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Mao M, Ahrens L, Luka J, Contreras F, Kurkina T, Bienstein M, Sárria Pereira de Passos M, Schirinzi G, Mehn D, Valsesia A, Desmet C, Serra MÁ, Gilliland D, Schwaneberg U. Material-specific binding peptides empower sustainable innovations in plant health, biocatalysis, medicine and microplastic quantification. Chem Soc Rev 2024; 53:6445-6510. [PMID: 38747901 DOI: 10.1039/d2cs00991a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
Material-binding peptides (MBPs) have emerged as a diverse and innovation-enabling class of peptides in applications such as plant-/human health, immobilization of catalysts, bioactive coatings, accelerated polymer degradation and analytics for micro-/nanoplastics quantification. Progress has been fuelled by recent advancements in protein engineering methodologies and advances in computational and analytical methodologies, which allow the design of, for instance, material-specific MBPs with fine-tuned binding strength for numerous demands in material science applications. A genetic or chemical conjugation of second (biological, chemical or physical property-changing) functionality to MBPs empowers the design of advanced (hybrid) materials, bioactive coatings and analytical tools. In this review, we provide a comprehensive overview comprising naturally occurring MBPs and their function in nature, binding properties of short man-made MBPs (<20 amino acids) mainly obtained from phage-display libraries, and medium-sized binding peptides (20-100 amino acids) that have been reported to bind to metals, polymers or other industrially produced materials. The goal of this review is to provide an in-depth understanding of molecular interactions between materials and material-specific binding peptides, and thereby empower the use of MBPs in material science applications. Protein engineering methodologies and selected examples to tailor MBPs toward applications in agriculture with a focus on plant health, biocatalysis, medicine and environmental monitoring serve as examples of the transformative power of MBPs for various industrial applications. An emphasis will be given to MBPs' role in detecting and quantifying microplastics in high throughput, distinguishing microplastics from other environmental particles, and thereby assisting to close an analytical gap in food safety and monitoring of environmental plastic pollution. In essence, this review aims to provide an overview among researchers from diverse disciplines in respect to material-(specific) binding of MBPs, protein engineering methodologies to tailor their properties to application demands, re-engineering for material science applications using MBPs, and thereby inspire researchers to employ MBPs in their research.
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Affiliation(s)
- Maochao Mao
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Leon Ahrens
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Julian Luka
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Francisca Contreras
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Tetiana Kurkina
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Marian Bienstein
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | | | | | - Dora Mehn
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Andrea Valsesia
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | - Cloé Desmet
- European Commission, Joint Research Centre (JRC), Ispra, Italy
| | | | | | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
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Puginier C, Libourel C, Otte J, Skaloud P, Haon M, Grisel S, Petersen M, Berrin JG, Delaux PM, Dal Grande F, Keller J. Phylogenomics reveals the evolutionary origins of lichenization in chlorophyte algae. Nat Commun 2024; 15:4452. [PMID: 38789482 PMCID: PMC11126685 DOI: 10.1038/s41467-024-48787-z] [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: 10/25/2023] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Mutualistic symbioses have contributed to major transitions in the evolution of life. Here, we investigate the evolutionary history and the molecular innovations at the origin of lichens, which are a symbiosis established between fungi and green algae or cyanobacteria. We de novo sequence the genomes or transcriptomes of 12 lichen algal symbiont (LAS) and closely related non-symbiotic algae (NSA) to improve the genomic coverage of Chlorophyte algae. We then perform ancestral state reconstruction and comparative phylogenomics. We identify at least three independent gains of the ability to engage in the lichen symbiosis, one in Trebouxiophyceae and two in Ulvophyceae, confirming the convergent evolution of the lichen symbioses. A carbohydrate-active enzyme from the glycoside hydrolase 8 (GH8) family was identified as a top candidate for the molecular-mechanism underlying lichen symbiosis in Trebouxiophyceae. This GH8 was acquired in lichenizing Trebouxiophyceae by horizontal gene transfer, concomitantly with the ability to associate with lichens fungal symbionts (LFS) and is able to degrade polysaccharides found in the cell wall of LFS. These findings indicate that a combination of gene family expansion and horizontal gene transfer provided the basis for lichenization to evolve in chlorophyte algae.
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Affiliation(s)
- Camille Puginier
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, INP, Toulouse, 31320, Castanet-Tolosan, France
| | - Cyril Libourel
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, INP, Toulouse, 31320, Castanet-Tolosan, France
| | - Juergen Otte
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Pavel Skaloud
- Department of Botany, Faculty of Science, Charles University, Benátská 2, CZ-12800, Praha 2, Czech Republic
| | - Mireille Haon
- INRAE, Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques (BBF), 13009, Marseille, France
- INRAE, Aix Marseille Université, 3PE Platform, 13009, Marseille, France
| | - Sacha Grisel
- INRAE, Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques (BBF), 13009, Marseille, France
- INRAE, Aix Marseille Université, 3PE Platform, 13009, Marseille, France
| | - Malte Petersen
- High Performance Computing & Analytics Lab, University of Bonn, Friedrich-Hirzebruch-Allee 8, 53115, Bonn, Germany
| | - Jean-Guy Berrin
- INRAE, Aix Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques (BBF), 13009, Marseille, France
- INRAE, Aix Marseille Université, 3PE Platform, 13009, Marseille, France
| | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, INP, Toulouse, 31320, Castanet-Tolosan, France.
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.
- Department of Biology, University of Padova, Padua, Italy.
| | - Jean Keller
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, UPS, INP, Toulouse, 31320, Castanet-Tolosan, France.
- Department of Insect Symbiosis, Max Planck Institute for Chemical Ecology, 07745, Jena, Germany.
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Suzuki M, Saito A, Kobayashi M, Yokoyama T, Omiya S, Li J, Sugita K, Miki K, Saito JI, Ando A. Crystal structure of the GH-46 subclass III chitosanase from Bacillus circulans MH-K1 in complex with chitotetraose. Biochim Biophys Acta Gen Subj 2024; 1868:130549. [PMID: 38158023 DOI: 10.1016/j.bbagen.2023.130549] [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: 06/22/2023] [Revised: 12/12/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND Chitosanases (EC 3.2.1.132) hydrolyze chitosan which is a polymer of glucosamine (GlcN) linked by β - 1,4 bonds, and show cleavage specificity against partially acetylated chitosan containing N-acetylglucosamine (GlcNAc) residues. Chitosanases' structural underpinnings for cleavage specificity and the conformational switch from open to closed structures are still a mystery. METHODS The GH-46 subclass III chitosanase from Bacillus circulans MH-K1 (MH-K1 chitosanase), which also catalyzes the hydrolysis of GlcN-GlcNAc bonds in addition to GlcN-GlcN, has had its chitotetraose [(GlcN)4]-complexed crystal structure solved at 1.35 Å resolution. RESULTS The MH-K1 chitosanase's (GlcN)4-bound structure has numerous structural similarities to other GH-46 chitosanases in terms of substrate binding and catalytic processes. However, subsite -1, which is absolutely specific for GlcN, seems to characterize the structure of a subclass III chitosanase due to its distinctive length and angle of a flexible loop. According to a comparison of the (GlcN)4-bound and apo-form structures, the particular binding of a GlcN residue at subsite -2 through Asp77 causes the backbone helix to kink, which causes the upper- and lower-domains to approach closely when binding a substrate. CONCLUSIONS Although GH-46 chitosanases vary in the finer details of the subsites defining cleavage specificity, they share similar structural characteristics in substrate-binding, catalytic processes, and potentially in conformational change. GENERAL SIGNIFICANCE The precise binding of a GlcN residue to the -2 subsite is essential for the conformational shift that occurs in all GH-46 chitosanases, as shown by the crystal structures of the apo- and substrate-bound forms of MH-K1 chitosanase.
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Affiliation(s)
- Michihiko Suzuki
- Molecular Analysis Center, Research Unit, R&D Division, Kyowa Kirin, Sunto-gun, Shizuoka 411-8731, Japan
| | - Akihiro Saito
- Department of Nanobiology, Graduate School of Advanced and Integration Science, Chiba University, Matsudo, Chiba 271-8510, Japan; Department of Materials and Life Science, Faculty of Science and Technology, Shizuoka Institute of Science and Technology, Fukuroi, Shizuoka 437-8555, Japan.
| | - Mariko Kobayashi
- Department of Nanobiology, Graduate School of Advanced and Integration Science, Chiba University, Matsudo, Chiba 271-8510, Japan
| | - Tomofumi Yokoyama
- Department of Nanobiology, Graduate School of Advanced and Integration Science, Chiba University, Matsudo, Chiba 271-8510, Japan
| | - Shoko Omiya
- Department of Nanobiology, Graduate School of Advanced and Integration Science, Chiba University, Matsudo, Chiba 271-8510, Japan
| | - Jian Li
- Department of Nanobiology, Graduate School of Advanced and Integration Science, Chiba University, Matsudo, Chiba 271-8510, Japan
| | - Kei Sugita
- Department of Nanobiology, Graduate School of Advanced and Integration Science, Chiba University, Matsudo, Chiba 271-8510, Japan
| | - Kunio Miki
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Jun-Ichi Saito
- Molecular Analysis Center, Research Unit, R&D Division, Kyowa Kirin, Sunto-gun, Shizuoka 411-8731, Japan
| | - Akikazu Ando
- Department of Nanobiology, Graduate School of Advanced and Integration Science, Chiba University, Matsudo, Chiba 271-8510, Japan
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Sun H, Zhao L, Mao X, Cao R, Liu Q. Identification of a Key Loop for Tuning Transglycosylation Activity in the Substrate-Binding Region of a Chitosanase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:5585-5591. [PMID: 37000127 DOI: 10.1021/acs.jafc.3c00110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Csn-PD, a glycoside family 46 chitosanase from Paenibacillus dendritiformis, exhibits endotype hydrolysis of chitosan and produces (GlcN)2 as the major product. Here, we report the crystal structure of Csn-PD at 1.68 Å resolution. The structure contains 14 α-helices and two β-strands that fold into two globular domains with the substrate bound between them. To evaluate the function of a loop in the substrate-binding region (residues 112-116, NDKHP), a mutant Csn-PDL1, in which this loop was deleted, was generated. Hydrolysis of chitosan by the mutant yielded chitooligosaccharides (COSs) with higher degrees of polymerization (DP) than the wild-type enzyme. Excitingly, (GlcN)6 was produced from smaller COSs via transglycosylation activity of the mutant. Hence, the catalytic performance of a chitosanase was altered by modification of a loop in the substrate-binding regions. Our novel data on a chitosanase with transglycosylation activity offer a promising way to produce COSs with high DP.
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Affiliation(s)
- Huihui Sun
- Department of Food Engineering and Nutrition, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Ling Zhao
- Department of Food Engineering and Nutrition, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Xiangzhao Mao
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Rong Cao
- Department of Food Engineering and Nutrition, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Qi Liu
- Department of Food Engineering and Nutrition, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
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Wang Q, Liu S, Li K, Xing R, Chen X, Li P. A Computational Biology Study on the Structure and Dynamics Determinants of Thermal Stability of the Chitosanase from Aspergillus fumigatus. Int J Mol Sci 2023; 24:ijms24076671. [PMID: 37047643 PMCID: PMC10095384 DOI: 10.3390/ijms24076671] [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: 02/19/2023] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 04/14/2023] Open
Abstract
Environmentally friendly and efficient biodegradation with chitosanase for degrading chitosan to oligosaccharide has been gaining more importance. Here, we studied a chitosanase from Aspergillus fumigatus with potential for production, but does not have the ideal thermal stability. The structure predicted by the Alphafold2 model, especially the binding site and two catalytic residues, has been found to have a high similarity with the experimental structure of the chitosanase V-CSN from the same family. The effects of temperature on structure and function were studied by dynamic simulation and the results showed that the binding site had high flexibility. After heating up from 300 K to 350 K, the RMSD and RMSF of the binding site increased significantly, in particular, the downward shift of loop6 closed the binding site, resulting in the spatial hindrance of binding. The time proportions of important hydrogen bonds at the binding site decreased sharply, indicating that serious disruption of hydrogen bonds should be the main interaction factor for conformational changes. The residues contributing energetically to binding were also revealed to be in the highly flexible region, which inevitably leads to the decrease in the activity stability at high temperature. These findings provide directions for the modification of thermal stability and perspectives on the research of proteins without experimental structures.
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Affiliation(s)
- Qian Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Song Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Kecheng Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Ronge Xing
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Xiaolin Chen
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Pengcheng Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
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Mendonça M, Barroca M, Collins T. Endo-1,4-β-xylanase-containing glycoside hydrolase families: Characteristics, singularities and similarities. Biotechnol Adv 2023; 65:108148. [PMID: 37030552 DOI: 10.1016/j.biotechadv.2023.108148] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 04/02/2023] [Accepted: 04/04/2023] [Indexed: 04/09/2023]
Abstract
Endo-1,4-β-xylanases (EC 3.2.1.8) are O-glycoside hydrolases that cleave the internal β-1,4-D-xylosidic linkages of the complex plant polysaccharide xylan. They are produced by a vast array of organisms where they play critical roles in xylan saccharification and plant cell wall hydrolysis. They are also important industrial biocatalysts with widespread application. A large and ever growing number of xylanases with wildly different properties and functionalites are known and a better understanding of these would enable a more effective use in various applications. The Carbohydrate-Active enZYmes database (CAZy), which classifies evolutionarily related proteins into a glycoside hydrolase family-subfamily organisational scheme has proven powerful in understanding these enzymes. Nevertheless, ambiguity currently exists as to the number of glycoside hydrolase families and subfamilies harbouring catalytic domains with true endoxylanase activity and as to the specific characteristics of each of these families/subfamilies. This review seeks to clarify this, identifying 9 glycoside hydrolase families containing enzymes with endo-1,4-β-xylanase activity and discussing their properties, similarities, differences and biotechnological perspectives. In particular, substrate specificities and hydrolysis patterns and the structural determinants of these are detailed, with taxonomic aspects of source organisms being also presented. Shortcomings in current knowledge and research areas that require further clarification are highlighted and suggestions for future directions provided. This review seeks to motivate further research on these enzymes and especially of the lesser known endo-1,4-β-xylanase containing families. A better understanding of these enzymes will serve as a foundation for the knowledge-based development of process-fitted endo-1,4-β-xylanases and will accelerate their development for use with even the most recalcitrant of substrates in the biobased industries of the future.
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Zhang RX, Wu ZW, Zhang SJ, Wei HM, Hua CW, Li L, Yang TY. Gene cloning and molecular characterization of a thermostable chitosanase from Bacillus cereus TY24. BMC Biotechnol 2022; 22:30. [PMID: 36303174 PMCID: PMC9615241 DOI: 10.1186/s12896-022-00762-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 10/18/2022] [Indexed: 11/24/2022] Open
Abstract
Background An important conceptual advance in health and the environment has been recognized that enzymes play a key role in the green processing industries. Of particular interest, chitosanase is beneficial for recycling the chitosan resource and producing chitosan oligosaccharides. Also, chitosan gene expression and molecular characterization will promote understanding of the biological function of bacterial chitosanase as well as explore chitosanase for utilizing chitosan resources. Results A chitosanase-producing bacterium TY24 was isolated and identified as Bacillus cereus. Moreover, the chitosanase gene was cloned and expressed in Escherichia coli. Sequence analysis reveals that the recombinant chitosanase (CHOE) belongs to the glycoside hydrolases 8 family. The purified CHOE has a molecular weight of about 48 kDa and the specific activity of 1150 U/mg. The optimal pH and temperature of CHOE were 5.5 and 65 °C, respectively. The enzyme was observed stable at the pH range of 4.5–7.5 and the temperature range of 30–65 °C. Especially, the half-life of CHOE at 65 °C was 161 min. Additionally, the activity of CHOE was remarkably enhanced in the presence of Mn2+, Cu2+, Mg2+ and K+, beside Ca2+ at 5 mM. Especially, the activity of CHOE was enhanced to more than 120% in the presence of 1% of various surfactants. CHOE exhibited the highest substrate specificity toward colloid chitosan. Conclusion A bacterial chitosanase was cloned from B. cereus and successfully expressed in E. coli (BL21) DE3. The recombinant enzyme displayed good stability under acid pH and high-temperature conditions. Supplementary Information The online version contains supplementary material available at 10.1186/s12896-022-00762-6.
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Affiliation(s)
- Rong-Xian Zhang
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, People's Republic of China.
| | - Zhong-Wei Wu
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, People's Republic of China
| | - Shu-Juan Zhang
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, People's Republic of China
| | - Hui-Min Wei
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, People's Republic of China
| | - Cheng-Wei Hua
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, People's Republic of China
| | - Lan Li
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, People's Republic of China
| | - Tian-You Yang
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, People's Republic of China
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Su H, Sun J, Jia Z, Zhao H, Mao X. Insights into promiscuous chitosanases: the known and the unknown. Appl Microbiol Biotechnol 2022; 106:6887-6898. [PMID: 36178516 DOI: 10.1007/s00253-022-12198-1] [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: 05/18/2022] [Revised: 09/18/2022] [Accepted: 09/21/2022] [Indexed: 11/30/2022]
Abstract
Chitosanase, a glycoside hydrolase (GH), catalyzes the cleavage of β-1,4-glycosidic bonds in polysaccharides and is widely distributed in nature. Many organisms produce chitosanases, and numerous chitosanases in the GH families have been intensely studied. The reported chitosanases mainly cleaved the inter-glucosamine glycosidic bonds, while substrate specificity is not strictly unique due to the existence of bifunctional or multifunctional activity profiles. The promiscuity of chitosanases is essential for the different pathways of biomass polysaccharide conversion and understanding of the chitosanase evolutionary process. However, the reviews for this aspect are completely unknown. This review provides an overview of the promiscuous activities, also considering the substrate and product specificity of chitosanases observed to date. These contribute to important implications for the future discovery and research of promiscuous chitosanases and applications related to biomass conversion. KEY POINTS: • The promiscuity of chitosanases is reviewed for the first time. • The current review provides insights into the substrate specificity of chitosanases. • The mode-product relationship and prospect of promiscuous chitosanases are highlighted.
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Affiliation(s)
- Haipeng Su
- College of Food Science and Engineering, Ocean University of China, No. 5 Yushan Road, Qingdao, 266003, China
| | - Jianan Sun
- College of Food Science and Engineering, Ocean University of China, No. 5 Yushan Road, Qingdao, 266003, China
| | - Zhenrong Jia
- College of Food Science and Engineering, Ocean University of China, No. 5 Yushan Road, Qingdao, 266003, China
| | - Hongjun Zhao
- College of Food Science and Engineering, Ocean University of China, No. 5 Yushan Road, Qingdao, 266003, China
| | - Xiangzhao Mao
- College of Food Science and Engineering, Ocean University of China, No. 5 Yushan Road, Qingdao, 266003, China. .,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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Xu Y, Li L, Cao S, Zhu B, Yao Z. An updated comprehensive review of advances on structural features, catalytic mechanisms, modification methods and applications of chitosanases. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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10
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Le Wang, Zhang XJ, Li YH. A Novel Reducing-end Xylose-releasing Exo-oligoxylanase (PphRex8A) from Paenibacillus physcomitrellae XB. Enzyme Microb Technol 2022; 160:110086. [DOI: 10.1016/j.enzmictec.2022.110086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 05/22/2022] [Accepted: 06/15/2022] [Indexed: 11/03/2022]
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Su H, Sun J, Guo C, Jia Z, Mao X. New Insights into Bifunctional Chitosanases with Hydrolysis Activity toward Chito- and Cello-Substrates. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:6168-6176. [PMID: 35549271 DOI: 10.1021/acs.jafc.2c01577] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In the present study, we carried out a comprehensive investigation of glycoside hydrolase (GH) 46 model-chitosanases based on cleavage specificity classification to understand their unknown bifunctional activity. We for the first time show that GH46 chitosanase CsnMHK1 from Bacillus circulans MH-K1, which was previously thought to be strictly exclusive to chitosan, can hydrolyze both chito- and cello-substrates. We determined the digestion direction of bifunctional chitosanase CsnMHK1 from class III and compared it with class II chitosanase belonging to GH8, providing insight into unique substrate specificities and a new perspective on its reclassification. The results lead us to challenge the current understanding of chitosanase substrate specificity based on GH taxonomy classification and suggest that the prevalence from the common bifunctional activity may have occurred. Altogether, these data contribute to the understanding of chitosanase recognition and hydrolysis toward chito- and cello-substrates, which is valuable for future studies on chitosanases.
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Affiliation(s)
- Haipeng Su
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Jianan Sun
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Chaoran Guo
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Zhenrong Jia
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Xiangzhao Mao
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
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12
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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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13
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Huang Z, Ni G, Zhao X, Wang F, Qu M. Characterization of a GH8 β-1,4-Glucanase from Bacillus subtilis B111 and Its Saccharification Potential for Agricultural Straws. J Microbiol Biotechnol 2021; 31:1446-1454. [PMID: 34409950 PMCID: PMC9705894 DOI: 10.4014/jmb.2105.05026] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/11/2021] [Accepted: 08/19/2021] [Indexed: 12/15/2022]
Abstract
Herein, we cloned and expressed an endo-β-1,4-glucanase gene (celA1805) from Bacillus subtilis B111 in Escherichia coli. The recombinant celA1805 contains a glycosyl hydrolase (GH) family 8 domain and shared 76.8% identity with endo-1,4-β-glucanase from Bacillus sp. KSM-330. Results showed that the optimal pH and temperature of celA1805 were 6.0 and 50°C, respectively, and it was stable at pH 3-9 and temperature ≤50°C. Metal ions slightly affected enzyme activity, but chemical agents generally inhibited enzyme activity. Moreover, celA1805 showed a wide substrate specificity to CMC, barley β-glucan, lichenin, chitosan, PASC and avicel. The Km and Vmax values of celA1805 were 1.78 mg/ml and 50.09 μmol/min/mg. When incubated with cellooligosaccharides ranging from cellotriose to cellopentose, celA1805 mainly hydrolyzed cellotetrose (G4) and cellopentose (G5) to cellose (G2) and cellotriose (G3), but hardly hydrolyzed cellotriose. The concentrations of reducing sugars saccharified by celA1805 from wheat straw, rape straw, rice straw, peanut straw, and corn straw were increased by 0.21, 0.51, 0.26, 0.36, and 0.66 mg/ml, respectively. The results obtained in this study suggest potential applications of celA1805 in biomass saccharification.
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Affiliation(s)
- Zhen Huang
- Key Laboratory of Animal Nutrition of Jiangxi Province, Nutritional Feed Development Engineering Research Center, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R. China
| | - Guorong Ni
- College of Land Resources and Environment, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R. China
| | - Xiaoyan Zhao
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R. China
| | - Fei Wang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R. China,Corresponding author F. Wang Phone/Fax: +86 791 83813459 E-mail:
| | - Mingren Qu
- Key Laboratory of Animal Nutrition of Jiangxi Province, Nutritional Feed Development Engineering Research Center, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R. China,
M. Qu E-mail:
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14
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Zhou Z, Wang X. Improve thermostability of Bacillus sp. TS chitosanase through structure-based alignment. Sci Rep 2021; 11:15846. [PMID: 34349190 PMCID: PMC8339078 DOI: 10.1038/s41598-021-95369-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/26/2021] [Indexed: 11/22/2022] Open
Abstract
Chitosanases can catalyze the release of chitooligosaccharides which have a number of medical applications. Therefore, Chitosanases are good candidates for large-scale enzymatic synthesis due to their favorable thermostability properties and high catalytic efficiency. To further improve the thermostability of a chitosanase from Bacillus sp. TS, which has a half-life of 5.32 min, we mutated specific serine residues that we identified as potentially relevant through structure comparison with thermophilic CelA from Clostridium thermocellum. Out of a total of 15 mutants, three, namely S265G, S276A, and S347G, show higher thermostability. Their half-lives at 60 °C were calculated as 34.57 min, 36.79 min and 7.2 min. The Km values of S265G, S276A and S347G mutants show substrate binding ability comparable to that of the wild-type enzyme, while the S265G mutant displays a significant decrease of enzymatic activities. Additionally, we studied the synergistic effects of combined mutations, observing that all double mutants and the triple mutant are more stable than the wild-type enzyme and single mutants. Finally, we investigated the mechanisms which might give a reasonable explanation for the improved thermostability via comparative analysis of the resulting 3D structures.
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Affiliation(s)
- Zhanping Zhou
- Tianjin Sinonocy Biological Technology Co. Ltd., Tianjin, 300308, China
| | - Xiao Wang
- Nanfang College of Sun Yat-Sen University, Guangzhou, 510970, China.
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15
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Jiang Z, Ma S, Guan L, Yan Q, Yang S. Biochemical characterization of a novel bifunctional chitosanase from Paenibacillus barengoltzii for chitooligosaccharide production. World J Microbiol Biotechnol 2021; 37:83. [PMID: 33855634 DOI: 10.1007/s11274-021-03051-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 04/07/2021] [Indexed: 10/21/2022]
Abstract
A novel chitosanase gene, designated as PbCsn8, was cloned from Paenibacillus barengoltzii. It shared the highest identity of 73% with the glycoside hydrolase (GH) family 8 chitosanase from Bacillus thuringiensis JAM-GG01. The gene was heterologously expressed in Bacillus subtilis as an extracellular protein, and the highest chitosanase yield of 1, 108 U/mL was obtained by high-cell density fermentation in a 5-L fermentor. The recombinant chitosanase (PbCsn8) was purified to homogeneity and biochemically characterized. PbCsn8 was most active at pH 5.5 and 70 °C, respectively. It was stable in a wide pH range of 5.0-11.0 and up to 55 °C. PbCsn8 was a bifunctional enzyme, exhibiting both chitosanase and glucanase activities, with the highest specificity towards chitosan (360 U/mg), followed by barley β-glucan (72 U/mg) and lichenan (13 U/mg). It hydrolyzed chitosan to release mainly chitooligosaccharides (COSs) with degree of polymerization (DP) 2-3, while hydrolyzed barley β-glucan to yield mainly glucooligosaccharides with DP > 5. PbCsn8 was further applied in COS production, and the highest COS yield of 79.3% (w/w) was obtained. This is the first report on a GH family 8 chitosanase from P. barengoltzii. The high yield and remarkable hydrolysis properties may make PbCsn8 a good candidate in industrial application.
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Affiliation(s)
- Zhenqiang Jiang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Suai Ma
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Leying Guan
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Qiaojuan Yan
- College of Engineering, China Agricultural University, Beijing, 100083, China
| | - Shaoqing Yang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
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16
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Bhuvanachandra B, Sivaramakrishna D, Alim S, Preethiba G, Rambabu S, Swamy MJ, Podile AR. New Class of Chitosanase from Bacillus amyloliquefaciens for the Generation of Chitooligosaccharides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:78-87. [PMID: 33393308 DOI: 10.1021/acs.jafc.0c05078] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Chitooligosaccharides (COS) generated from either chitin (chitin oligosaccharides) or chitosan (chitosan oligosaccharides) have a wide range of applications in agriculture, medicine, and other fields. Here, we report the characterization of a chitosanase from Bacillus amyloliquefaciens (BamCsn) and the importance of a tryptophan (Trp), W204, for BamCsn activity. BamCsn hydrolyzed the chitosan polymer by an endo mode. It also hydrolyzed chitin oligosaccharides and interestingly exhibited transglycosylation activity on chitotetraose and chitopentaose. Mutation of W204, a nonconserved amino acid in chitosanases, to W204A abolished the hydrolytic activity of BamCsn, with a change in the structure that resulted in a decreased affinity for the substrate and impaired the catalytic ability. Phylogenetic analysis revealed that BamCsn could belong to a new class of chitosanases that showed unique properties like transglycosylation, cleavage of chitin oligosaccharides, and the presence of W204 residues, which is important for activity. Chitosanases belonging to the BamCsn class showed a high potential to generate COS from chitinous substrates.
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Affiliation(s)
- Bhoopal Bhuvanachandra
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500 046, Telangana, India
| | - Dokku Sivaramakrishna
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500 046, Telangana, India
| | - Sk Alim
- School of Chemistry, University of Hyderabad, Gachibowli, Hyderabad 500 046, Telangana, India
| | - Gopi Preethiba
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500 046, Telangana, India
| | - Samudrala Rambabu
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500 046, Telangana, India
| | - Musti J Swamy
- School of Chemistry, University of Hyderabad, Gachibowli, Hyderabad 500 046, Telangana, India
| | - Appa Rao Podile
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500 046, Telangana, India
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17
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Wang Y, Qin Z, Fan L, Zhao L. Structure-function analysis of Gynuella sunshinyii chitosanase uncovers the mechanism of substrate binding in GH family 46 members. Int J Biol Macromol 2020; 165:2038-2048. [PMID: 33080262 DOI: 10.1016/j.ijbiomac.2020.10.066] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/21/2020] [Accepted: 10/09/2020] [Indexed: 01/10/2023]
Abstract
Chitooligosaccharides (COS) is a kind of functional carbohydrates with great application potential as its various biological functions in food, cosmetics, and pharmaceutical fields. Exploring the relationship between structure and function of chitosanase is essential for the controllable preparation of chitooligosaccharides with the specific degree of polymerization (DP). GsCsn46A is a cold-adapted glycosyl hydrolase (GH) family 46 chitosanase with application potential for the controllable preparation of chitooligosaccharides. Here, we present two complex structures with substrate chitopentaose and chitotetraose of GsCsn46A, respectively. The overall structure of GsCsn46A contains nine α-helices and two β-strands that folds into two globular domains with the substrate between them. The unique binding positions of both chitopentaose and chitotetraose revealed two novel sugar residues in the negatively-numbered subsites of GH family 46 chitosanases. The structure-function analysis of GsCsn46A uncovers the substrate binding and catalysis mechanism of GH family 46 chitosanases. Structural basis mutagenesis in GsCsn46A indicated that altering interactions near +3 subsite would help produce hydrolysis products with higher DP. Specifically, the mutant N21W of GsCsn46A nearly eliminated the ability of hydrolyzing chitotetraose after long-time degradation.
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Affiliation(s)
- Yani Wang
- School of Biotechnology, State Key Laboratory of Bioreactor Engineering, R&D Center of Separation and Extraction Technology in Fermentation Industry, East China University of Science and Technology, Shanghai 200237, China
| | - Zhen Qin
- School of Life Science, Shanghai University, Shanghai 200444, China
| | - Liqiang Fan
- School of Biotechnology, State Key Laboratory of Bioreactor Engineering, R&D Center of Separation and Extraction Technology in Fermentation Industry, East China University of Science and Technology, Shanghai 200237, China
| | - Liming Zhao
- School of Biotechnology, State Key Laboratory of Bioreactor Engineering, R&D Center of Separation and Extraction Technology in Fermentation Industry, East China University of Science and Technology, Shanghai 200237, China; Shanghai Collaborative Innovation Center for Biomanufacturing Technology (SCICBT), Shanghai 200237, China.
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18
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Sun H, Gao L, Xue C, Mao X. Marine-polysaccharide degrading enzymes: Status and prospects. Compr Rev Food Sci Food Saf 2020; 19:2767-2796. [PMID: 33337030 DOI: 10.1111/1541-4337.12630] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 08/04/2020] [Accepted: 08/06/2020] [Indexed: 12/19/2022]
Abstract
Marine-polysaccharide degrading enzymes have recently been studied extensively. They are particularly interesting as they catalyze the cleavage of glycosidic bonds in polysaccharide macromolecules and produce oligosaccharides with low degrees of polymerization. Numerous findings have demonstrated that marine polysaccharides and their biotransformed products possess beneficial properties including antitumor, antiviral, anticoagulant, and anti-inflammatory activities, and they have great value in healthcare, cosmetics, the food industry, and agriculture. Exploitation of enzymes that can degrade marine polysaccharides is in the ascendant, and is important for high-value use of marine biomass resources. In this review, we describe research and prospects regarding the classification, biochemical properties, and catalytic mechanisms of the main types of marine-polysaccharide degrading enzymes, focusing on chitinase, chitosanase, alginate lyase, agarase, and carrageenase, and their product oligosaccharides. The state-of-the-art discussion of marine-polysaccharide degrading enzymes and their properties offers information that might enable more efficient production of marine oligosaccharides. We also highlight current problems in the field of marine-polysaccharide degrading enzymes and trends in their development. Understanding the properties, catalytic mechanisms, and modification of known enzymes will aid the identification of novel enzymes to degrade marine polysaccharides and facilitation of their use in various biotechnological processes.
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Affiliation(s)
- Huihui Sun
- College of Food Science and Engineering, Ocean University of China, Qingdao, China.,Department of Food Engineering and Nutrition, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Li Gao
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Changhu Xue
- College of Food Science and Engineering, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiangzhao Mao
- College of Food Science and Engineering, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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19
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Jiménez‐Ortega E, Valenzuela S, Ramírez‐Escudero M, Pastor FJ, Sanz‐Aparicio J. Structural analysis of the reducing‐end xylose‐releasing exo‐oligoxylanase Rex8A from
Paenibacillus barcinonensis
BP‐23 deciphers its molecular specificity. FEBS J 2020; 287:5362-5374. [DOI: 10.1111/febs.15332] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/27/2020] [Accepted: 04/09/2020] [Indexed: 12/26/2022]
Affiliation(s)
- Elena Jiménez‐Ortega
- Macromolecular Crystallography and Structural Biology Department Institute of Physical‐Chemistry ‘Rocasolano’ CSIC Madrid Spain
| | - Susana Valenzuela
- Department of Microbiology Faculty of Biology University of Barcelona Spain
- Institute of Nanoscience and Nanotechnology (IN2UB) University of Barcelona Spain
| | - Mercedes Ramírez‐Escudero
- Macromolecular Crystallography and Structural Biology Department Institute of Physical‐Chemistry ‘Rocasolano’ CSIC Madrid Spain
| | - Francisco Javier Pastor
- Department of Microbiology Faculty of Biology University of Barcelona Spain
- Institute of Nanoscience and Nanotechnology (IN2UB) University of Barcelona Spain
| | - Julia Sanz‐Aparicio
- Macromolecular Crystallography and Structural Biology Department Institute of Physical‐Chemistry ‘Rocasolano’ CSIC Madrid Spain
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20
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Regel EK, Evers M, Liss M, Cord-Landwehr S, Moerschbacher BM. High-Throughput Screening Using UHPLC-MS To Characterize the Subsite Specificities of Chitosanases or Chitinases. Anal Chem 2020; 92:3246-3252. [PMID: 31940178 DOI: 10.1021/acs.analchem.9b05049] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Partially acetylated chitosan oligosaccharides (paCOS), consisting of β-1,4-linked N-acetyl-d-glucosamine and d-glucosamine units, possess diverse bioactivities that can be used for applications in, e.g., biomedicine, agriculture, and pharmaceutics. Establishing structure-function relationships and revealing modes of action requires the availability of structurally defined paCOS that can best be produced using chitin- and chitosan-modifying enzymes, such as chitinases and chitosanases, with known and defined subsite specificities. To enlarge the spectrum of such enzymes and, consequently, defined paCOS available, we have developed a two-step, microtiter plate-based high-throughput screening assay that allows quantification of the activity and subsite specificities of chitosan hydrolases. In a first step, the activities of the enzymes are quantified using a reducing end assay, and enzymes with sufficient activity are then screened for their subsite specificities using mass spectrometric analysis of their products when acting on well-defined chitosan polymers as substrates. The rapid UHPLC-ELSD-ESI-MS2 method does not require labeling steps or addition of standards, and the principal component analysis of the fragment ion intensities of just two isomeric oligomer groups, GlcNAc1GlcN3 and GlcNAc2GlcN2, sufficed to identify, in a directed evolution, the site-saturation mutagenesis library of Bacillus sp. MN chitosanase consisting of 167 muteins, enzymes that significantly differed in their subsite specificities from the wildtype enzyme. Detailed analyses of a few selected muteins proved that the screening method is efficient and accurate in predicting altered subsite specificities.
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Affiliation(s)
- Eva K Regel
- Institute for Biology and Biotechnology of Plants , University of Münster , Schlossplatz 8 , 48143 Münster , Germany
| | - Maximilian Evers
- Institute for Biology and Biotechnology of Plants , University of Münster , Schlossplatz 8 , 48143 Münster , Germany
| | - Michael Liss
- Thermo Fisher Scientific GENEART GmbH , Im Gewerbepark B35 , 93059 Regensburg , Germany
| | - Stefan Cord-Landwehr
- Institute for Biology and Biotechnology of Plants , University of Münster , Schlossplatz 8 , 48143 Münster , Germany
| | - Bruno M Moerschbacher
- Institute for Biology and Biotechnology of Plants , University of Münster , Schlossplatz 8 , 48143 Münster , Germany
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21
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Chen F, Ye J, Sista Kameshwar AK, Wu X, Ren J, Qin W, Li DW. A Novel Cold-Adaptive Endo-1,4-β-Glucanase From Burkholderia pyrrocinia JK-SH007: Gene Expression and Characterization of the Enzyme and Mode of Action. Front Microbiol 2020; 10:3137. [PMID: 32038571 PMCID: PMC6987409 DOI: 10.3389/fmicb.2019.03137] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 12/26/2019] [Indexed: 11/30/2022] Open
Abstract
The efficient industrial conversion of plant-derived cellulose to simple sugars and other value-added chemicals requires various highly stable and reactive enzymes. Industrial processes especially synchronous saccharification and fermentation (SSF)-based production of cellulosic bio-ethanol require enzymes that are active at lower temperatures. In this study, we have identified, characterized, and expressed the cold-adaptive endo-1,4-β-glucanase (BpEG) isolated from the Burkholderia pyrrocinia JK-SH007. The analysis of the predicted amino acid sequence indicated that BpEG belongs to GH family 8. The BpEG without the signal peptide was cloned into the expression vector pET32a and significantly expressed in Escherichia coli BL21 (DE3) competent cells. The SDS-PAGE and Western blot analysis of BpEG revealed that the recombinant BpEG was approximately 60 kDa. Purified recombinant BpEG exhibited hydrolytic activity against carboxymethyl cellulose (CMC) and phosphoric acid swollen cellulose (PASC), but not crystalline cellulose and xylan substrates. High performance, anion exchange, chromatography-pulsed amperometric detector (HPAEC-PAD) analysis of the enzymatic products obtained from depolymerization of 1,4-β-linked biopolymers of different lengths revealed an interesting cutting mechanism employed by endoglucanases. The recombinant BpEG exhibited 6.0 of optimum pH and 35°C of optimum temperature, when cultured with CMC substrate. The BpEG enzyme exhibited stable activity between pH 5.0 and 9.0 at 35°C. Interestingly, BpEG retained about 42% of its enzymatic activity at 10°C compared to its optimal temperature. This new cold-adaptive cellulase could potentially achieve synchronous saccharification and fermentation (SSF) making BpEG a promising candidate in the fields of biofuel, biorefining, food and pharmaceutical industries.
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Affiliation(s)
- Feifei Chen
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Co-innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China.,Department of Biology, Lakehead University, Thunder Bay, ON, Canada
| | - Jianren Ye
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Co-innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | | | - Xuelian Wu
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Co-innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Jiahong Ren
- Department of Biology Science and Technology, Changzhi College, Changzhi, China
| | - Wensheng Qin
- Department of Biology, Lakehead University, Thunder Bay, ON, Canada
| | - De-Wei Li
- Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Co-innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China.,The Connecticut Agricultural Experiment Station, Valley Laboratory, Windsor, CT, United States
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22
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Yang G, Sun H, Cao R, Liu Q, Mao X. Characterization of a novel glycoside hydrolase family 46 chitosanase, Csn-BAC, from Bacillus sp. MD-5. Int J Biol Macromol 2020; 146:518-523. [PMID: 31917207 DOI: 10.1016/j.ijbiomac.2020.01.031] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 01/03/2020] [Accepted: 01/04/2020] [Indexed: 10/25/2022]
Abstract
Chitosanases play an important role in chitosan degradation, and the enzymatic degradation products of chitosan show various biological activities. Here, a novel glycoside hydrolase family 46 chitosanase (named Csn-BAC) from Bacillus sp. MD-5 was heterologously expressed in Escherichia coli BL21 (DE3). The recombinant enzyme was purified by Ni-NTA affinity chromatography, and its molecular weight was estimated to be 35 kDa by SDS-PAGE. Csn-BAC showed maximal activity toward colloidal chitosan at pH 7 and 40 °C. The enzymatic activity of Csn-BAC was enhanced by Mn2+, Cu2+ and Co2+ at 1 mM, and by Mn2+ at 5 mM. Thin-layer chromatography and electrospray ionization-mass spectrometry results demonstrated that Csn-BAC exhibited an endo-type cleavage pattern and hydrolyzed chitosan to yield, mainly, (GlcN)2 and (GlcN)3. The enzymatic properties of this chitosanase may make it a good candidate for use in oligosaccharide production-based industries.
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Affiliation(s)
- Guosong Yang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Huihui Sun
- Department of Food Engineering and Nutrition, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Rong Cao
- Department of Food Engineering and Nutrition, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
| | - Qi Liu
- Department of Food Engineering and Nutrition, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Xiangzhao Mao
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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23
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A thermostable GH8 endoglucanase of Enterobacter sp. R1 is suitable for β-glucan deconstruction. Food Chem 2019; 298:124999. [DOI: 10.1016/j.foodchem.2019.124999] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 06/09/2019] [Accepted: 06/11/2019] [Indexed: 12/13/2022]
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24
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Gercke D, Regel EK, Singh R, Moerschbacher BM. Rational protein design of Bacillus sp. MN chitosanase for altered substrate binding and production of specific chitosan oligomers. J Biol Eng 2019; 13:23. [PMID: 30918529 PMCID: PMC6419424 DOI: 10.1186/s13036-019-0152-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/21/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Partially acetylated chito-oligosaccharides (paCOS) have a variety of potential applications in different fields, but to harness their benefits, pure paCOS or well-defined paCOS mixtures are essential. For example, if one could produce fully acetylated (A4) and fully deacetylated (D4) tetramers in abundance, all possible variants of tetrameric paCOS could be generated reliably from them. A promising approach for generating defined paCOS is by enzymatic depolymerization of chitosan polymers using chitosanases, since these enzymes' subsite specificities directly influence the composition of the paCOS produced; however, enzymatic production of e.g. D4 is challenging because the substrate is generally hydrolyzed further by most chitosanases. To overcome this, chitosanases could potentially be engineered so that upon hydrolyzing chitosan, they are unable to hydrolyze certain substrates, leaving well-defined oligomers intact in the hydrolysate. RESULTS For this purpose, we performed rational protein engineering on the extensively studied GH 8 chitosanase CSN from Bacillus sp. MN. By specifically targeting residues with a predicted function in substrate binding, we created new muteins incapable of efficiently hydrolyzing the fully deacetylated tetramer D4, and we were able to demonstrate efficient large-scale production of D4 with an altered version of CSN. Furthermore, we were able to uncover differences in the substrate positioning and subsite specificities of the muteins, which result in altered paCOS mixtures produced from partially acetylated chitosan polymers, with possibly altered bioactivities. CONCLUSION The value of protein engineering as a tool for the more efficient production of pure oligomers and potentially bioactive paCOS mixtures was demonstrated by the results and the suitability of specific muteins for the large-scale production of strictly defined, pure paCOS in a batch process was shown using the example of D4.
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Affiliation(s)
- David Gercke
- University of Muenster, Institute for Biology and Biotechnology of Plants, Schlossplatz 8, 48143 Münster, Germany
| | - Eva K. Regel
- University of Muenster, Institute for Biology and Biotechnology of Plants, Schlossplatz 8, 48143 Münster, Germany
| | - Ratna Singh
- University of Muenster, Institute for Biology and Biotechnology of Plants, Schlossplatz 8, 48143 Münster, Germany
| | - Bruno M. Moerschbacher
- University of Muenster, Institute for Biology and Biotechnology of Plants, Schlossplatz 8, 48143 Münster, Germany
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Singh R, Weikert T, Basa S, Moerschbacher BM. Structural and biochemical insight into mode of action and subsite specificity of a chitosan degrading enzyme from Bacillus spec. MN. Sci Rep 2019; 9:1132. [PMID: 30718524 PMCID: PMC6362164 DOI: 10.1038/s41598-018-36213-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 11/14/2018] [Indexed: 12/14/2022] Open
Abstract
Chitosans, partially de-N-acetylated derivatives of chitin, are multifunctional biopolymers. In nature, biological activities of partially acetylated chitosan polymers are mediated in part by their oligomeric breakdown products, which are generated in situ by the action of chitosanolytic enzymes. Understanding chitosanolytic enzymes, therefore, can lead to the production of chitosan oligomers with fully defined structures that may confer specific bioactivities. To address whether defined oligomer products can be produced via chitosanolytic enzymes, we here characterized a GH8 family chitosanase from Bacillus spec. MN, determining its mode of action and product profiles. We found that the enzyme has higher activity towards polymers with lower degree of acetylation. Oligomeric products were dominated by GlcN3, GlcN3GlcNAc1, and GlcN4GlcNAc1. The product distribution from oligomers were GlcN3 > GlcN2. Modeling and simulations show that the binding site comprises subsites ranging from (-3) to (+3), and a putative (+4) subsite, with defined preferences for GlcN or GlcNAc at each subsite. Flexible loops at the binding site facilitate enzyme-substrate interactions and form a cleft at the active site which can open and close. The detailed insight gained here will help to engineer enzyme variants to produce tailored chitosan oligomers with defined structures that can then be used to probe their specific biological activities.
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Affiliation(s)
- Ratna Singh
- Institute for Biology and Biotechnology of Plants, University of Münster, Schlossplatz 8, 48143, Münster, Germany
| | - Tobias Weikert
- Institute for Biology and Biotechnology of Plants, University of Münster, Schlossplatz 8, 48143, Münster, Germany
| | - Sven Basa
- Institute for Biology and Biotechnology of Plants, University of Münster, Schlossplatz 8, 48143, Münster, Germany
| | - Bruno M Moerschbacher
- Institute for Biology and Biotechnology of Plants, University of Münster, Schlossplatz 8, 48143, Münster, Germany.
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26
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Cloning, purification and characterization of a novel GH46 family chitosanase, Csn-CAP, from Staphylococcus capitis. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.09.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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27
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Fowler CA, Hemsworth GR, Cuskin F, Hart S, Turkenburg J, Gilbert HJ, Walton PH, Davies GJ. Structure and function of a glycoside hydrolase family 8 endoxylanase from Teredinibacter turnerae. Acta Crystallogr D Struct Biol 2018; 74:946-955. [PMID: 30289404 PMCID: PMC6173055 DOI: 10.1107/s2059798318009737] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/09/2018] [Indexed: 12/13/2022] Open
Abstract
The biological conversion of lignocellulosic matter into high-value chemicals or biofuels is of increasing industrial importance as the sector slowly transitions away from nonrenewable sources. Many industrial processes involve the use of cellulolytic enzyme cocktails - a selection of glycoside hydrolases and, increasingly, polysaccharide oxygenases - to break down recalcitrant plant polysaccharides. ORFs from the genome of Teredinibacter turnerae, a symbiont hosted within the gills of marine shipworms, were identified in order to search for enzymes with desirable traits. Here, a putative T. turnerae glycoside hydrolase from family 8, hereafter referred to as TtGH8, is analysed. The enzyme is shown to be active against β-1,4-xylan and mixed-linkage (β-1,3,β-1,4) marine xylan. Kinetic parameters, obtained using high-performance anion-exchange chromatography with pulsed amperometric detection and 3,5-dinitrosalicyclic acid reducing-sugar assays, show that TtGH8 catalyses the hydrolysis of β-1,4-xylohexaose with a kcat/Km of 7.5 × 107 M-1 min-1 but displays maximal activity against mixed-linkage polymeric xylans, hinting at a primary role in the degradation of marine polysaccharides. The three-dimensional structure of TtGH8 was solved in uncomplexed and xylobiose-, xylotriose- and xylohexaose-bound forms at approximately 1.5 Å resolution; the latter was consistent with the greater kcat/Km for hexasaccharide substrates. A 2,5B boat conformation observed in the -1 position of bound xylotriose is consistent with the proposed conformational itinerary for this class of enzyme. This work shows TtGH8 to be effective at the degradation of xylan-based substrates, notably marine xylan, further exemplifying the potential of T. turnerae for effective and diverse biomass degradation.
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Affiliation(s)
- Claire A. Fowler
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Glyn R. Hemsworth
- School of Molecular and Cellular Biology, The Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, England
| | - Fiona Cuskin
- School of Natural and Environmental Science, Newcastle University, Newcastle upon Tyne NE1 7RU, England
| | - Sam Hart
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Johan Turkenburg
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Harry J. Gilbert
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, England
| | - Paul H. Walton
- Department of Chemistry, The University of York, York YO10 5DD, England
| | - Gideon J. Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
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Regel EK, Weikert T, Niehues A, Moerschbacher BM, Singh R. Protein-engineering of chitosanase from Bacillus sp. MN to alter its substrate specificity. Biotechnol Bioeng 2018; 115:863-873. [PMID: 29280476 DOI: 10.1002/bit.26533] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/30/2017] [Accepted: 12/18/2017] [Indexed: 01/29/2023]
Abstract
Partially acetylated chitosan oligosaccharides (paCOS) have various potential applications in agriculture, biomedicine, and pharmaceutics due to their suitable bioactivities. One method to produce paCOS is partial chemical hydrolysis of chitosan polymers, but that leads to poorly defined mixtures of oligosaccharides. However, the effective production of defined paCOS is crucial for fundamental research and for developing applications. A more promising approach is enzymatic depolymerization of chitosan using chitinases or chitosanases, as the substrate specificity of the enzyme determines the composition of the oligomeric products. Protein-engineering of these enzymes to alter their substrate specificity can overcome the limitations associated with naturally occurring enzymes and expand the spectrum of specific paCOS that can be produced. Here, engineering the substrate specificity of Bacillus sp. MN chitosanase is described for the first time. Two muteins with active site substitutions can accept N-acetyl-D-glucosamine units at their subsite (-2), which is impossible for the wildtype enzyme.
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Affiliation(s)
- Eva K Regel
- Institute for Biology and Biotechnology of Plants, University of Münster, Münster, Germany
| | - Tobias Weikert
- Institute for Biology and Biotechnology of Plants, University of Münster, Münster, Germany
| | - Anna Niehues
- Institute for Biology and Biotechnology of Plants, University of Münster, Münster, Germany
| | - Bruno M Moerschbacher
- Institute for Biology and Biotechnology of Plants, University of Münster, Münster, Germany
| | - Ratna Singh
- Institute for Biology and Biotechnology of Plants, University of Münster, Münster, Germany
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29
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Weikert T, Niehues A, Cord-Landwehr S, Hellmann MJ, Moerschbacher BM. Reassessment of chitosanase substrate specificities and classification. Nat Commun 2017; 8:1698. [PMID: 29167423 PMCID: PMC5700058 DOI: 10.1038/s41467-017-01667-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 10/05/2017] [Indexed: 01/09/2023] Open
Abstract
Chitosanases can be used to produce partially acetylated chitosan oligosaccharides (paCOS) for different applications, provided they are thoroughly characterized. However, recent studies indicate that the established classification system for chitosanases is too simplistic. Here, we apply a highly sensitive method for quantitatively sequencing paCOS to reassess the substrate specificities of the best-characterized class I–III chitosanases. The enzymes’ abilities to cleave bonds at GlcNAc residues positioned at subsite (−1) or (+1), on which the classification system is based, vary especially when the substrates have different fractions of acetylation (FA). Conflicts with the recent classification are observed at higher FA, which were not investigated in prior specificity determinations. Initial analyses of pectin-degrading enzymes reveal that classifications of other polysaccharide-degrading enzymes should also be critically reassessed. Based on our results, we tentatively suggest a chitosanase classification system which is based on specificities and preferences of subsites (−2) to (+2). Chitosanases are classified according to their specificity in cleaving bonds at GlcNAc residues but the current system may be too simplistic. Here, the authors use quantitative mass spectrometry to revisit chitosanase specificity and propose additional determinants for their classification.
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Affiliation(s)
- Tobias Weikert
- Institute for Biology and Biotechnology of Plants, University of Münster, Schlossplatz 8, 48143, Münster, Germany
| | - Anna Niehues
- Institute for Biology and Biotechnology of Plants, University of Münster, Schlossplatz 8, 48143, Münster, Germany
| | - Stefan Cord-Landwehr
- Institute for Biology and Biotechnology of Plants, University of Münster, Schlossplatz 8, 48143, Münster, Germany
| | - Margareta J Hellmann
- Institute for Biology and Biotechnology of Plants, University of Münster, Schlossplatz 8, 48143, Münster, Germany
| | - Bruno M Moerschbacher
- Institute for Biology and Biotechnology of Plants, University of Münster, Schlossplatz 8, 48143, Münster, Germany.
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30
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Zitouni M, Viens P, Ghinet MG, Brzezinski R. Diversity of family GH46 chitosanases in Kitasatospora setae KM-6054. Appl Microbiol Biotechnol 2017; 101:7877-7888. [PMID: 28924834 PMCID: PMC5635096 DOI: 10.1007/s00253-017-8517-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 08/18/2017] [Accepted: 09/05/2017] [Indexed: 11/26/2022]
Abstract
The genome of Kitasatospora setae KM-6054, a soil actinomycete, has three genes encoding chitosanases belonging to GH46 family. The genes (csn1-3) were cloned in Streptomyces lividans and the corresponding enzymes were purified from the recombinant cultures. The csn2 clone yielded two proteins (Csn2BH and Csn2H) differing by the presence of a carbohydrate-binding domain. Sequence analysis showed that Csn1 and Csn2H were canonical GH46 chitosanases, while Csn3 resembled chitosanases from bacilli. The activity of the four chitosanases was tested in a variety of conditions and on diverse chitosan forms, including highly N-deacetylated chitosan or chitosan complexed with humic or polyphosphoric acid. Kinetic parameters were also determined. These tests unveiled the biochemical diversity among these chitosanases and the peculiarity of Csn3 compared with the other three enzymes. The observed biochemical diversity is discussed based on structural 3D models and sequence alignment. This is a first study of all the GH46 chitosanases produced by a single microbial strain.
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Affiliation(s)
- Mina Zitouni
- Centre d'Étude et de Valorisation de la Diversité Microbienne; Département de Biologie; Faculté des Sciences, Université de Sherbrooke, 2500, boul.de l'Université, Sherbrooke, Québec, J1K 2R1, Canada
| | - Pascal Viens
- Centre d'Étude et de Valorisation de la Diversité Microbienne; Département de Biologie; Faculté des Sciences, Université de Sherbrooke, 2500, boul.de l'Université, Sherbrooke, Québec, J1K 2R1, Canada
- Innomalt Inc, Sherbrooke, Québec, Canada
| | - Mariana G Ghinet
- Centre d'Étude et de Valorisation de la Diversité Microbienne; Département de Biologie; Faculté des Sciences, Université de Sherbrooke, 2500, boul.de l'Université, Sherbrooke, Québec, J1K 2R1, Canada
- Département de Pharmacologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Ryszard Brzezinski
- Centre d'Étude et de Valorisation de la Diversité Microbienne; Département de Biologie; Faculté des Sciences, Université de Sherbrooke, 2500, boul.de l'Université, Sherbrooke, Québec, J1K 2R1, Canada.
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31
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Scapin SMN, Souza FHM, Zanphorlin LM, de Almeida TS, Sade YB, Cardoso AM, Pinheiro GL, Murakami MT. Structure and function of a novel GH8 endoglucanase from the bacterial cellulose synthase complex of Raoultella ornithinolytica. PLoS One 2017; 12:e0176550. [PMID: 28448629 PMCID: PMC5407803 DOI: 10.1371/journal.pone.0176550] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/12/2017] [Indexed: 02/02/2023] Open
Abstract
Cellulose synthesis in bacteria is a complex process involving the concerted action of several enzymes whose genes are often organized in operons. This process influences many fundamental physiological aspects such as bacteria and host interaction, biofilm formation, among others. Although it might sound contradictory, the participation of cellulose-degrading enzymes is critical to this process. The presence of endoglucanases from family 8 of glycosyl hydrolases (GH8) in bacterial cellulose synthase (Bcs) complex has been described in different bacteria, including the model organism Komagataeibacter xylinus; however, their role in this process is not completely understood. In this study, we describe the biochemical characterization and three-dimensional structure of a novel GH8 member from Raoultella ornithinolytica, named AfmE1, which was previously identified by our group from the metagenomic analysis of the giant snail Achatina fulica. Our results demonstrated that AfmE1 is an endo-β-1,4-glucanase, with maximum activity in acidic to neutral pH over a wide temperature range. This enzyme cleaves cello-oligosaccharides with a degree of polymerization ≥ 5 and presents six glucosyl-binding subsites. The structural comparison of AfmE1 with other GH8 endoglucanases showed significant structural dissimilarities in the catalytic cleft, particularly in the subsite +3, which correlate with different functional mechanisms, such as the recognition of substrate molecules having different arrangements and crystallinities. Together, these findings provide new insights into molecular and structural features of evolutionarily conserved endoglucanases from the bacterial cellulose biosynthetic machinery.
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Affiliation(s)
- Sandra Mara Naressi Scapin
- Division of Metrology Applied to Life Sciences, National Institute of Metrology, Quality and Technology, Duque de Caxias, Rio de Janeiro, Brazil
- * E-mail: (SMNS); (MTM)
| | - Flavio Henrique Moreira Souza
- Brazilian Bioethanol Science and Technology Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Leticia Maria Zanphorlin
- Brazilian Bioethanol Science and Technology Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Thamyres Silva de Almeida
- Division of Metrology Applied to Life Sciences, National Institute of Metrology, Quality and Technology, Duque de Caxias, Rio de Janeiro, Brazil
| | - Youssef Bacila Sade
- Division of Metrology Applied to Life Sciences, National Institute of Metrology, Quality and Technology, Duque de Caxias, Rio de Janeiro, Brazil
| | - Alexander Machado Cardoso
- Division of Metrology Applied to Life Sciences, National Institute of Metrology, Quality and Technology, Duque de Caxias, Rio de Janeiro, Brazil
| | - Guilherme Luiz Pinheiro
- Division of Metrology Applied to Life Sciences, National Institute of Metrology, Quality and Technology, Duque de Caxias, Rio de Janeiro, Brazil
| | - Mario Tyago Murakami
- Brazilian Bioethanol Science and Technology Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
- * E-mail: (SMNS); (MTM)
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Shinya S, Fukamizo T. Interaction between chitosan and its related enzymes: A review. Int J Biol Macromol 2017; 104:1422-1435. [PMID: 28223213 DOI: 10.1016/j.ijbiomac.2017.02.040] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 01/17/2017] [Accepted: 02/09/2017] [Indexed: 10/20/2022]
Abstract
Chitosan-related enzymes including chitosanases, exo-β-glucosaminidases, and enzymes having chitosan-binding modules recognize ligands through electrostatic interactions between the acidic amino acids in proteins and amino groups of chitosan polysaccharides. However, in GH8 chitosanases, several aromatic residues are also involved in substrate recognition through stacking interactions, and these enzymes consequently hydrolyze β-1,4-glucan as well as chitosan. The binding grooves of these chitosanases are extended and opened at both ends of the grooves, so that the enzymes can clamp a long chitosan polysaccharide. The association/dissociation of positively charged glucosamine residues to/from the binding pocket of a GH2 exo-β-glucosaminidase controls the p Ka of the catalytic acid, thereby maintaining the high catalytic potency of the enzyme. In contrast to chitosanases, chitosan-binding modules only accommodate a couple of glucosamine residues, predominantly recognizing the non-reducing end glucosamine residue of chitosan by electrostatic interactions and a hydrogen-bonding network. These structural findings on chitosan-related enzymes may contribute to future applications for the efficient conversion of the chitin/chitosan biomass.
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Affiliation(s)
- Shoko Shinya
- Department of Advanced Bioscience, Kindai University, 3327-204 Nakamachi, Nara 631-8505, Japan
| | - Tamo Fukamizo
- Department of Advanced Bioscience, Kindai University, 3327-204 Nakamachi, Nara 631-8505, Japan.
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33
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Baek SC, Ho TH, Lee HW, Jung WK, Gang HS, Kang LW, Kim H. Improvement of enzyme activity of β-1,3-1,4-glucanase from Paenibacillus sp. X4 by error-prone PCR and structural insights of mutated residues. Appl Microbiol Biotechnol 2017; 101:4073-4083. [PMID: 28180917 DOI: 10.1007/s00253-017-8145-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 01/16/2017] [Accepted: 01/22/2017] [Indexed: 11/29/2022]
Abstract
β-1,3-1,4-Glucanase (BGlc8H) from Paenibacillus sp. X4 was mutated by error-prone PCR or truncated using termination primers to improve its enzyme properties. The crystal structure of BGlc8H was determined at a resolution of 1.8 Å to study the possible roles of mutated residues and truncated regions of the enzyme. In mutation experiments, three clones of EP 2-6, 2-10, and 5-28 were finally selected that exhibited higher specific activities than the wild type when measured using their crude extracts. Enzyme variants of BG2-6, BG2-10, and BG5-28 were mutated at two, two, and six amino acid residues, respectively. These enzymes were purified homogeneously by Hi-Trap Q and CHT-II chromatography. Specific activity of BG5-28 was 2.11-fold higher than that of wild-type BGwt, whereas those of BG2-6 and BG2-10 were 0.93- and 1.19-fold that of the wild type, respectively. The optimum pH values and temperatures of the variants were nearly the same as those of BGwt (pH 5.0 and 40 °C, respectively). However, the half-life of the enzyme activity and catalytic efficiency (k cat/K m) of BG5-28 were 1.92- and 2.12-fold greater than those of BGwt at 40 °C, respectively. The catalytic efficiency of BG5-28 increased to 3.09-fold that of BGwt at 60 °C. These increases in the thermostability and catalytic efficiency of BG5-28 might be useful for the hydrolysis of β-glucans to produce fermentable sugars. Of the six mutated residues of BG5-28, five residues were present in mature BGlc8H protein, and two of them were located in the core scaffold of BGlc8H and the remaining three residues were in the substrate-binding pocket forming loop regions. In truncation experiments, three forms of C-terminal truncated BGlc8H were made, which comprised 360, 286, and 215 amino acid residues instead of the 409 residues of the wild type. No enzyme activity was observed for these truncated enzymes, suggesting the complete scaffold of the α6/α6-double-barrel structure is essential for enzyme activity.
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Affiliation(s)
- Seung Cheol Baek
- Department of Pharmacy, Sunchon National University, Suncheon, 57922, Republic of Korea.,Department of Agricultural Chemistry, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Thien-Hoang Ho
- Department of Biological Sciences, Konkuk University, Gwangjin-gu, Seoul, 05029, Republic of Korea
| | - Hyun Woo Lee
- Department of Pharmacy, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Won Kyeong Jung
- Research Institute of Life Pharmaceutical Sciences, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Hyo-Seung Gang
- Department of Agricultural Chemistry, Sunchon National University, Suncheon, 57922, Republic of Korea
| | - Lin-Woo Kang
- Department of Biological Sciences, Konkuk University, Gwangjin-gu, Seoul, 05029, Republic of Korea.
| | - Hoon Kim
- Department of Pharmacy, Sunchon National University, Suncheon, 57922, Republic of Korea. .,Research Institute of Life Pharmaceutical Sciences, Sunchon National University, Suncheon, 57922, Republic of Korea.
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Yorinaga Y, Kumasaka T, Yamamoto M, Hamada K, Kawamukai M. Crystal structure of a family 80 chitosanase fromMitsuaria chitosanitabida. FEBS Lett 2017; 591:540-547. [DOI: 10.1002/1873-3468.12557] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 01/09/2017] [Accepted: 01/10/2017] [Indexed: 01/08/2023]
Affiliation(s)
- Yutaka Yorinaga
- Department of Life Science and Biotechnology; Faculty of Life and Environmental Science; Shimane University; Matsue Japan
| | - Takashi Kumasaka
- Japan Synchrotron Radiation Research Institute (JASRI); Sayo Hyogo Japan
| | | | - Kensaku Hamada
- X-ray Research Laboratory; Rigaku Co.; Akishima Tokyo Japan
| | - Makoto Kawamukai
- Department of Life Science and Biotechnology; Faculty of Life and Environmental Science; Shimane University; Matsue Japan
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35
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Deciphering the factors defining the pH-dependence of a commercial glycoside hydrolase family 8 enzyme. Enzyme Microb Technol 2017; 96:163-169. [DOI: 10.1016/j.enzmictec.2016.10.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 10/13/2016] [Accepted: 10/17/2016] [Indexed: 01/05/2023]
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36
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The Glycoside Hydrolase Family 8 Reducing-End Xylose-Releasing Exo-oligoxylanase Rex8A from Paenibacillus barcinonensis BP-23 Is Active on Branched Xylooligosaccharides. Appl Environ Microbiol 2016; 82:5116-24. [PMID: 27316951 DOI: 10.1128/aem.01329-16] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 05/27/2016] [Indexed: 01/06/2023] Open
Abstract
UNLABELLED A GH8 family enzyme involved in xylan depolymerization has been characterized. The enzyme, Rex8A, is a reducing-end xylose-releasing exo-oligoxylanase (Rex) that efficiently hydrolyzes xylooligosaccharides and shows minor activity on polymeric xylan. Rex8A hydrolyzes xylooligomers of 3 to 6 xylose units to xylose and xylobiose in long-term incubations. Kinetic constants of Rex8A were determined on xylotriose, showing a Km of 1.64 ± 0.03 mM and a kcat value of 118.8 s(-1) Besides linear xylooligosaccharides, the enzyme hydrolyzed decorated xylooligomers. The catalytic activity on branched xylooligosaccharides, i.e., the release of xylose from the reducing end, is a newly described trait of xylose-releasing exo-oligoxylanases, as the exo-activity on these substrates has not been reported for the few of these enzymes characterized to date. Modeling of the three-dimensional (3D) structure of Rex8A shows an (α/α)6 barrel fold where the loops connecting the α-helices contour the active site. These loops, which show high sequence diversity among GH8 enzymes, shape a catalytic cleft with a -2 subsite that can accommodate methyl-glucuronic acid decorations. The hydrolytic ability of Rex8A on branched oligomers can be crucial for the complete depolymerization of highly substituted xylans, which is indispensable to accomplish biomass deconstruction and to generate efficient catalysts. IMPORTANCE A GH8 family enzyme involved in xylan depolymerization has been characterized. The Rex8A enzyme from Paenibacillus barcinonensis is involved in depolymerization of glucuronoxylan, a major component of the lignocellulosic substrates. The study shows that Rex8A is a reducing-end xylose-releasing exo-oligoxylanase that efficiently hydrolyzes xylose from neutral and acidic xylooligosaccharides generated by the action of other xylanases also secreted by the strain. The activity of a Rex enzyme on branched xylooligosaccharides has not been described to date. This report provides original and useful information on the properties of a new example of the rarely studied Rex enzymes. Depolymerization of highly substituted xylans is crucial for biomass valorization as a platform for generation of biofuels, chemicals, and solvents.
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Das SN, Wagenknecht M, Nareddy PK, Bhuvanachandra B, Niddana R, Balamurugan R, Swamy MJ, Moerschbacher BM, Podile AR. Amino Groups of Chitosan Are Crucial for Binding to a Family 32 Carbohydrate Binding Module of a Chitosanase from Paenibacillus elgii. J Biol Chem 2016; 291:18977-90. [PMID: 27405759 DOI: 10.1074/jbc.m116.721332] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Indexed: 11/06/2022] Open
Abstract
We report here the role and mechanism of specificity of a family 32 carbohydrate binding module (CBM32) of a glycoside hydrolase family 8 chitosanase from Paenibacillus elgii (PeCsn). Both the activity and mode of action of PeCsn toward soluble chitosan polymers were not different with/without the CBM32 domain of P. elgii (PeCBM32). The decreased activity of PeCsn without PeCBM32 on chitosan powder suggested that PeCBM32 increases the relative concentration of enzyme on the substrate and thereby enhanced enzymatic activity. PeCBM32 specifically bound to polymeric and oligomeric chitosan and showed very weak binding to chitin and cellulose. In isothermal titration calorimetry, the binding stoichiometry of 2 and 1 for glucosamine monosaccharide (GlcN) and disaccharide (GlcN)2, respectively, was indicative of two binding sites in PeCBM32. A three-dimensional model-guided site-directed mutagenesis and the use of defined disaccharides varying in the pattern of acetylation suggested that the amino groups of chitosan and the polar residues Glu-16 and Glu-38 of PeCBM32 play a crucial role for the observed binding. The specificity of CBM32 has been further elucidated by a generated fusion protein PeCBM32-eGFP that binds to the chitosan exposing endophytic infection structures of Puccinia graminis f. sp. tritici Phylogenetic analysis showed that CBM32s appended to chitosanases are highly conserved across different chitosanase families suggesting their role in chitosan recognition and degradation. We have identified and characterized a chitosan-specific CBM32 useful for in situ staining of chitosans in the fungal cell wall during plant-fungus interaction.
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Affiliation(s)
| | - Martin Wagenknecht
- the Institute of Plant Biology and Biotechnology, Westphalian Wilhelms-University of Münster, 48143 Münster, Germany
| | | | | | - Ramana Niddana
- School of Chemistry, University of Hyderabad, 500046-Hyderabad, India and
| | | | - Musti J Swamy
- School of Chemistry, University of Hyderabad, 500046-Hyderabad, India and
| | - Bruno M Moerschbacher
- the Institute of Plant Biology and Biotechnology, Westphalian Wilhelms-University of Münster, 48143 Münster, Germany
| | - Appa Rao Podile
- From the Department of Plant Sciences, School of Life Sciences,
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A highly Conserved Aspartic Acid Residue of the Chitosanase from Bacillus Sp. TS Is Involved in the Substrate Binding. Appl Biochem Biotechnol 2016; 180:1167-1179. [PMID: 27318711 DOI: 10.1007/s12010-016-2159-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 06/06/2016] [Indexed: 02/07/2023]
Abstract
The chitosanase from Bacillus sp. TS (CsnTS) is an enzyme belonging to the glycoside hydrolase family 8. The sequence of CsnTS shares 98 % identity with the chitosanase from Bacillus sp. K17. Crystallography analysis and site-direct mutagenesis of the chitosanase from Bacillus sp. K17 identified the important residues involved in the catalytic interaction and substrate binding. However, despite progress in understanding the catalytic mechanism of the chitosanase from the family GH8, the functional roles of some residues that are highly conserved throughout this family have not been fully elucidated. This study focused on one of these residues, i.e., the aspartic acid residue at position 318. We found that apart from asparagine, mutation of Asp318 resulted in significant loss of enzyme activity. In-depth investigations showed that mutation of this residue not only impaired enzymatic activity but also affected substrate binding. Taken together, our results showed that Asp318 plays an important role in CsnTS activity.
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Lin L, Fu C, Huang W. Improving the activity of the endoglucanase, Cel8M from Escherichia coli by error-prone PCR. Enzyme Microb Technol 2016; 86:52-8. [DOI: 10.1016/j.enzmictec.2016.01.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 01/19/2016] [Accepted: 01/20/2016] [Indexed: 11/29/2022]
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40
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First report of a tropical Lysobacter enzymogenes producing bifunctional endoglucanase activity towards carboxymethylcellulose and chitosan. ANN MICROBIOL 2015. [DOI: 10.1007/s13213-015-1170-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Substrate-binding specificity of chitinase and chitosanase as revealed by active-site architecture analysis. Carbohydr Res 2015; 418:50-56. [PMID: 26545262 DOI: 10.1016/j.carres.2015.10.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 10/03/2015] [Accepted: 10/06/2015] [Indexed: 11/21/2022]
Abstract
Chitinases and chitosanases, referred to as chitinolytic enzymes, are two important categories of glycoside hydrolases (GH) that play a key role in degrading chitin and chitosan, two naturally abundant polysaccharides. Here, we investigate the active site architecture of the major chitosanase (GH8, GH46) and chitinase families (GH18, GH19). Both charged (Glu, His, Arg, Asp) and aromatic amino acids (Tyr, Trp, Phe) are observed with higher frequency within chitinolytic active sites as compared to elsewhere in the enzyme structure, indicating significant roles related to enzyme function. Hydrogen bonds between chitinolytic enzymes and the substrate C2 functional groups, i.e. amino groups and N-acetyl groups, drive substrate recognition, while non-specific CH-π interactions between aromatic residues and substrate mainly contribute to tighter binding and enhanced processivity evident in GH8 and GH18 enzymes. For different families of chitinolytic enzymes, the number, type, and position of substrate atoms bound in the active site vary, resulting in different substrate-binding specificities. The data presented here explain the synergistic action of multiple enzyme families at a molecular level and provide a more reasonable method for functional annotation, which can be further applied toward the practical engineering of chitinases and chitosanases.
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Novel characteristics of chitin deacetylase from Colletotrichum lindemuthianum: Production of fully acetylated chitooligomers, and hydrolysis of deacetylated chitooligomers. Process Biochem 2014. [DOI: 10.1016/j.procbio.2014.07.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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43
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Isogawa D, Morisaka H, Kuroda K, Kusaoke H, Kimoto H, Suye SI, Ueda M. Evaluation of chitosan-binding amino acid residues of chitosanase from Paenibacillus fukuinensis. Biosci Biotechnol Biochem 2014; 78:1177-82. [DOI: 10.1080/09168451.2014.917263] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Abstract
Chitosan oligosaccharides longer than a hexamer have higher bioactivity than polymer or shorter oligosaccharides, such as the monomer or dimer. In our previous work, we generated Paenibacillus fukuinensis chitosanase-displaying yeast using yeast cell surface displaying system and demonstrated the catalytic base. Here we investigated the specific function of putative four amino acid residues Trp159, Trp228, Tyr311, and Phe406 engaged in substrate binding. Using this system, we generated chitosanase mutants in which the four amino acid residues were substituted with Ala and the chitosanase activity assay and HPLC analysis were performed. Based on these results, we demonstrated that Trp159 and Phe406 were critical for hydrolyzing both polymer and oligosaccharide, and Trp228 and Tyr311 were especially important for binding to oligosaccharide, such as the chitosan-hexamer, not to the chitosan polymer. From the results, we suggested the possibility of the effective strategy for designing useful mutants that produce chitosan oligosaccharides holding higher bioactivity.
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Affiliation(s)
- Danya Isogawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Hironobu Morisaka
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kouichi Kuroda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Hideo Kusaoke
- Department of Environmental and Biotechnological Frontier Engineering, Fukui University of Technology, Fukui, Japan
| | - Hisashi Kimoto
- Faculty of Biotechnology, Department of Bioscience, Fukui Prefectural University, Fukui, Japan
| | - Shin-ichiro Suye
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, Fukui, Japan
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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Abstract
We present the first chitosanase–substrate complex structure, and, in combination with a mutagenesis and thermal stability assay, we elucidate the chitosanase–substrate binding mechanism precisely for the first time. The structural basis for chitosanase cleavage specificity is analysed as well.
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Fuenzalida JP, Weikert T, Hoffmann S, Vila-Sanjurjo C, Moerschbacher BM, Goycoolea FM, Kolkenbrock S. Affinity protein-based FRET tools for cellular tracking of chitosan nanoparticles and determination of the polymer degree of acetylation. Biomacromolecules 2014; 15:2532-9. [PMID: 24835451 DOI: 10.1021/bm500394v] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Chitosan (CS) is a family of linear polysaccharides with diverse applications in medicine, agriculture, and industry. Its bioactive properties are determined by parameters such as the degree of acetylation (DA), but current techniques to measure the DA are laborious and require large amounts of substrate and sophisticated equipment. It is also challenging to monitor the fate of chitosan-based nanoparticles (CS-NPs) in vitro because current tools cannot measure their enzymatic or chemical degradation. We have developed a method based on the Förster resonance energy transfer (FRET) that occurs between two independent fluorescent proteins fused to a CS-binding domain, who interact with CS polymers or CS-NPs. We used this approach to calibrate a simple and rapid analytical method that can determine the DA of CS substrates. We showed unequivocally that FRET occurs on the surface of CS-NPs and that the FRET signal is quenched by enzymatic degradation of the CS substrate. Finally, we provide in vitro proof-of-concept that these approaches can be used to label CS-NPs and colocalize them following their interactions with mammalian cells.
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Affiliation(s)
- J P Fuenzalida
- IBBP, Westfälische Wilhelms-Universität Münster Schlossgarten 3, 48149, Münster, Germany
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Characterization of an alkalophilic extracellular chitosanase from Bacillus cereus GU-02. J Biosci Bioeng 2014; 117:684-9. [DOI: 10.1016/j.jbiosc.2013.11.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 10/16/2013] [Accepted: 11/04/2013] [Indexed: 12/16/2022]
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Function and Structure Studies of GH Family 31 and 97 α-Glycosidases. Biosci Biotechnol Biochem 2014; 75:2269-77. [DOI: 10.1271/bbb.110610] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Production and purification of a fungal chitosanase and chitooligomers from Penicillium janthinellum D4 and discovery of the enzyme activators. Carbohydr Polym 2014; 108:331-7. [PMID: 24751281 DOI: 10.1016/j.carbpol.2014.02.053] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 02/13/2014] [Accepted: 02/16/2014] [Indexed: 11/20/2022]
Abstract
Chitosanases have received much attention because of their wide range of applications. Although most fungal chitosanases use sugar as their major carbon source, in the present work, a chitosanase was induced from a squid pen powder (SPP)-containing Penicillium janthinellum D4 medium and purified by ammonium sulphate precipitation and combined column chromatography. The purified D4 chitosanase exhibited optimum activity at pH 7-9, 60°C and was stable at pH 7-11, 25-50°C. The D4 chitosanase that was used for chitooligomers preparation was studied. The enzyme products revealed various chitooligomers with different degrees of polymerisation (DP) from 3 to 9, as determined by a MALDI-TOF mass spectrometer, confirming the endo-type nature of the D4 chitosanase. D4 chitosanase activity was significantly inhibited by Cu(2+), Mn(2+), and EDTA. However, Fe(2+) activated or inhibited D4 chitosanases at different concentrations. The D4 chitosanase was also activated by some small synthetic boron-containing molecules with boronate ester side chains.
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β-xylosidases and α-L-arabinofuranosidases: accessory enzymes for arabinoxylan degradation. Biotechnol Adv 2013; 32:316-32. [PMID: 24239877 DOI: 10.1016/j.biotechadv.2013.11.005] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 10/28/2013] [Accepted: 11/09/2013] [Indexed: 11/22/2022]
Abstract
Arabinoxylan (AX) is among the most abundant hemicelluloses on earth and one of the major components of feedstocks that are currently investigated as a source for advanced biofuels. As global research into these sustainable biofuels is increasing, scientific knowledge about the enzymatic breakdown of AX advanced significantly over the last decade. This review focuses on the exo-acting AX hydrolases, such as α-arabinofuranosidases and β-xylosidases. It aims to provide a comprehensive overview of the diverse substrate specificities and corresponding structural features found in the different glycoside hydrolase families. A careful review of the available literature reveals a marked difference in activity between synthetically labeled and naturally occurring substrates, often leading to erroneous enzymatic annotations. Therefore, special attention is given to enzymes with experimental evidence on the hydrolysis of natural polymers.
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Buschmann MD, Merzouki A, Lavertu M, Thibault M, Jean M, Darras V. Chitosans for delivery of nucleic acids. Adv Drug Deliv Rev 2013; 65:1234-70. [PMID: 23872012 PMCID: PMC7103275 DOI: 10.1016/j.addr.2013.07.005] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 05/22/2013] [Accepted: 07/05/2013] [Indexed: 01/19/2023]
Abstract
Alternatives to efficient viral vectors in gene therapy are desired because of their poor safety profiles. Chitosan is a promising non-viral nucleotide delivery vector because of its biocompatibility, biodegradability, low immunogenicity and ease of manufacturing. Since the transfection efficiency of chitosan polyplexes is relatively low compared to viral counterparts, there is an impetus to gain a better understanding of the structure-performance relationship. Recent progress in preparation and characterisation has enabled coupling analysis of chitosans structural parameters that has led to increased TE by tailoring of chitosan's structure. In this review, we summarize the recent advances that have lead to a more rational design of chitosan polyplexes. We present an integrated review of all major areas of chitosan-based transfection, including preparation, chitosan and polyplexes physicochemical characterisation, in vitro and in vivo assessment. In each, we present the obstacles to efficient transfection and the strategies adopted over time to surmount these impediments.
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Affiliation(s)
- Michael D Buschmann
- Dept. Chemical Engineering and Inst. Biomedical Engineering, Ecole Polytechnique, Montreal, QC, Canada.
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