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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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Consuming fresh macroalgae induces specific catabolic pathways, stress reactions and Type IX secretion in marine flavobacterial pioneer degraders. THE ISME JOURNAL 2022; 16:2027-2039. [PMID: 35589967 PMCID: PMC9296495 DOI: 10.1038/s41396-022-01251-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 04/28/2022] [Accepted: 05/09/2022] [Indexed: 12/20/2022]
Abstract
Macroalgae represent huge amounts of biomass worldwide, largely recycled by marine heterotrophic bacteria. We investigated the strategies of bacteria within the flavobacterial genus Zobellia to initiate the degradation of whole algal tissues, which has received little attention compared to the degradation of isolated polysaccharides. Zobellia galactanivorans DsijT has the capacity to use fresh brown macroalgae as a sole carbon source and extensively degrades algal tissues via the secretion of extracellular enzymes, even in the absence of physical contact with the algae. Co-cultures experiments with the non-degrading strain Tenacibaculum aestuarii SMK-4T showed that Z. galactanivorans can act as a pioneer that initiates algal breakdown and shares public goods with other bacteria. A comparison of eight Zobellia strains, and strong transcriptomic shifts in Z. galactanivorans cells using fresh macroalgae vs. isolated polysaccharides, revealed potential overlooked traits of pioneer bacteria. Besides brown algal polysaccharide degradation, they notably include oxidative stress resistance proteins, type IX secretion system proteins and novel uncharacterized polysaccharide utilization loci. Overall, this work highlights the relevance of studying fresh macroalga degradation to fully understand the metabolic and ecological strategies of pioneer microbial degraders, key players in macroalgal biomass remineralization.
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Biochemical characterization and cleavage pattern analysis of a novel chitosanase with cellulase activity. Appl Microbiol Biotechnol 2022; 106:1979-1990. [PMID: 35175399 DOI: 10.1007/s00253-022-11829-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 02/05/2022] [Accepted: 02/08/2022] [Indexed: 11/02/2022]
Abstract
Chitosanases are critical tools for the preparation of active oligosaccharides, whose composition is related to the cleavage pattern of the enzyme. Although numerous chitosanases have been characterized, the glycoside hydrolase (GH) family 5 chitosanases with other activities have rarely been investigated. Herein, a novel and second GH5 chitosanase OUC-Csngly from Streptomyces bacillaris was cloned and further characterized by expression in Escherichia coli BL21 (DE3). Interestingly, OUC-Csngly possessed dual chitosanase and cellulase activities. Molecular docking analysis showed that the C-2 group of sugar units affected the binding of the enzyme to oligosaccharides, which could result in different cleavage patterns toward chito-oligosaccharides (COSs) and cello-oligosaccharides. Further, we characterized OUC-Csngly's distinctive cleavage patterns toward two different types of oligosaccharides. Meanwhile, endo-type chitosanase OUC-Csngly generated (GlcN) - (GlcN)4 from chitosan, was significantly different from other chitosanases. To our knowledge, this is the first report to investigate the different cleavage patterns of chitosanase for COSs and cello-oligosaccharides.Key points• The molecular docking showed C-2 group of sugar units in substrate affecting the cleavage pattern.• The first chitosanase exhibited different cleavage patterns towards chito- and cello-oligosaccharides.• The groups at C-2 influence the subsite composition of the enzyme's active cleft.
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Glasgow EM, Kemna EI, Bingman CA, Ing N, Deng K, Bianchetti CM, Takasuka TE, Northen TR, Fox BG. A structural and kinetic survey of GH5_4 endoglucanases reveals determinants of broad substrate specificity and opportunities for biomass hydrolysis. J Biol Chem 2021; 295:17752-17769. [PMID: 33454012 DOI: 10.1074/jbc.ra120.015328] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/15/2020] [Indexed: 11/06/2022] Open
Abstract
Broad-specificity glycoside hydrolases (GHs) contribute to plant biomass hydrolysis by degrading a diverse range of polysaccharides, making them useful catalysts for renewable energy and biocommodity production. Discovery of new GHs with improved kinetic parameters or more tolerant substrate-binding sites could increase the efficiency of renewable bioenergy production even further. GH5 has over 50 subfamilies exhibiting selectivities for reaction with β-(1,4)-linked oligo- and polysaccharides. Among these, subfamily 4 (GH5_4) contains numerous broad-selectivity endoglucanases that hydrolyze cellulose, xyloglucan, and mixed-linkage glucans. We previously surveyed the whole subfamily and found over 100 new broad-specificity endoglucanases, although the structural origins of broad specificity remained unclear. A mechanistic understanding of GH5_4 substrate specificity would help inform the best protein design strategies and the most appropriate industrial application of broad-specificity endoglucanases. Here we report structures of 10 new GH5_4 enzymes from cellulolytic microbes and characterize their substrate selectivity using normalized reducing sugar assays and MS. We found that GH5_4 enzymes have the highest catalytic efficiency for hydrolysis of xyloglucan, glucomannan, and soluble β-glucans, with opportunistic secondary reactions on cellulose, mannan, and xylan. The positions of key aromatic residues determine the overall reaction rate and breadth of substrate tolerance, and they contribute to differences in oligosaccharide cleavage patterns. Our new composite model identifies several critical structural features that confer broad specificity and may be readily engineered into existing industrial enzymes. We demonstrate that GH5_4 endoglucanases can have broad specificity without sacrificing high activity, making them a valuable addition to the biomass deconstruction toolset.
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Affiliation(s)
- Evan M Glasgow
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA; Great Lakes Bioenergy Research Center, Madison, Wisconsin, USA
| | - Elias I Kemna
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA; Great Lakes Bioenergy Research Center, Madison, Wisconsin, USA
| | - Nicole Ing
- Joint BioEnergy Institute, Emeryville, California, USA; Sandia National Laboratories, Livermore, California, USA
| | - Kai Deng
- Joint BioEnergy Institute, Emeryville, California, USA; Sandia National Laboratories, Livermore, California, USA
| | - Christopher M Bianchetti
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA; Great Lakes Bioenergy Research Center, Madison, Wisconsin, USA
| | | | - Trent R Northen
- Joint BioEnergy Institute, Emeryville, California, USA; Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Brian G Fox
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin, USA; Great Lakes Bioenergy Research Center, Madison, Wisconsin, USA.
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Li K, Jiang C, Tan H, Li J, Xu Y, Tang D, Zhao X, Liu Q, Li J, Yin H. Identification and characterization of a novel glucomannanase from Paenibacillus polymyxa. 3 Biotech 2021; 11:129. [PMID: 33680694 PMCID: PMC7892656 DOI: 10.1007/s13205-021-02676-0] [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: 11/05/2020] [Accepted: 02/01/2021] [Indexed: 10/22/2022] Open
Abstract
Konjac glucomannan oligosaccharide has attracted much attention due to its broad biological activities. Specific glucomannan degrading enzymes are effective tools for the production of oligosaccharides from konjac glucomannan. However, there are still few reports of commercial enzymes that can specifically degrade konjac glucomannan. The gene ppgluB encoding a glucomannanase consisting of 553 amino acids (61.5 kDa) from Paenibacillus polymyxa 3-3 was cloned and heterologous expressed in Escherichia coli BL21 (DE3). The recombinant PpGluB showed high specificity for the degradation of konjac glucomannan. Moreover, the hydrolytic products of PpGluB degrade konjac glucomannan were a series of oligosaccharides with degrees of polymerisation of 2-12. Furthermore, the biochemical properties indicated that PpGluB is the optimal active at 45 to 55 °C and pH 5.0-6.0, and shows highly pH stability over a very broad pH range. The present characteristics indicated that PpGluB is a potential tool to be used to produce oligosaccharides from konjac glucomannan.
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Affiliation(s)
- Kuikui Li
- Key Laboratory of Se-enriched Products Development and Quality Control, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Laboratory of Se-enriched Food Development, Ankang, 725000 Shaanxi China
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, CAS, Dalian, 116023 China
| | - Chaofeng Jiang
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, CAS, Dalian, 116023 China
| | - Haidong Tan
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, CAS, Dalian, 116023 China
| | - Junyan Li
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, CAS, Dalian, 116023 China
| | - Yali Xu
- Key Laboratory of Se-enriched Products Development and Quality Control, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Laboratory of Se-enriched Food Development, Ankang, 725000 Shaanxi China
| | - Dejian Tang
- Key Laboratory of Se-enriched Products Development and Quality Control, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Laboratory of Se-enriched Food Development, Ankang, 725000 Shaanxi China
| | - Xiaoming Zhao
- Key Laboratory of Se-enriched Products Development and Quality Control, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Laboratory of Se-enriched Food Development, Ankang, 725000 Shaanxi China
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, CAS, Dalian, 116023 China
| | - Qishun Liu
- Key Laboratory of Se-enriched Products Development and Quality Control, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Laboratory of Se-enriched Food Development, Ankang, 725000 Shaanxi China
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, CAS, Dalian, 116023 China
| | - Jianguo Li
- Key Laboratory of Se-enriched Products Development and Quality Control, Ministry of Agriculture and Rural Affairs, National-Local Joint Engineering Laboratory of Se-enriched Food Development, Ankang, 725000 Shaanxi China
- Ankang Agro-Tech Extension and Service Center, Ankang, 725000 Shaanxi China
| | - Heng Yin
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, CAS, Dalian, 116023 China
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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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