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Itoh T. Structures and functions of carbohydrate-active enzymes of chitinolytic bacteria Paenibacillus sp. str. FPU-7. Biosci Biotechnol Biochem 2021; 85:1314-1323. [PMID: 33792636 DOI: 10.1093/bbb/zbab058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 03/22/2021] [Indexed: 11/14/2022]
Abstract
Chitin and its derivatives have valuable potential applications in various fields that include medicine, agriculture, and food industries. Paenibacillus sp. str. FPU-7 is one of the most potent chitin-degrading bacteria identified. This review introduces the chitin degradation system of P. str. FPU-7. In addition to extracellular chitinases, P. str. FPU-7 uses a unique multimodular chitinase (ChiW) to hydrolyze chitin to oligosaccharides on the cell surface. Chitin oligosaccharides are converted to N-acetyl-d-glucosamine by β-N-acetylhexosaminidase (PsNagA) in the cytosol. The functions and structures of ChiW and PsNagA are also summarized. The genome sequence of P. str. FPU-7 provides opportunities to acquire novel enzymes. Genome mining has identified a novel alginate lyase, PsAly. The functions and structure of PsAly are reviewed. These findings will inform further improvement of the sustainable conversion of polysaccharides to functional materials.
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Affiliation(s)
- Takafumi Itoh
- Department of Bioscience and Biotechnology, Fukui Prefectural University, Yoshida-gun, Fukui, Japan
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Cherry P, Yadav S, Strain CR, Allsopp PJ, McSorley EM, Ross RP, Stanton C. Prebiotics from Seaweeds: An Ocean of Opportunity? Mar Drugs 2019; 17:E327. [PMID: 31159359 PMCID: PMC6627129 DOI: 10.3390/md17060327] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/27/2019] [Accepted: 05/29/2019] [Indexed: 02/07/2023] Open
Abstract
Seaweeds are an underexploited and potentially sustainable crop which offer a rich source of bioactive compounds, including novel complex polysaccharides, polyphenols, fatty acids, and carotenoids. The purported efficacies of these phytochemicals have led to potential functional food and nutraceutical applications which aim to protect against cardiometabolic and inflammatory risk factors associated with non-communicable diseases, such as obesity, type 2 diabetes, metabolic syndrome, cardiovascular disease, inflammatory bowel disease, and some cancers. Concurrent understanding that perturbations of gut microbial composition and metabolic function manifest throughout health and disease has led to dietary strategies, such as prebiotics, which exploit the diet-host-microbe paradigm to modulate the gut microbiota, such that host health is maintained or improved. The prebiotic definition was recently updated to "a substrate that is selectively utilised by host microorganisms conferring a health benefit", which, given that previous discussion regarding seaweed prebiotics has focused upon saccharolytic fermentation, an opportunity is presented to explore how non-complex polysaccharide components from seaweeds may be metabolised by host microbial populations to benefit host health. Thus, this review provides an innovative approach to consider how the gut microbiota may utilise seaweed phytochemicals, such as polyphenols, polyunsaturated fatty acids, and carotenoids, and provides an updated discussion regarding the catabolism of seaweed-derived complex polysaccharides with potential prebiotic activity. Additional in vitro screening studies and in vivo animal studies are needed to identify potential prebiotics from seaweeds, alongside untargeted metabolomics to decipher microbial-derived metabolites from seaweeds. Furthermore, controlled human intervention studies with health-related end points to elucidate prebiotic efficacy are required.
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Affiliation(s)
- Paul Cherry
- Nutrition Innovation Centre for Food and Health, Ulster University, Cromore Road, Coleraine, Co. Londonderry BT52 1SA, UK.
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, P61 C996, Ireland.
- APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland.
| | - Supriya Yadav
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, P61 C996, Ireland.
| | - Conall R Strain
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, P61 C996, Ireland.
- APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland.
| | - Philip J Allsopp
- Nutrition Innovation Centre for Food and Health, Ulster University, Cromore Road, Coleraine, Co. Londonderry BT52 1SA, UK.
| | - Emeir M McSorley
- Nutrition Innovation Centre for Food and Health, Ulster University, Cromore Road, Coleraine, Co. Londonderry BT52 1SA, UK.
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland.
- College of Science, Engineering and Food Science, University College Cork, Cork T12 K8AF, Ireland.
| | - Catherine Stanton
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, P61 C996, Ireland.
- APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland.
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Itoh T, Hibi T, Suzuki F, Sugimoto I, Fujiwara A, Inaka K, Tanaka H, Ohta K, Fujii Y, Taketo A, Kimoto H. Crystal Structure of Chitinase ChiW from Paenibacillus sp. str. FPU-7 Reveals a Novel Type of Bacterial Cell-Surface-Expressed Multi-Modular Enzyme Machinery. PLoS One 2016; 11:e0167310. [PMID: 27907169 PMCID: PMC5132251 DOI: 10.1371/journal.pone.0167310] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/13/2016] [Indexed: 12/03/2022] Open
Abstract
The Gram-positive bacterium Paenibacillus sp. str. FPU-7 effectively hydrolyzes chitin by using a number of chitinases. A unique chitinase with two catalytic domains, ChiW, is expressed on the cell surface of this bacterium and has high activity towards various chitins, even crystalline chitin. Here, the crystal structure of ChiW at 2.1 Å resolution is presented and describes how the enzyme degrades chitin on the bacterial cell surface. The crystal structure revealed a unique multi-modular architecture composed of six domains to function efficiently on the cell surface: a right-handed β-helix domain (carbohydrate-binding module family 54, CBM-54), a Gly-Ser-rich loop, 1st immunoglobulin-like (Ig-like) fold domain, 1st β/α-barrel catalytic domain (glycoside hydrolase family 18, GH-18), 2nd Ig-like fold domain and 2nd β/α-barrel catalytic domain (GH-18). The structure of the CBM-54, flexibly linked to the catalytic region of ChiW, is described here for the first time. It is similar to those of carbohydrate lyases but displayed no detectable carbohydrate degradation activities. The CBM-54 of ChiW bound to cell wall polysaccharides, such as chin, chitosan, β-1,3-glucan, xylan and cellulose. The structural and biochemical data obtained here also indicated that the enzyme has deep and short active site clefts with endo-acting character. The affinity of CBM-54 towards cell wall polysaccharides and the degradation pattern of the catalytic domains may help to efficiently decompose the cell wall chitin through the contact surface. Furthermore, we clarify that other Gram-positive bacteria possess similar cell-surface-expressed multi-modular enzymes for cell wall polysaccharide degradation.
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Affiliation(s)
- Takafumi Itoh
- Department of Bioscience, Fukui Prefectural University, Yoshida-gun, Fukui, Japan
- * E-mail: (TI); (HK)
| | - Takao Hibi
- Department of Bioscience, Fukui Prefectural University, Yoshida-gun, Fukui, Japan
| | - Fumiko Suzuki
- Department of Bioscience, Fukui Prefectural University, Yoshida-gun, Fukui, Japan
| | - Ikumi Sugimoto
- Department of Bioscience, Fukui Prefectural University, Yoshida-gun, Fukui, Japan
| | - Akihiro Fujiwara
- Department of Bioscience, Fukui Prefectural University, Yoshida-gun, Fukui, Japan
| | - Koji Inaka
- Maruwa Foods and Biosciences Inc., Yamatokoriyama, Nara, Japan
| | | | - Kazunori Ohta
- Japan Aerospace Exploration Agency, Tsukuba, Ibaraki, Japan
| | - Yutaka Fujii
- Department of Molecular Biology and Chemistry, Faculty of Medicine, University of Fukui, Yoshida-gun, Fukui, Japan
| | - Akira Taketo
- Department of Environmental and Biotechnological Frontier Engineering, Fukui University of Technology, Fukui, Fukui, Japan
| | - Hisashi Kimoto
- Department of Bioscience, Fukui Prefectural University, Yoshida-gun, Fukui, Japan
- * E-mail: (TI); (HK)
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