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Daunoras J, Kačergius A, Gudiukaitė R. Role of Soil Microbiota Enzymes in Soil Health and Activity Changes Depending on Climate Change and the Type of Soil Ecosystem. BIOLOGY 2024; 13:85. [PMID: 38392304 PMCID: PMC10886310 DOI: 10.3390/biology13020085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/25/2024] [Accepted: 01/27/2024] [Indexed: 02/24/2024]
Abstract
The extracellular enzymes secreted by soil microorganisms play a pivotal role in the decomposition of organic matter and the global cycles of carbon (C), phosphorus (P), and nitrogen (N), also serving as indicators of soil health and fertility. Current research is extensively analyzing these microbial populations and enzyme activities in diverse soil ecosystems and climatic regions, such as forests, grasslands, tropics, arctic regions and deserts. Climate change, global warming, and intensive agriculture are altering soil enzyme activities. Yet, few reviews have thoroughly explored the key enzymes required for soil fertility and the effects of abiotic factors on their functionality. A comprehensive review is thus essential to better understand the role of soil microbial enzymes in C, P, and N cycles, and their response to climate changes, soil ecosystems, organic farming, and fertilization. Studies indicate that the soil temperature, moisture, water content, pH, substrate availability, and average annual temperature and precipitation significantly impact enzyme activities. Additionally, climate change has shown ambiguous effects on these activities, causing both reductions and enhancements in enzyme catalytic functions.
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Affiliation(s)
- Jokūbas Daunoras
- Life Sciences Center, Vilnius University, Sauletekis Av. 7, LT-10257 Vilnius, Lithuania
| | - Audrius Kačergius
- Lithuanian Research Centre for Agriculture and Forestry, Kedainiai Distr., LT-58344 Akademija, Lithuania
| | - Renata Gudiukaitė
- Life Sciences Center, Vilnius University, Sauletekis Av. 7, LT-10257 Vilnius, Lithuania
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Liu Y, Yan Q, Ma J, Wang J, Jiang Z, Yang S. Directed evolution of a β-N-acetylhexosaminidase from Haloferula sp. for lacto-N-triose II and lacto-N-neotetraose synthesis from chitin. Enzyme Microb Technol 2023; 164:110177. [PMID: 36549095 DOI: 10.1016/j.enzmictec.2022.110177] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 12/06/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022]
Abstract
In our previous study, a β-N-acetylhexosaminidase (HaHex74) from Haloferula sp. showing high human milk oligosaccharides (HMOs) synthesis ability was identified and characterized. In this study, HaHex74 was further engineered by directed evolution and site-saturation mutagenesis to improve its transglycosylation activity for HMOs synthesis. A mutant (mHaHex74) with improved transglycosylation activity (HaHex74-Asn401Ile/His394Leu) was obtained and characterized. mHaHex74 exhibited maximal activity at pH 5.5 and 35 °C, respectively, which were distinct from that of HaHex74 (pH 6.5 and 45 °C). Moreover, mHaHex74 showed the highest LNT2 conversion ratio of 28.2% from N,N'-diacetyl chitobiose (GlcNAc2), which is 2.2 folds higher than that of HaHex74. A three-enzyme cascade reaction for the synthesis of LNT2 and LNnT from chitin was performed in a 5-L reactor, and the contents of LNT2 and LNnT reached up to 15.0 g L1 and 4.9 g L1, respectively. Therefore, mHaHex74 maybe a good candidate for enzymatic synthesis of HMOs.
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Affiliation(s)
- Yihao Liu
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Engineering, China Agricultural University, No.17 Qinghua East Road, Haidian, Beijing 100083, China
| | - Qiaojuan Yan
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Engineering, China Agricultural University, No.17 Qinghua East Road, Haidian, Beijing 100083, China
| | - Junwen Ma
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Engineering, China Agricultural University, No.17 Qinghua East Road, Haidian, Beijing 100083, China
| | - Jianyu Wang
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Engineering, China Agricultural University, No.17 Qinghua East Road, Haidian, Beijing 100083, China
| | - Zhengqiang Jiang
- Department of Nutrition and Health, College of Food Science and Nutritional Engineering, China Agricultural University, No.17 Qinghua East Road, Haidian, Beijing 100083, China.
| | - Shaoqing Yang
- Department of Nutrition and Health, College of Food Science and Nutritional Engineering, China Agricultural University, No.17 Qinghua East Road, Haidian, Beijing 100083, China.
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2017-2018. MASS SPECTROMETRY REVIEWS 2023; 42:227-431. [PMID: 34719822 DOI: 10.1002/mas.21721] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2018. Also included are papers that describe methods appropriate to glycan and glycoprotein analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, new methods, matrices, derivatization, MALDI imaging, fragmentation and the use of arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Most of the applications are presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and highlights the impact that MALDI imaging is having across a range of diciplines. MALDI is still an ideal technique for carbohydrate analysis and advancements in the technique and the range of applications continue steady progress.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
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Rajput M, Kumar M, Pareek N. Myco-chitinases as versatile biocatalysts for translation of coastal residual resources to eco-competent chito-bioactives. FUNGAL BIOL REV 2022. [DOI: 10.1016/j.fbr.2022.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Doan CT, Tran TN, Wang SL. Production of Thermophilic Chitinase by Paenibacillus sp. TKU052 by Bioprocessing of Chitinous Fishery Wastes and Its Application in N-acetyl-D-glucosamine Production. Polymers (Basel) 2021; 13:3048. [PMID: 34577952 PMCID: PMC8471714 DOI: 10.3390/polym13183048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/05/2021] [Accepted: 09/07/2021] [Indexed: 01/15/2023] Open
Abstract
The bioprocessing of chitinous fishery wastes (CFWs) to chitinases through fermentation approaches has gained importance owing to its great benefits in reducing the enzyme production cost, and utilizing chitin waste. In this work, our study of the chitinase production of Paenibacillus sp. TKU052 in the presence of different kinds of CFWs revealed a preference for demineralized crab shells powder (deCSP); furthermore, a 72 kDa chitinase was isolated from the 0.5% deCSP-containing medium. The Paenibacillus sp. TKU052 chitinase displayed maximum activity at 70 °C and pH 4-5, while Zn2+, Fe3+, Triton X-100, Tween 40, and SDS exerted a negative effect on its activity, whereas Mn2+ and 2-mercaptoethanol were found to potentially enhance the activity. Among various kinds of polysaccharide, Paenibacillus sp. TKU052 chitinase exhibited the best catalytic activity on colloidal chitin (CC) with Km = 9.75 mg/mL and Vmax = 2.43 μmol/min. The assessment of the hydrolysis of CC and N-acetyl chitooligosaccharides revealed that Paenibacillus sp. TKU052 chitinase possesses multiple catalytic functions, including exochitinase, endochitinase, and N-acetyl-β-D-glucosaminidase activities. Finally, the combination of Paenibacillus sp. TKU052 chitinase and Streptomyces speibonae TKU048 N-acetyl-β-D-glucosaminidase could efficiently convert CC to N-acetyl-D-glucosamine (GlcNAc) with a production yield of 94.35-98.60% in 12-24 h.
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Affiliation(s)
- Chien Thang Doan
- Faculty of Natural Sciences and Technology, Tay Nguyen University, Buon Ma Thuot 630000, Vietnam; (C.T.D.); (T.N.T.)
- Department of Chemistry, Tamkang University, New Taipei City 25137, Taiwan
| | - Thi Ngoc Tran
- Faculty of Natural Sciences and Technology, Tay Nguyen University, Buon Ma Thuot 630000, Vietnam; (C.T.D.); (T.N.T.)
- Doctoral Program in Applied Sciences, College of Science, Tamkang University, New Taipei City 25137, Taiwan
| | - San-Lang Wang
- Department of Chemistry, Tamkang University, New Taipei City 25137, Taiwan
- Life Science Development Center, Tamkang University, New Taipei City 25137, Taiwan
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Zhang A, Mo X, Zhou N, Wang Y, Wei G, Chen J, Chen K, Ouyang P. A novel bacterial β- N-acetyl glucosaminidase from Chitinolyticbacter meiyuanensis possessing transglycosylation and reverse hydrolysis activities. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:115. [PMID: 32612678 PMCID: PMC7324980 DOI: 10.1186/s13068-020-01754-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/20/2020] [Indexed: 05/31/2023]
Abstract
BACKGROUND N-Acetyl glucosamine (GlcNAc) and N-Acetyl chitooligosaccharides (N-Acetyl COSs) exhibit many biological activities, and have been widely used in the pharmaceutical, agriculture, food, and chemical industries. Particularly, higher N-Acetyl COSs with degree of polymerization from 4 to 7 ((GlcNAc)4-(GlcNAc)7) show good antitumor and antimicrobial activity, as well as possessing strong stimulating activity toward natural killer cells. Thus, it is of great significance to discover a β-N-acetyl glucosaminidase (NAGase) that can not only produce GlcNAc, but also synthesize N-Acetyl COSs. RESULTS The gene encoding the novel β-N-acetyl glucosaminidase, designated CmNAGase, was cloned from Chitinolyticbacter meiyuanensis SYBC-H1. The deduced amino acid sequence of CmNAGase contains a glycoside hydrolase family 20 catalytic module that shows low identity (12-35%) with the corresponding domain of most well-characterized NAGases. The CmNAGase gene was highly expressed with an active form in Escherichia coli BL21 (DE3) cells. The specific activity of purified CmNAGase toward p-nitrophenyl-N-acetyl glucosaminide (pNP-GlcNAc) was 4878.6 U/mg of protein. CmNAGase had a molecular mass of 92 kDa, and its optimum activity was at pH 5.4 and 40 °C. The V max, K m, K cat, and K cat/K m of CmNAGase for pNP-GlcNAc were 16,666.67 μmol min-1 mg-1, 0.50 μmol mL-1, 25,555.56 s-1, and 51,111.12 mL μmol-1 s-1, respectively. Analysis of the hydrolysis products of N-Acetyl COSs and colloidal chitin revealed that CmNAGase is a typical exo-acting NAGase. Particularly, CmNAGase can synthesize higher N-Acetyl COSs ((GlcNAc)3-(GlcNAc)7) from (GlcNAc)2-(GlcNAc)6, respectively, showed that it possesses transglycosylation activity. In addition, CmNAGase also has reverse hydrolysis activity toward GlcNAc, synthesizing various linked GlcNAc dimers. CONCLUSIONS The observations recorded in this study that CmNAGase is a novel NAGase with exo-acting, transglycosylation, and reverse hydrolysis activities, suggest a possible application in the production of GlcNAc or higher N-Acetyl COSs.
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Affiliation(s)
- Alei Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800 People’s Republic of China
| | - Xiaofang Mo
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800 People’s Republic of China
| | - Ning Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800 People’s Republic of China
| | - Yingying Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800 People’s Republic of China
| | - Guoguang Wei
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800 People’s Republic of China
| | - Jie Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800 People’s Republic of China
| | - Kequan Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800 People’s Republic of China
| | - Pingkai Ouyang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800 People’s Republic of China
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Liu Y, Jiang Z, Ma J, Ma S, Yan Q, Yang S. Biochemical Characterization and Structural Analysis of a β- N-Acetylglucosaminidase from Paenibacillus barengoltzii for Efficient Production of N-Acetyl-d-glucosamine. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:5648-5657. [PMID: 32338008 DOI: 10.1021/acs.jafc.9b08085] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Bioproduction of N-acetyl-d-glucosamine (GlcNAc) from chitin, the second most abundant natural renewable polymer on earth, is of great value in which chitinolytic enzymes play key roles. In this study, a novel glycoside hydrolase family-18 β-N-acetylglucosaminidase (PbNag39) from Paenibacillus barengoltzii suitable for GlcNAc production was identified and biochemically characterized. It possessed a unique shallow catalytic groove (5.8 Å) as well as a smaller C-terminal domain (solvent-accessible surface area, 5.1 × 103 Å2) and exhibited strict substrate specificity toward N-acetyl chitooligosaccharides (COS) with GlcNAc as the sole product, showing a typical manner of action of β-N-acetylglucosaminidases. Thus, an environmentally friendly bioprocess for GlcNAc production from ball-milled powdery chitin by an enzyme cocktail reaction was further developed. By using the new route, the powdery chitin conversion rate increased from 23.3% (v/v) to 75.3% with a final GlcNAc content of 22.6 mg mL-1. The efficient and environmentally friendly bioprocess may have great application potential in GlcNAc production.
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Affiliation(s)
- Yihao Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Engineering, China Agricultural University, No.17 Qinghua East Road, Haidian District, Beijing 100083, China
| | - Zhengqiang Jiang
- College of Food Science and Nutritional Engineering, China Agricultural University, No.17 Qinghua East Road, Haidian District, Beijing 100083, China
| | - Junwen Ma
- College of Food Science and Nutritional Engineering, China Agricultural University, No.17 Qinghua East Road, Haidian District, Beijing 100083, China
| | - Shuai Ma
- College of Engineering, China Agricultural University, No.17 Qinghua East Road, Haidian District, Beijing 100083, China
| | - Qiaojuan Yan
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Engineering, China Agricultural University, No.17 Qinghua East Road, Haidian District, Beijing 100083, China
| | - Shaoqing Yang
- College of Food Science and Nutritional Engineering, China Agricultural University, No.17 Qinghua East Road, Haidian District, Beijing 100083, China
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Zhou B, Huang N, Zeng W, Zhang H, Chen G, Liang Z. Development of a strategy for the screening of α-glucosidase-producing microorganisms. J Microbiol 2020; 58:163-172. [PMID: 31993989 DOI: 10.1007/s12275-020-9267-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 12/12/2019] [Accepted: 12/16/2019] [Indexed: 11/28/2022]
Abstract
α-Glucosidase is a crucial enzyme for the production of isomaltooligosaccharide. In this study, a novel method comprising eosin Y (EY) and α-D-methylglucoside (AMG) in glass plates was tested for the primary screening of α-glucosidaseproducing strains. First, α-glucosidase-producing Aspergillus niger strains were selected on plates containing EY and AMG based on transparent zone formation resulting from the solubilization of EY by the hydrolyzed product. Conventional methods that use trypan blue (TB) and p-nitrophenyl-α-D-glucopyranoside (pPNP) as indicators were then compared with the new strategy. The results showed that EY-containing plates provide the advantages of low price and higher specificity for the screening of α-glucosidase-producing strains. We then evaluated the correlation between the hydrolytic activity of α-glucosidase and diffusion distance, and found that good linearity could be established within a 6-75 U/ml enzyme concentration range. Finally, the hydrolytic and transglycosylation activities of α-glucosidase obtained from the target isolates were determined by EY plate assay and 3,5-dinitrosalicylic acid-Saccharomyces cerevisiae assay, respectively. The results showed that the diameter of the transparent zone varied among isolates was positively correlated with α-glucosidase hydrolytic activity, while good linearity could also be established between α-glucosidase transglycosylation activity and non-fermentable reducing sugars content. With this strategy, 7 Aspergillus niger mutants with high yield of α-glucosidase from 200 obvious single colonies on the primary screen plate were obtained.
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Affiliation(s)
- Bo Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Microorganism and Enzyme Research Center of Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, P. R. China
| | - Nan Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Microorganism and Enzyme Research Center of Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, P. R. China
| | - Wei Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Microorganism and Enzyme Research Center of Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, P. R. China
| | - Hao Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Microorganism and Enzyme Research Center of Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, P. R. China
| | - Guiguang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Microorganism and Enzyme Research Center of Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, P. R. China
| | - Zhiqun Liang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Microorganism and Enzyme Research Center of Engineering Technology, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, P. R. China.
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