but this adaptation is incomplete. This is probably related to the short straight carnivore-like gut structure of the giant panda, preventing the colonization of some efficient functional but anaerobic-preferred flora.
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Affiliation(s)
- Mingye Zhan
- College of Environmental Science and Engineering, Institute of Pollution Control and Ecological Safety, Tongji University, Shanghai, China
| | | | | | - Yingmin Zhou
- China Conservation and Research Center for the Giant Panda, Dujiangyan, China
| | | | - Xiaohua Fu
- College of Environmental Science and Engineering, Institute of Pollution Control and Ecological Safety, Tongji University, Shanghai, China
| | | | | | - Lei Wang
- College of Environmental Science and Engineering, Institute of Pollution Control and Ecological Safety, Tongji University, Shanghai, China
- *Correspondence: Lei Wang,
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Escuder-Rodríguez JJ, González-Suarez M, deCastro ME, Saavedra-Bouza A, Becerra M, González-Siso MI. Characterization of a novel thermophilic metagenomic GH5 endoglucanase heterologously expressed in Escherichia coli and Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:76. [PMID: 35799200 PMCID: PMC9264688 DOI: 10.1186/s13068-022-02172-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/24/2022] [Indexed: 01/05/2023]
Abstract
Background Endoglucanases from thermophilic microorganisms are a valuable resource as they can be used in a wide variety of biotechnological applications including the valorisation of biomass and the production of biofuels. In the present work we analysed the metagenome from the hot spring Muiño da Veiga, located in the northwest of Spain (in the Galicia region), in search for novel thermostable endoglucanases. Results Sequence analysis of the metagenome revealed a promising enzyme (Cel776). Predictions on protein structure and conserved amino acid sequences were conducted, as well as expression in heterologous systems with Escherichia coli and Saccharomyces cerevisiae as the host. Cel776Ec was correctly expressed and purified by taking advantage of the His-Tag system, with a yield of 0.346 U/mL in the eluted fraction. Cel776Sc was expressed extracellulary and was easily recovered from the supernatant without the need of further purification, requiring only a concentration step by ultrafiltration, with a significantly higher yield of 531.95 U/mL, revealing a much more suitable system for production of large amounts of the enzyme. Their biochemical characterization revealed biotechnologically interesting enzymes. Both Cel776Ec and Cel776Sc had an optimal temperature of 80 °C and optimal pH of 5. Cel776Ec exhibited high thermostability maintaining its activity for 24 h at 60 °C and maintained its activity longer than Cel776Sc at increasing incubation temperatures. Moreover, its substrate specificity allowed the degradation of both cellulose and xylan. Whereas Cel776Ec was more active in the presence of calcium and magnesium, manganese was found to increase Cel776Sc activity. A stronger inhibitory effect was found for Cel776Ec than Cel776Sc adding detergent SDS to the reaction mix, whereas EDTA only significantly affected Cel776Sc activity. Conclusions Our study reports the discovery of a new promising biocatalyst for its application in processes, such as the production of biofuel and the saccharification of plant biomass, due to its bifunctional enzymatic activity as an endoglucanase and as a xylanase, as well as highlights the advantages of a yeast expression system over bacteria. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02172-4.
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Affiliation(s)
- Juan-José Escuder-Rodríguez
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071, A Coruña, Spain
| | - María González-Suarez
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071, A Coruña, Spain
| | - María-Eugenia deCastro
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071, A Coruña, Spain
| | - Almudena Saavedra-Bouza
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071, A Coruña, Spain
| | - Manuel Becerra
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071, A Coruña, Spain.
| | - María-Isabel González-Siso
- Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, 15071, A Coruña, Spain.
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Mohammadi S, Tarrahimofrad H, Arjmand S, Zamani J, Haghbeen K, Aminzadeh S. Expression, characterization, and activity optimization of a novel cellulase from the thermophilic bacteria Cohnella sp. A01. Sci Rep 2022; 12:10301. [PMID: 35717508 PMCID: PMC9206686 DOI: 10.1038/s41598-022-14651-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 06/09/2022] [Indexed: 11/09/2022] Open
Abstract
Cellulases are hydrolytic enzymes with wide scientific and industrial applications. We described a novel cellulase, CelC307, from the thermophilic indigenous Cohnella sp. A01. The 3-D structure of the CelC307 was predicted by comparative modeling. Docking of CelC307 with specific inhibitors and molecular dynamic (MD) simulation revealed that these ligands bound in a non-competitive manner. The CelC307 protein was purified and characterized after recombinant expression in Escherichia coli (E. coli) BL21. Using CMC 1% as the substrate, the thermodynamic values were determined as Km 0.46 mM, kcat 104.30 × 10-3 (S-1), and kcat/Km 226.73 (M-1 S-1). The CelC307 was optimally active at 40 °C and pH 7.0. The culture condition was optimized for improved CelC307 expression using Plackett-Burman and Box-Behnken design as follows: temperature 20 °C, pH 7.5, and inoculation concentration with an OD600 = 1. The endoglucanase activity was positively modulated in the presence of Na+, Li+, Ca2+, 2-mercaptoethanol (2-ME), and glycerol. The thermodynamic parameters calculated for CelC307 confirmed its inherent thermostability. The characterized CelC307 may be a suitable candidate for various biotechnological applications.
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Affiliation(s)
- Shima Mohammadi
- Bioprocess Engineering Group, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Hossein Tarrahimofrad
- Bioprocess Engineering Group, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Sareh Arjmand
- Protein Research Center, Shahid Beheshti University, Tehran, Iran
| | - Javad Zamani
- Bioprocess Engineering Group, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Kamahldin Haghbeen
- Bioprocess Engineering Group, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Saeed Aminzadeh
- Bioprocess Engineering Group, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
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11
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Gavande PV, Nath P, Kumar K, Ahmed N, Fontes CMGA, Goyal A. Highly efficient, processive and multifunctional recombinant endoglucanase RfGH5_4 from Ruminococcus flavefaciens FD-1 v3 for recycling lignocellulosic plant biomasses. Int J Biol Macromol 2022; 209:801-813. [PMID: 35421411 DOI: 10.1016/j.ijbiomac.2022.04.059] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/18/2022] [Accepted: 04/08/2022] [Indexed: 11/26/2022]
Abstract
Gene encoding endoglucanase, RfGH5_4 from R. flavefaciens FD-1 v3 was cloned, expressed in Escherichia coli BL21(DE3) cells and purified. RfGH5_4 showed molecular size 41 kDa and maximum activity at pH 5.5 and 55 °C. It was stable between pH 5.0-8.0, retaining 85% activity and between 5 °C-45 °C, retaining 75% activity, after 60 min. RfGH5_4 displayed maximum activity (U/mg) against barley β-D-glucan (665) followed by carboxymethyl cellulose (450), xyloglucan (343), konjac glucomannan (285), phosphoric acid swollen cellulose (86), beechwood xylan (21.7) and carob galactomannan (16), thereby displaying the multi-functionality. Catalytic efficiency (mL.mg-1 s-1) of RfGH5_4 against carboxymethyl cellulose (146) and konjac glucomannan (529) was significantly high. TLC and MALDI-TOF-MS analyses of RfGH5_4 treated hydrolysates of cellulosic and hemicellulosic polysaccharides displayed oligosaccharides of degree of polymerization (DP) between DP2-DP11. TLC, HPLC and Processivity-Index analyses revealed RfGH5_4 to be a processive endoglucanase as initially, for 30 min it hydrolysed cellulose to cellotetraose followed by persistent release of cellotriose and cellobiose. RfGH5_4 yielded sufficiently high Total Reducing Sugar (TRS, mg/g) from saccharification of alkali pre-treated sorghum (72), finger millet (62), sugarcane bagasse (38) and cotton (27) in a 48 h saccharification reaction. Thus, RfGH5_4 can be considered as a potential endoglucanase for renewable energy applications.
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Affiliation(s)
- Parmeshwar Vitthal Gavande
- Department of Biosciences and Bioengineering, Carbohydrate Enzyme Biotechnology Laboratory, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Priyanka Nath
- Department of Biosciences and Bioengineering, Carbohydrate Enzyme Biotechnology Laboratory, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Krishan Kumar
- Department of Biosciences and Bioengineering, Carbohydrate Enzyme Biotechnology Laboratory, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Nazneen Ahmed
- Department of Biosciences and Bioengineering, Carbohydrate Enzyme Biotechnology Laboratory, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Carlos M G A Fontes
- CIISA - Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisbon, Portugal; NZYTech - Genes & Enzymes, Estrada do Paço do Lumiar, Campus do Lumiar, Edifício, Lisbon, Portugal
| | - Arun Goyal
- Department of Biosciences and Bioengineering, Carbohydrate Enzyme Biotechnology Laboratory, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India.
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12
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Drula E, Garron ML, Dogan S, Lombard V, Henrissat B, Terrapon N. The carbohydrate-active enzyme database: functions and literature. Nucleic Acids Res 2021; 50:D571-D577. [PMID: 34850161 PMCID: PMC8728194 DOI: 10.1093/nar/gkab1045] [Citation(s) in RCA: 769] [Impact Index Per Article: 256.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/13/2021] [Accepted: 10/14/2021] [Indexed: 02/01/2023] Open
Abstract
Thirty years have elapsed since the emergence of the classification of carbohydrate-active enzymes in sequence-based families that became the CAZy database over 20 years ago, freely available for browsing and download at www.cazy.org. In the era of large scale sequencing and high-throughput Biology, it is important to examine the position of this specialist database that is deeply rooted in human curation. The three primary tasks of the CAZy curators are (i) to maintain and update the family classification of this class of enzymes, (ii) to classify sequences newly released by GenBank and the Protein Data Bank and (iii) to capture and present functional information for each family. The CAZy website is updated once a month. Here we briefly summarize the increase in novel families and the annotations conducted during the last 8 years. We present several important changes that facilitate taxonomic navigation, and allow to download the entirety of the annotations. Most importantly we highlight the considerable amount of work that accompanies the analysis and report of biochemical data from the literature.
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Affiliation(s)
- Elodie Drula
- Aix Marseille Univ, CNRS, UMR7257 AFMB, Marseille, France.,INRAE, USC1408 AFMB, Marseille, France
| | - Marie-Line Garron
- Aix Marseille Univ, CNRS, UMR7257 AFMB, Marseille, France.,INRAE, USC1408 AFMB, Marseille, France
| | - Suzan Dogan
- Aix Marseille Univ, CNRS, UMR7257 AFMB, Marseille, France.,INRAE, USC1408 AFMB, Marseille, France
| | - Vincent Lombard
- Aix Marseille Univ, CNRS, UMR7257 AFMB, Marseille, France.,INRAE, USC1408 AFMB, Marseille, France
| | - Bernard Henrissat
- Aix Marseille Univ, CNRS, UMR7257 AFMB, Marseille, France.,INRAE, USC1408 AFMB, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.,Technical University of Denmark, DTU Bioengineering, Kgs Lyngby, Denmark
| | - Nicolas Terrapon
- Aix Marseille Univ, CNRS, UMR7257 AFMB, Marseille, France.,INRAE, USC1408 AFMB, Marseille, France
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13
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Glasgow E, Vander Meulen K, Kuch N, Fox BG. Multifunctional cellulases are potent, versatile tools for a renewable bioeconomy. Curr Opin Biotechnol 2021; 67:141-148. [PMID: 33550093 PMCID: PMC8366578 DOI: 10.1016/j.copbio.2020.12.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 12/09/2020] [Accepted: 12/28/2020] [Indexed: 11/21/2022]
Abstract
Enzyme performance is critical to the future bioeconomy based on renewable plant materials. Plant biomass can be efficiently hydrolyzed by multifunctional cellulases (MFCs) into sugars suitable for conversion into fuels and chemicals, and MFCs fall into three functional categories. Recent work revealed MFCs with broad substrate specificity, dual exo-activity/endo-activity on cellulose, and intramolecular synergy, among other novel characteristics. Binding modules and accessory catalytic domains amplify MFC and xylanase activity in a wide variety of ways, and processive endoglucanases achieve autosynergy on cellulose. Multidomain MFCs from Caldicellulosiruptor are heat-tolerant, adaptable to variable cellulose crystallinity, and may provide interchangeable scaffolds for recombinant design. Further studies of MFC properties and their reactivity with plant biomass are recommended for increasing biorefinery yields.
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Affiliation(s)
- Evan Glasgow
- Dept. of Biochemistry, University of Wisconsin - Madison, 433 Babcock Dr., Madison, WI, 53706, United States; Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, 1552 University Ave, Madison, WI, 53726, United States
| | - Kirk Vander Meulen
- Dept. of Biochemistry, University of Wisconsin - Madison, 433 Babcock Dr., Madison, WI, 53706, United States; Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, 1552 University Ave, Madison, WI, 53726, United States
| | - Nate Kuch
- Dept. of Biochemistry, University of Wisconsin - Madison, 433 Babcock Dr., Madison, WI, 53706, United States; Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, 1552 University Ave, Madison, WI, 53726, United States
| | - Brian G Fox
- Dept. of Biochemistry, University of Wisconsin - Madison, 433 Babcock Dr., Madison, WI, 53706, United States; Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, 1552 University Ave, Madison, WI, 53726, United States.
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