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Bacterial chitinases: genetics, engineering and applications. World J Microbiol Biotechnol 2022; 38:252. [DOI: 10.1007/s11274-022-03444-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022]
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Li J, Wang S, Liu C, Li Y, Wei Y, Fu G, Liu P, Ma H, Huang D, Lin J, Zhang D. Going Beyond the Local Catalytic Activity Space of Chitinase Using a Simulation-Based Iterative Saturation Mutagenesis Strategy. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jinlong Li
- Tianjin Institutes of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Sijia Wang
- Tianjin Institutes of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Cui Liu
- Tianjin Institutes of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Yixin Li
- Tianjin Institutes of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Yu Wei
- College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, P. R. China
| | - Gang Fu
- Tianjin Institutes of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Pi Liu
- Tianjin Institutes of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Hongwu Ma
- Tianjin Institutes of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Biodesign Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Dawei Huang
- College of Life Sciences, Nankai University, Tianjin 300071, P. R. China
| | - Jianping Lin
- College of Pharmacy, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, P. R. China
| | - Dawei Zhang
- Tianjin Institutes of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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Madland E, Forsberg Z, Wang Y, Lindorff-Larsen K, Niebisch A, Modregger J, Eijsink VGH, Aachmann FL, Courtade G. Structural and functional variation of chitin-binding domains of a lytic polysaccharide monooxygenase from Cellvibrio japonicus. J Biol Chem 2021; 297:101084. [PMID: 34411561 PMCID: PMC8449059 DOI: 10.1016/j.jbc.2021.101084] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 11/28/2022] Open
Abstract
Among the extensive repertoire of carbohydrate-active enzymes, lytic polysaccharide monooxygenases (LPMOs) have a key role in recalcitrant biomass degradation. LPMOs are copper-dependent enzymes that catalyze oxidative cleavage of glycosidic bonds in polysaccharides such as cellulose and chitin. Several LPMOs contain carbohydrate-binding modules (CBMs) that are known to promote LPMO efficiency. However, structural and functional properties of some CBMs remain unknown, and it is not clear why some LPMOs, like CjLPMO10A from the soil bacterium Cellvibrio japonicus, have multiple CBMs (CjCBM5 and CjCBM73). Here, we studied substrate binding by these two CBMs to shine light on their functional variation and determined the solution structures of both by NMR, which constitutes the first structure of a member of the CBM73 family. Chitin-binding experiments and molecular dynamics simulations showed that, while both CBMs bind crystalline chitin with Kd values in the micromolar range, CjCBM73 has higher affinity for chitin than CjCBM5. Furthermore, NMR titration experiments showed that CjCBM5 binds soluble chitohexaose, whereas no binding of CjCBM73 to this chitooligosaccharide was detected. These functional differences correlate with distinctly different arrangements of three conserved aromatic amino acids involved in substrate binding. In CjCBM5, these residues show a linear arrangement that seems compatible with the experimentally observed affinity for single chitin chains. On the other hand, the arrangement of these residues in CjCBM73 suggests a wider binding surface that may interact with several chitin chains. Taken together, these results provide insight into natural variation among related chitin-binding CBMs and the possible functional implications of such variation.
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Affiliation(s)
- Eva Madland
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Zarah Forsberg
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Yong Wang
- Structural Biology and NMR Laboratory, Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Department of Biology, Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Finn L Aachmann
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Gaston Courtade
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway.
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Ueda M, Nakadoi K, Tsukamoto K, Sakurai S. Effect of LPMO on the Hydrolysis of Crystalline Chitin by Chitinase A and β- N-Acetylglucosaminidase from Paenibacillus sp. Mol Biotechnol 2021. [DOI: 10.5772/intechopen.93761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We performed cloning and expression of chitinase A (Pb-ChiA), β-GlcNAcase (Pb-GlcNAcase), and lytic polysaccharide monooxygenase (Pb-LPMO) genes from Paenibacillus sp. The analysis of the hydrolysis products indicated Pb-ChiA to be an exo-type chitinase with 10-fold activity toward β-chitin as compared with α-chitin. The sequence of Pb-GlcNAcase was found to be similar to that of β-N-acetylhexosaminidase from P. barengoltzii (99%, WP_016313754.1). Pb-LPMO was expressed in the Brevibacillus expression system. Pb-ChiA was found to have affinity toward crystalline chitin higher than that of Pb-LPMO. Pb-LPMO boosted the activity of Pb-ChiA toward crystalline α-chitin but not toward crystalline β-chitin. When Pb-LPMO (3 μM) was added to the reaction mixture during the hydrolysis of crystalline α-chitin by Pb-ChiA, hydrolysis products at two-fold concentration were obtained. However, the hydrolysis products decreased upon addition of more than 3 μM Pb-LPMO to the reaction mixture.
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Xu T, Qi M, Liu H, Cao D, Xu C, Wang L, Qi B. Chitin degradation potential and whole-genome sequence of Streptomyces diastaticus strain CS1801. AMB Express 2020; 10:29. [PMID: 32036475 PMCID: PMC7007918 DOI: 10.1186/s13568-020-0963-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 01/23/2020] [Indexed: 12/22/2022] Open
Abstract
The aim of this study was to evaluate the chitin degradation potential and whole-genome sequence of Streptomyces diastaticus strain CS1801, which had been screened out in our previous work. The results of fermentation revealed that CS1801 can convert the chitin derived from crab shells, colloidal chitin and N-acetylglucosamine to chitooligosaccharide. Additional genome-wide analysis of CS1801 was also performed to explore the genomic basis for chitin degradation. The results showed that CS1801 possesses a chromosome with 5,611,479 bp (73% GC) and a plasmid with 1,388,284 bp (73% GC). The CS1801 genome consists of 7584 protein-coding genes, 90 tRNA and 21 rRNA operons. In addition, the results of genomic CAZyme analysis indicated that CS1801 comprises 103 glycoside hydrolase family genes, which could regulate the glycoside hydrolases that contribute to chitin degradation. The whole-genome information of CS1801 could highlight the mechanism underlying the chitin degradation activity of CS1801, strongly indicating that CS1801 is characterized by a substantial number of genes encoding chitinases and the complete metabolic pathway of chitin, conferring CS1801 with promising potential applicability in chitooligosaccharide production.
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Tanaka H, Akutsu H, Yabuta I, Hara M, Sugimoto H, Ikegami T, Watanabe T, Fujiwara T. A novel chitin‐binding mode of the chitin‐binding domain of chitinase A1 from
Bacillus circulans
WL
‐12 revealed by solid‐state
NMR. FEBS Lett 2018; 592:3173-3182. [DOI: 10.1002/1873-3468.13226] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 08/13/2018] [Accepted: 08/16/2018] [Indexed: 11/08/2022]
Affiliation(s)
- Hiroki Tanaka
- Institute for Protein Research Osaka University Suita Japan
| | - Hideo Akutsu
- Institute for Protein Research Osaka University Suita Japan
- Graduate School of Medical Life Science Yokohama City University Tsurumi‐ku Yokohama Japan
| | - Izumi Yabuta
- Institute for Protein Research Osaka University Suita Japan
| | - Masashi Hara
- Department of Applied Biological Chemistry Faculty of Agriculture Niigata University Niigata Japan
| | - Hayuki Sugimoto
- Department of Applied Biological Chemistry Faculty of Agriculture Niigata University Niigata Japan
| | - Takahisa Ikegami
- Institute for Protein Research Osaka University Suita Japan
- Graduate School of Medical Life Science Yokohama City University Tsurumi‐ku Yokohama Japan
| | - Takeshi Watanabe
- Department of Applied Biological Chemistry Faculty of Agriculture Niigata University Niigata Japan
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Vogt S, Kelkenberg M, Nöll T, Steinhoff B, Schönherr H, Merzendorfer H, Nöll G. Rapid determination of binding parameters of chitin binding domains using chitin-coated quartz crystal microbalance sensor chips. Analyst 2018; 143:5255-5263. [DOI: 10.1039/c8an01453a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Chitin present in fungal cell walls has been considered as a diagnostic polymer for the detection of fungal infections.
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Affiliation(s)
- Stephan Vogt
- Organic Chemistry
- Department of Chemistry and Biology
- University of Siegen
- 57076 Siegen
- Germany
| | - Marco Kelkenberg
- Molecular Biology
- Department of Chemistry and Biology
- University of Siegen
- 57076 Siegen
- Germany
| | - Tanja Nöll
- Organic Chemistry
- Department of Chemistry and Biology
- University of Siegen
- 57076 Siegen
- Germany
| | - Benedikt Steinhoff
- Physical Chemistry I and Research Center of Micro and Nanochemistry and Engineering (Cμ)
- Department of Chemistry and Biology
- University of Siegen
- 57076 Siegen
- Germany
| | - Holger Schönherr
- Physical Chemistry I and Research Center of Micro and Nanochemistry and Engineering (Cμ)
- Department of Chemistry and Biology
- University of Siegen
- 57076 Siegen
- Germany
| | - Hans Merzendorfer
- Molecular Biology
- Department of Chemistry and Biology
- University of Siegen
- 57076 Siegen
- Germany
| | - Gilbert Nöll
- Organic Chemistry
- Department of Chemistry and Biology
- University of Siegen
- 57076 Siegen
- Germany
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Sánchez-Vallet A, Mesters JR, Thomma BP. The battle for chitin recognition in plant-microbe interactions. FEMS Microbiol Rev 2015; 39:171-83. [DOI: 10.1093/femsre/fuu003] [Citation(s) in RCA: 171] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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Joshi S, Satyanarayana T. In vitro engineering of microbial enzymes with multifarious applications: prospects and perspectives. BIORESOURCE TECHNOLOGY 2015; 176:273-283. [PMID: 25435065 DOI: 10.1016/j.biortech.2014.10.151] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 10/28/2014] [Accepted: 10/29/2014] [Indexed: 06/04/2023]
Abstract
The discovery of a novel enzyme from a microbial source takes anywhere between months to years, and therefore, there has been an immense interest in modifying the existing microbial enzymes to suit the present day needs of the industry. The redesigning of industrially useful enzymes for improving their performance has become a challenge because bioinformatics databases have been revealing new facts on a day-to-day basis. Modification of the existing enzymes has become a trend for fine tuning of biocatalysts in the biotech industry. Hydrolases are employed in pharmaceutical, biofuel, detergent, food and feed industries that significantly contribute to the global annual revenue, and therefore, the emphasis has been on engineering them. Although a large data is accumulating on making alterations in microbial enzymes, there is a lack of definite information on redesigning industrial enzymes. This review focuses on the recent developments in improving the characteristics of various biotechnologically important enzymes.
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Affiliation(s)
- Swati Joshi
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India
| | - Tulasi Satyanarayana
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India.
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Mine S, Nakamura T, Sato T, Ikegami T, Uegaki K. Solution structure of the chitin-binding domain 1 (ChBD1) of a hyperthermophilic chitinase from Pyrococcus furiosus. ACTA ACUST UNITED AC 2013; 155:115-22. [DOI: 10.1093/jb/mvt104] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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