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Moran CL, Debowski A, Vrielink A, Stubbs K, Sarkar-Tyson M. N-acetyl-β-hexosaminidase activity is important for chitooligosaccharide metabolism and biofilm formation in Burkholderia pseudomallei. Environ Microbiol 2024; 26:e16571. [PMID: 38178319 DOI: 10.1111/1462-2920.16571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/18/2023] [Indexed: 01/06/2024]
Abstract
Burkholderia pseudomallei is a saprophytic Gram-negative bacillus that can cause the disease melioidosis. Although B. pseudomallei is a recognised member of terrestrial soil microbiomes, little is known about its contribution to the saprophytic degradation of polysaccharides within its niche. For example, while chitin is predicted to be abundant within terrestrial soils the chitinolytic capacity of B. pseudomallei is yet to be defined. This study identifies and characterises a putative glycoside hydrolase, bpsl0500, which is expressed by B. pseudomallei K96243. Recombinant BPSL0500 was found to exhibit activity against substrate analogues and GlcNAc disaccharides relevant to chitinolytic N-acetyl-β-d-hexosaminidases. In B. pseudomallei, bpsl0500 was found to be essential for both N-acetyl-β-d-hexosaminidase activity and chitooligosaccharide metabolism. Furthermore, bpsl0500 was also observed to significantly affect biofilm deposition. These observations led to the identification of BPSL0500 activity against model disaccharide linkages that are present in biofilm exopolysaccharides, a feature that has not yet been described for chitinolytic enzymes. The results in this study indicate that chitinolytic N-acetyl-β-d-hexosaminidases like bpsl0500 may facilitate biofilm disruption as well as chitin assimilation, providing dual functionality for saprophytic bacteria such as B. pseudomallei within the competitive soil microbiome.
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Affiliation(s)
- Clare L Moran
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Nedlands, Australia
| | - Aleksandra Debowski
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Nedlands, Australia
| | - Alice Vrielink
- School of Molecular Sciences, The University of Western Australia, Crawley, Australia
| | - Keith Stubbs
- School of Molecular Sciences, The University of Western Australia, Crawley, Australia
- ARC Training Centre for Next-Gen Technologies in Biomedical Analysis, School of Molecular Sciences, University of Western Australia, Crawley, Australia
| | - Mitali Sarkar-Tyson
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Nedlands, Australia
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2
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Phengsakun G, Boonyarit B, Rungrotmongkol T, Suginta W. Structure-based virtual screening for potent inhibitors of GH-20 β-N-acetylglucosaminidase: classical and machine learning scoring functions, and molecular dynamics simulations. Comput Biol Chem 2023; 104:107856. [PMID: 37003097 DOI: 10.1016/j.compbiolchem.2023.107856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023]
Abstract
GH-20 β-N-acetylglucosaminidases (GlcNAcases) are promising targets in the development of antimicrobial agents against Vibrio infections in humans and aquatic animals. In this study, we set up structure-based virtual screening to identify potential GH-20 GlcNAcase inhibitors from the Reaxys commercial database, using VhGlcNAcase from V. campbellii type strain ATCC® BAA 1116 as the protein target and Redoxal as the reference ligand. Using ChemPLP and RF-Score-VS machine learning scoring functions, eight lead compounds were identified and further evaluated for protein interaction preference and pharmacological properties. Protein-ligand analysis demonstrated that all selected compounds interacted exclusively at subsite - 1 with five hydrophobic residues W487, W505, W546, W582 and V544 at site S1, and with two polar residues, D437 and E438, at site 3. For subsite + 1, the most common residues were R274 and E584 at site 2 and I397 and Q398 at site 4. Based on the data obtained from binding free energy changes (ΔG°binding), pharmacological property analysis and molecular dynamic simulations, two ChemPLP compounds, 338175 and 1146525, and one RF-Score-VS compound, 337447, were considered as the likely lead compounds. The most promising compound, 1146525, could serve as a scaffold for the future design of novel antimicrobial agents against Vibrio infections.
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Ding Z, Li T, Chen M, Fang Y, Hou X, Yang G, Lu J, Ye Q, Zhu R, He F, Xia M, Liu S. Purification and characterization of a chitinase from Aeromonas media CZW001 as a biocatalyst for producing chitinpentaose and chitinhexaose. Biotechnol Appl Biochem 2023; 70:281-289. [PMID: 35578780 DOI: 10.1002/bab.2351] [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: 11/30/2021] [Accepted: 03/25/2022] [Indexed: 11/07/2022]
Abstract
Developing chitinase suitable for the bioconversion of chitin to chitin oligosaccharides has attracted significant attention due to its benefits in environmental protection. In this study, chitinase from Aeromonas media CZW001 (AmChi) was purified and characterized. The molecular weight of AmChi was approximately 40 kDa. AmChi exhibited maximum catalytic activity at pH 8.0 with an optimum temperature of 55°C and showed broad stability between 15 and 65°C and between pH 5.0 and 9.0. AmChi was activated by Mg2+ , Na+ , and K+ and inhibited by Hg+ , Co2+ , Fe2+ , Ca2+ , Ag+ , Zn2+ , and EDTA. The main products of AmChi on colloidal chitin were chitinhexaose and chitinpentaose. AmChi had better substrate specificity for powdered chitin than colloidal chitin and had a higher catalytic efficiency toward (GlcNAc)5 than colloidal chitin. AmChi inhibited fungal growth in a dose-dependent manner. These results suggest that AmChi could be used for the enzymatic degradation of chitin to produce chitinhexaose and chitinpentaose, which have several industrial applications.
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Affiliation(s)
- Zhiwen Ding
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China.,Co-Innovation Center of Jiangsu Marine Bioindustry Technology, Jiangsu Ocean University, Lianyungang, China.,School of Food Science and Engineering, Jiangsu Ocean University, Lianyungang, China.,Jiangsu Marine Resources Development Research Institute, Jiangsu Ocean University, Lianyungang, China
| | - Tian Li
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China.,Co-Innovation Center of Jiangsu Marine Bioindustry Technology, Jiangsu Ocean University, Lianyungang, China.,School of Food Science and Engineering, Jiangsu Ocean University, Lianyungang, China.,Jiangsu Marine Resources Development Research Institute, Jiangsu Ocean University, Lianyungang, China
| | - Meng Chen
- Lianyungang Inspection and Testing Center for Food and Drug Control, Lianyungang, China
| | - Yaowei Fang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China.,Co-Innovation Center of Jiangsu Marine Bioindustry Technology, Jiangsu Ocean University, Lianyungang, China.,School of Food Science and Engineering, Jiangsu Ocean University, Lianyungang, China.,Jiangsu Marine Resources Development Research Institute, Jiangsu Ocean University, Lianyungang, China
| | - Xiaoyue Hou
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China.,Co-Innovation Center of Jiangsu Marine Bioindustry Technology, Jiangsu Ocean University, Lianyungang, China.,School of Food Science and Engineering, Jiangsu Ocean University, Lianyungang, China
| | - Gaung Yang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China.,Co-Innovation Center of Jiangsu Marine Bioindustry Technology, Jiangsu Ocean University, Lianyungang, China.,School of Food Science and Engineering, Jiangsu Ocean University, Lianyungang, China
| | - Jing Lu
- School of Food Science and Engineering, Jiangsu Ocean University, Lianyungang, China
| | - Qinwen Ye
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China.,Co-Innovation Center of Jiangsu Marine Bioindustry Technology, Jiangsu Ocean University, Lianyungang, China.,School of Food Science and Engineering, Jiangsu Ocean University, Lianyungang, China
| | - Rongjun Zhu
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China.,Co-Innovation Center of Jiangsu Marine Bioindustry Technology, Jiangsu Ocean University, Lianyungang, China.,School of Food Science and Engineering, Jiangsu Ocean University, Lianyungang, China
| | - Fuxiang He
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China.,Co-Innovation Center of Jiangsu Marine Bioindustry Technology, Jiangsu Ocean University, Lianyungang, China.,School of Food Science and Engineering, Jiangsu Ocean University, Lianyungang, China
| | - Mengjie Xia
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China.,Co-Innovation Center of Jiangsu Marine Bioindustry Technology, Jiangsu Ocean University, Lianyungang, China.,School of Food Science and Engineering, Jiangsu Ocean University, Lianyungang, China
| | - Shu Liu
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang, China.,Co-Innovation Center of Jiangsu Marine Bioindustry Technology, Jiangsu Ocean University, Lianyungang, China.,School of Food Science and Engineering, Jiangsu Ocean University, Lianyungang, China.,Jiangsu Marine Resources Development Research Institute, Jiangsu Ocean University, Lianyungang, China
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Lee ME, Shin SK, Oh JJ, Hwang DH, Ko YJ, Hyeon JE, Han SO. Enzymatic production of sugar from fungi and fungi-infected lignocellulosic biomass by a new cellulosomal enzyme harboring N-acetyl-β-d-glucosaminidase activity. BIORESOURCE TECHNOLOGY 2021; 319:124242. [PMID: 33254465 DOI: 10.1016/j.biortech.2020.124242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 06/12/2023]
Abstract
Cellulosomes are scaffold proteins displaying enzymes on the cell wall to efficiently obtain nutrient sources. CcGlcNAcase is a novel cellulosomal component. Based on sequence analysis, CcGlcNAcase was predicted to be a chitinolytic enzyme based on high homology with the discoidin domain-containing protein and chitobiase/ β-hexosaminidase C terminal domain. CcGlcNAcase expression was notably increased when chitin was present. CcGlcNAcase produced N-acetyl-d-glucosamine from various lengths of N-acetyl-d-glucosamine. CcGlcNAcase bound to chitin (89%) and fungi (54.10%), whereas CcGlcNAcase exhibited a low binding ability to cellulose and xylan. CcGlcNAcase hydrolyzed fungi, yielding maximum 3.90 g/L N-acetyl-d-glucosamine. CcGlcNAcase enhanced cellulase toward fungi-infected lignocellulosic biomass, yielding 18 mg/L glucose (1.32-fold) and 1.72-fold increased total reducing sugar levels, whereas cellulase alone produced 13 mg/L glucose. Taken together, CcGlcNAcase can be utilized to enhance the degradation of fungi-infected lignocellulosic biomass and exhibits potential applications in the wood and sugar industry.
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Affiliation(s)
- Myeong-Eun Lee
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Sang Kyu Shin
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Jeong-Joo Oh
- Division of Environmental Science & Ecological Engineering, Korea University, Seoul 01133, Republic of Korea
| | - Dong-Hyeok Hwang
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Young Jin Ko
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Jeong Eun Hyeon
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea; Department of Food Science and Biotechnology, College of Knowledge-Based Services Engineering, Sungshin Women's University, Seoul 01133, Republic of Korea; Department of Food and Nutrition, College of Health & Wellness, Sungshin Women's University, Seoul 01133, Republic of Korea
| | - Sung Ok Han
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea.
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Morimoto Y, Takahashi S, Isoda Y, Nokami T, Fukamizo T, Suginta W, Ohnuma T. Kinetic and thermodynamic insights into the inhibitory mechanism of TMG-chitotriomycin on Vibrio campbellii GH20 exo-β-N-acetylglucosaminidase. Carbohydr Res 2020; 499:108201. [PMID: 33243428 DOI: 10.1016/j.carres.2020.108201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 12/20/2022]
Abstract
We investigated the inhibition kinetics of VhGlcNAcase, a GH20 exo-β-N-acetylglucosaminidase (GlcNAcase) from the marine bacterium Vibrio campbellii (formerly V. harveyi) ATCC BAA-1116, using TMG-chitotriomycin, a natural enzyme inhibitor specific for GH20 GlcNAcases from chitin-processing organisms, with p-nitrophenyl N-acetyl-β-d-glucosaminide (pNP-GlcNAc) as the substrate. TMG-chitotriomycin inhibited VhGlcNAcase with an IC50 of 3.0 ± 0.7 μM. Using Dixon plots, the inhibition kinetics indicated that TMG-chitotriomycin is a competitive inhibitor, with an inhibition constant Ki of 2.2 ± 0.3 μM. Isothermal titration calorimetry experiments provided the thermodynamic parameters for the binding of TMG-chitotriomycin to VhGlcNAcase and revealed that binding was driven by both favorable enthalpy and entropy changes (ΔH° = -2.5 ± 0.1 kcal/mol and -TΔS° = -5.8 ± 0.3 kcal/mol), resulting in a free energy change, ΔG°, of -8.2 ± 0.2 kcal/mol. Dissection of the entropic term showed that a favorable solvation entropy change (-TΔSsolv° = -16 ± 2 kcal/mol) is the main contributor to the entropic term.
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Affiliation(s)
- Yusuke Morimoto
- Department of Advanced Bioscience, Kindai University, 3327-204 Nakamachi, Nara, 631-8505, Japan
| | - Shuji Takahashi
- Department of Chemistry and Biotechnology, Tottori University, 4-101 Koyama-minami, Tottori, 680-8552, Japan
| | - Yuta Isoda
- Department of Chemistry and Biotechnology, Tottori University, 4-101 Koyama-minami, Tottori, 680-8552, Japan
| | - Toshiki Nokami
- Department of Chemistry and Biotechnology, Tottori University, 4-101 Koyama-minami, Tottori, 680-8552, Japan
| | - Tamo Fukamizo
- Department of Advanced Bioscience, Kindai University, 3327-204 Nakamachi, Nara, 631-8505, Japan; School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Tumbol Payupnai, Wangchan Valley, Rayong, 21210, Thailand
| | - Wipa Suginta
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Tumbol Payupnai, Wangchan Valley, Rayong, 21210, Thailand
| | - Takayuki Ohnuma
- Department of Advanced Bioscience, Kindai University, 3327-204 Nakamachi, Nara, 631-8505, Japan; Agricultural Technology and Innovation Research Institute, Kindai University, Nara, Japan.
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