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Lin Y, Dong Y, Li X, Cai J, Cai L, Zhang G. Enzymatic production of xylooligosaccharide from lignocellulosic and marine biomass: A review of current progress, challenges, and its applications in food sectors. Int J Biol Macromol 2024; 277:134014. [PMID: 39047995 DOI: 10.1016/j.ijbiomac.2024.134014] [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: 09/18/2023] [Revised: 04/03/2024] [Accepted: 07/17/2024] [Indexed: 07/27/2024]
Abstract
Over the last decade, xylooligosaccharides (XOS) have attracted great attentions because of their unique chemical properties and excellent prebiotic effects. Among the current strategies for XOS production, enzymatic hydrolysis is preferred due to its green and safe process, simplicity in equipment, and high control of the degrees of polymerization. This paper comprehensively summarizes various lignocellulosic biomass and marine biomass employed in enzymatic production of XOS. The importance and advantages of enzyme immobilization in XOS production are also discussed. Many novel immobilization techniques for xylanase are presented. In addition, bioinformatics techniques for the mining and designing of new xylanase are also described. Moreover, XOS has exhibited great potential applications in the food industry as diverse roles, such as a sugar replacer, a fat replacer, and cryoprotectant. This review systematically summarizes the current research progress on the applications of XOS in food sectors, including beverages, bakery products, dairy products, meat products, aquatic products, food packaging film, wall materials, and others. It is anticipated that this paper will act as a reference for the further development and application of XOS in food sectors and other fields.
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Affiliation(s)
- Yuanqing Lin
- College of Environment and Public Health, Xiamen Huaxia University, Xiamen 361024, Fujian, China
| | - Yuting Dong
- College of Environment and Public Health, Xiamen Huaxia University, Xiamen 361024, Fujian, China; Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, Fujian, China
| | - Xiangling Li
- Thayer School of Engineering, Dartmouth College, Hanover, NH 03755, United States
| | - Jinzhong Cai
- College of Environment and Public Health, Xiamen Huaxia University, Xiamen 361024, Fujian, China
| | - Lixi Cai
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, Fujian, China; College of Basic Medicine, Putian University, Putian 351100, Fujian, China.
| | - Guangya Zhang
- Department of Bioengineering and Biotechnology, Huaqiao University, Xiamen 361021, Fujian, China.
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2
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Nam KH. Temperature-dependent structural changes in xylanase II from Trichoderma longibrachiatum. Carbohydr Res 2024; 541:109173. [PMID: 38833820 DOI: 10.1016/j.carres.2024.109173] [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: 04/29/2024] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/06/2024]
Abstract
Endo-β-1,4-xylanases degrade heteroxylans that constitute the lignocellulosic plant cell wall. This enzyme is widely used in the food, paper, textile, and biorefinery industries. Temperature affects the optimum activity of xylanase and is an important factor in its application. Various structural analyses of xylanase have been performed, but its structural influence by temperature is not fully elucidated. To better understand the structural influence of xylanase due to temperature, the crystal structure of xylanase II from Trichoderma longibrachiatum (TloXynII) at room and cryogenic temperatures was determined at 2.1 and 1.9 Å resolution, respectively. The room-temperature structure of TloXynII (TloXynIIRT) showed a B-factor value 2.09 times higher than that of the cryogenic-temperature structure of TloXynII (TloXynIICryo). Subtle movement of the catalytic and substrate binding residues was observed between TloXynIIRT and TloXynIICryo. In TloXynIIRT, the thumb domain exhibited high flexibility, whereas in TloXynIICryo, the finger domain exhibited high flexibility. The substrate binding cleft of TloXynIIRT was narrower than that of TloXynIICryo, indicating a distinct finger domain conformation. Numerous water molecule networks were observed in the substrate binding cleft of TloXynIICryo, whereas only a few water molecules were observed in TloXynIIRT. These structural analyses expand our understanding of the temperature-dependent conformational changes in xylanase.
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Affiliation(s)
- Ki Hyun Nam
- College of General Education, Kookmin University, Seoul, 02707, Republic of Korea.
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3
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Bhairamkar S, Kadam P, Anjulal H, Joshi A, Chaudhari R, Bagul D, Javdekar V, Zinjarde S. Comprehensive updates on the biological features and metabolic potential of the versatile extremophilic actinomycete Nocardiopsis dassonvillei. Res Microbiol 2024; 175:104171. [PMID: 37995890 DOI: 10.1016/j.resmic.2023.104171] [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: 09/15/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 11/25/2023]
Abstract
Nocardiopsis dassonvillei prevails under harsh environmental conditions and the purpose of this review is to highlight its biological features and recent biotechnological applications. The organism prevails in salt-rich soils/marine systems and some strains endure extreme temperatures and pH. A few isolates are associated with marine organisms and others cause human diseases. Comparative genomic analysis indicates its versatility in producing biotechnologically relevant metabolites. Antimicrobial, cytotoxic, anticancer and growth promoting biomolecules are obtained from this organism. It also synthesizes biotechnologically important enzymes. Bioactive compounds and enzymes obtained from this actinomycete provide evidence regarding its metabolic competence and its potential economic value.
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Affiliation(s)
- Shivani Bhairamkar
- Department of Biotechnology (With Jointly Merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, Pune, 411007, India
| | - Pratik Kadam
- Department of Biotechnology (With Jointly Merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, Pune, 411007, India
| | - H Anjulal
- Department of Biotechnology (With Jointly Merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, Pune, 411007, India
| | - Avani Joshi
- Department of Biotechnology (With Jointly Merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, Pune, 411007, India
| | - Riddhi Chaudhari
- Department of Biotechnology (With Jointly Merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, Pune, 411007, India
| | - Dimpal Bagul
- Department of Biotechnology (With Jointly Merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, Pune, 411007, India
| | - Vaishali Javdekar
- Department of Biotechnology (With Jointly Merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, Pune, 411007, India
| | - Smita Zinjarde
- Department of Biotechnology (With Jointly Merged Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, Pune, 411007, India.
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Akram F, Fatima T, Ibrar R, Shabbir I, Shah FI, Haq IU. Trends in the development and current perspective of thermostable bacterial hemicellulases with their industrial endeavors: A review. Int J Biol Macromol 2024; 265:130993. [PMID: 38508567 DOI: 10.1016/j.ijbiomac.2024.130993] [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: 07/15/2023] [Revised: 03/12/2024] [Accepted: 03/17/2024] [Indexed: 03/22/2024]
Abstract
Hemicellulases are enzymes that hydrolyze hemicelluloses, common polysaccharides in nature. Thermophilic hemicellulases, derived from microbial strains, are extensively studied as natural biofuel sources due to the complex structure of hemicelluloses. Recent research aims to elucidate the catalytic principles, mechanisms and specificity of hemicellulases through investigations into their high-temperature stability and structural features, which have applications in biotechnology and industry. This review article targets to serve as a comprehensive resource, highlighting the significant progress in the field and emphasizing the vital role of thermophilic hemicellulases in eco-friendly catalysis. The primary goal is to improve the reliability of hemicellulase enzymes obtained from thermophilic bacterial strains. Additionally, with their ability to break down lignocellulosic materials, hemicellulases hold immense potential for biofuel production. Despite their potential, the commercial viability is hindered by their high enzyme costs, necessitating the development of efficient bioprocesses involving waste pretreatment with microbial consortia to overcome this challenge.
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Affiliation(s)
- Fatima Akram
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan.
| | - Taseer Fatima
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | - Ramesha Ibrar
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | - Ifrah Shabbir
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | | | - Ikram Ul Haq
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan; Pakistan Academy of Sciences, Islamabad, Pakistan
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Cao L, Lin M, Ning J, Meng X, Pu X, Zhang R, Wu Q, Huang Z, Zhou J. Critical Roles of Acidic Residues in Loop Regions of the Structural Surface for the Salt Tolerance of a GH39 β-d-Xylosidase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:5805-5815. [PMID: 38451212 DOI: 10.1021/acs.jafc.3c07957] [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: 03/08/2024]
Abstract
Xylan is the main component of hemicellulose. Complete hydrolysis of xylan requires synergistically acting xylanases, such as β-d-xylosidases. Salt-tolerant β-d-xylosidases have significant application benefits, but few reports have explored the critical amino acids affecting the salt tolerance of xylosidases. Herein, the site-directed mutation was used to demonstrate that negative electrostatic potentials generated by 19 acidic residues in the loop regions of the structural surface positively correlated with the improved salt tolerance of GH39 β-d-xylosidase JB13GH39P28. These mutants showed reduced negative potentials on structural surfaces as well as a 13-43% decrease in stability in 3.0-30.0% (w/v) NaCl. Six key residue sites, D201, D259, D297, D377, D395, and D474, were confirmed to influence both the stability and activity of GH39 β-d-xylosidase. The activity of the GH39 β-d-xylosidase was found promoting by SO42- and inhibiting by NO3-. Values of Km and Kcat/Km decreased aggravatedly in 30.0% (w/v) NaCl when mutation operated on residues E179 and D182 in the loop regions of the catalytic domain. Taken together, mutation on acidic residues in loop regions from catalytic and noncatalytic domains may cause the deformation of catalytic pocket and aggregation of protein particles then decrease the stability, binding affinity, and catalytic efficiency of the β-d-xylosidase.
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Affiliation(s)
- Lijuan Cao
- College of Life Sciences, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Mingyue Lin
- College of Life Sciences, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Juan Ning
- College of Life Sciences, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Xin Meng
- College of Life Sciences, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Xiong Pu
- College of Life Sciences, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Rui Zhang
- College of Life Sciences, Yunnan Normal University, Kunming 650500, People's Republic of China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming 650500, People's Republic of China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan 650500, People's Republic of China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Qian Wu
- College of Life Sciences, Yunnan Normal University, Kunming 650500, People's Republic of China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming 650500, People's Republic of China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan 650500, People's Republic of China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Zunxi Huang
- College of Life Sciences, Yunnan Normal University, Kunming 650500, People's Republic of China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming 650500, People's Republic of China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan 650500, People's Republic of China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Junpei Zhou
- College of Life Sciences, Yunnan Normal University, Kunming 650500, People's Republic of China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming 650500, People's Republic of China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan 650500, People's Republic of China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Yunnan Normal University, Kunming 650500, People's Republic of China
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Lu H, Xue M, Nie X, Luo H, Tan Z, Yang X, Shi H, Li X, Wang T. Glycoside hydrolases in the biodegradation of lignocellulosic biomass. 3 Biotech 2023; 13:402. [PMID: 37982085 PMCID: PMC10654287 DOI: 10.1007/s13205-023-03819-1] [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: 09/04/2023] [Accepted: 10/15/2023] [Indexed: 11/21/2023] Open
Abstract
Lignocellulose is a plentiful and intricate biomass substance made up of cellulose, hemicellulose, and lignin. Cellulose and hemicellulose are polysaccharides characterized by different compositions and degrees of polymerization. As renewable resources, their applications are eco-friendly and can help reduce reliance on petrochemical resources. This review aims to illustrate cellulose, hemicellulose, and their structures and hydrolytic enzymes. To obtain desirable enzyme sources for the high hydrolysis of lignocellulose, highly stable, efficient and thermophilic enzyme sources, and new technologies, such as rational design and machine learning, have been introduced in detail. Generally, the efficient biodegradation of abundant natural biomass into fermentable sugars or other intermediates has great potential in practical applications. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03819-1.
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Affiliation(s)
- Honglin Lu
- Faculty of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003 China
| | - Maoyuan Xue
- Faculty of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003 China
| | - Xinling Nie
- Faculty of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003 China
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-Forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037 China
| | - Hongzheng Luo
- Faculty of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003 China
| | - Zhongbiao Tan
- Faculty of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003 China
| | - Xiao Yang
- Department of Poultry Science, The University of Georgia, Athens, GA 30602 USA
| | - Hao Shi
- Faculty of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003 China
| | - Xun Li
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-Forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037 China
| | - Tao Wang
- Department of Microbiology, The University of Georgia, Athens, GA 30602 USA
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Liu Y, Tang S, Wang X, Wang X, Tang X, Wu Q, Huang Z, Ding J. A novel thermostable and salt-tolerant carboxylesterase involved in the initial aerobic degradation pathway for pyrethroids in Glycomyces salinus. JOURNAL OF HAZARDOUS MATERIALS 2023; 451:131128. [PMID: 36893599 DOI: 10.1016/j.jhazmat.2023.131128] [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: 12/21/2022] [Revised: 02/25/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
The long-term and excessive use of pyrethroid pesticides poses substantial health risks and ecosystem concerns. Several bacteria and fungi have been reported that could degrade pyrethroids. The ester-bond hydrolysis using hydrolases is the initial regulatory metabolic reaction of pyrethroids. However, the thoroughly biochemical characterization of hydrolases involved in this process is limited. Here, a novel carboxylesterase, designated as EstGS1 that could hydrolyze pyrethroid pesticides was characterized. EstGS1 showed low sequence identity (<27.03%) compared to other reported pyrethroid hydrolases and belonged to the hydroxynitrile lyase family that preferred short short-chain acyl esters (C2 to C8). EstGS1 displayed the maximal activity of 213.38 U/mg at 60 °C and pH 8.5 using pNPC2 as substrate, with Km and Vmax were 2.21 ± 0.72 mM and 212.90 ± 41.78 µM/min, respectively. EstGS1 is a halotolerant esterase and remains stable in 5.1 M NaCl. Based on molecular docking and mutational analysis, the catalytic triad of S74-D181-H212 and three other substrate-binding residues I108, S159, and G75 are critical for the enzymatic activity of EstGS1. Additionally, 61 and 40 mg/L of deltamethrin and λ-cyhalothrin were hydrolyzed by 20 U of EstGS1 in 4 h. This work presents the first report on a pyrethroid pesticide hydrolase characterized from a halophilic actinobacteria.
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Affiliation(s)
- Yan Liu
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming 650500, China
| | - Shukun Tang
- Yunnan Institute of Microbiology, Key Laboratory for Conservation and Utilization of Bio-Resource, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Xu Wang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming 650500, China
| | - Xiaoliang Wang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming 650500, China
| | - Xianghua Tang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming 650500, China
| | - Qian Wu
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming 650500, China
| | - Zunxi Huang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming 650500, China; Key Laboratory of Yunnan Province for Biomass Energy and Environmental Biotechnology, Yunnan Normal University, Kunming 650500, China
| | - Junmei Ding
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming 650500, China; Key Laboratory of Yunnan Province for Biomass Energy and Environmental Biotechnology, Yunnan Normal University, Kunming 650500, China.
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8
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Li N, Zhang R, Zhou J, Huang Z. Structures, Biochemical Characteristics, and Functions of β-Xylosidases. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:7961-7976. [PMID: 37192316 DOI: 10.1021/acs.jafc.3c01425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The complete degradation of abundant xylan derived from plants requires the participation of β-xylosidases to produce the xylose which can be converted to xylitol, ethanol, and other valuable chemicals. Some phytochemicals can also be hydrolyzed by β-xylosidases into bioactive substances, such as ginsenosides, 10-deacetyltaxol, cycloastragenol, and anthocyanidins. On the contrary, some hydroxyl-containing substances such as alcohols, sugars, and phenols can be xylosylated by β-xylosidases into new chemicals such as alkyl xylosides, oligosaccharides, and xylosylated phenols. Thus, β-xylosidases shows great application prospects in food, brewing, and pharmaceutical industries. This review focuses on the molecular structures, biochemical properties, and bioactive substance transformation function of β-xylosidases derived from bacteria, fungi, actinomycetes, and metagenomes. The molecular mechanisms of β-xylosidases related to the properties and functions are also discussed. This review will serve as a reference for the engineering and application of β-xylosidases in food, brewing, and pharmaceutical industries.
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Affiliation(s)
- Na Li
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming 650500, People's Republic of China
- College of Life Sciences, Yunnan Normal University, Kunming 650500, People's Republic of China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming 650500, People's Republic of China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Kunming 650500, People's Republic of China
| | - Rui Zhang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming 650500, People's Republic of China
- College of Life Sciences, Yunnan Normal University, Kunming 650500, People's Republic of China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming 650500, People's Republic of China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Kunming 650500, People's Republic of China
| | - Junpei Zhou
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming 650500, People's Republic of China
- College of Life Sciences, Yunnan Normal University, Kunming 650500, People's Republic of China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming 650500, People's Republic of China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Kunming 650500, People's Republic of China
| | - Zunxi Huang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming 650500, People's Republic of China
- College of Life Sciences, Yunnan Normal University, Kunming 650500, People's Republic of China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming 650500, People's Republic of China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Kunming 650500, People's Republic of China
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Dionisi HM, Lozada M, Campos E. Diversity of GH51 α-L-arabinofuranosidase homolog sequences from subantarctic intertidal sediments. Biologia (Bratisl) 2023. [DOI: 10.1007/s11756-023-01382-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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10
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Eliminating host-guest incompatibility via enzyme mining enables the high-temperature production of N-acetylglucosamine. iScience 2022; 26:105774. [PMID: 36636338 PMCID: PMC9829697 DOI: 10.1016/j.isci.2022.105774] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 10/09/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
The host-guest incompatibility between a production host and non-native enzymes has posed an arduous challenge for synthetic biology, particularly between mesophile-derived enzymes and a thermophilic chassis. In the present study, we develop a thermophilic enzyme mining strategy comprising an automated co-evolution-based screening pipeline (http://cem.sjtu.edu.cn), computation-based enzyme characterization, and gene synthesis-based function validation. Using glucosamine-6-phosphate acetyltransferase (GNA1) as an example, we successfully mined four novel GNA1s with excellent thermostabilities and catalytic performances. Calculation and analysis based on AlphaFold2-generated structures were also conducted to uncover the mechanism underlying their excellent properties. Finally, our mined GNA1s were used to enable the high-temperature N-acetylglucosamine (GlcNAc) production with high titers of up to 119.3 g/L, with the aid of systems metabolic engineering and temperature programming. This study demonstrates the effectiveness of the enzyme mining strategy, highlighting the application prospects of mining new enzymes from massive databases and providing an effective solution for tackling host-guest incompatibility.
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Genomic Analysis to Elucidate the Lignocellulose Degrading Capability of a New Halophile Robertkochia solimangrovi. Genes (Basel) 2022; 13:genes13112135. [DOI: 10.3390/genes13112135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 11/19/2022] Open
Abstract
Robertkochia solimangrovi is a proposed marine bacterium isolated from mangrove soil. So far, the study of this bacterium is limited to taxonomy only. In this report, we performed a genomic analysis of R. solimangrovi that revealed its lignocellulose degrading ability. Genome mining of R. solimangrovi revealed a total of 87 lignocellulose degrading enzymes. These enzymes include cellulases (GH3, GH5, GH9 and GH30), xylanases (GH5, GH10, GH43, GH51, GH67, and GH115), mannanases (GH2, GH26, GH27 and GH113) and xyloglucanases (GH2, GH5, GH16, GH29, GH31 and GH95). Most of the lignocellulolytic enzymes encoded in R. solimangrovi were absent in the genome of Robertkochia marina, the closest member from the same genus. Furthermore, current work also demonstrated the ability of R. solimangrovi to produce lignocellulolytic enzymes to deconstruct oil palm empty fruit bunch (EFB), a lignocellulosic waste found abundantly in palm oil industry. The metabolic pathway taken by R. solimangrovi to transport and process the reducing sugars after the action of lignocellulolytic enzymes on EFB was also inferred based on genomic data. Collectively, genomic analysis coupled with experimental studies elucidated R. solimangrovi to serve as a promising candidate in seawater based-biorefinery industry.
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Xu L, Zhang Y, Liu N, Wei Z, Wang Z, Wang Y, Wang S. Purification and characterization of cold-adapted and salt-tolerant dextranase from Cellulosimicrobium sp. THN1 and its potential application for treatment of dental plaque. Front Microbiol 2022; 13:1012957. [PMID: 36439846 PMCID: PMC9691899 DOI: 10.3389/fmicb.2022.1012957] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 10/17/2022] [Indexed: 10/28/2023] Open
Abstract
The cold-adapted and/or salt-tolerant enzymes from marine microorganisms were confirmed to be meritorious tools to enhance the efficiency of biocatalysis in industrial biotechnology. We purified and characterized a dextranase CeDex from the marine bacterium Cellulosimicrobium sp. THN1. CeDex acted in alkaline pHs (7.5-8.5) and a broad temperature range (10-50°C) with sufficient pH stability and thermostability. Remarkably, CeDex retained approximately 40% of its maximal activities at 4°C and increased its activity to 150% in 4 M NaCl, displaying prominently cold adaptation and salt tolerance. Moreover, CeDex was greatly stimulated by Mg2+, Na+, Ba2+, Ca2+ and Sr2+, and sugarcane juice always contains K+, Ca2+, Mg2+ and Na+, so CeDex will be suitable for removing dextran in the sugar industry. The main hydrolysate of CeDex was isomaltotriose, accompanied by isomaltotetraose, long-chain IOMs, and a small amount of isomaltose. The amino acid sequence of CeDex was identified from the THN1 genomic sequence by Nano LC-MS/MS and classified into the GH49 family. Notably, CeDex could prevent the formation of Streptococcus mutans biofilm and disassemble existing biofilms at 10 U/ml concentration and would have great potential to defeat biofilm-related dental caries.
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Affiliation(s)
- Linxiang Xu
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, China
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, China
| | - Yan Zhang
- School of Marine Science and Fisheries, Jiangsu Ocean University, Lianyungang, China
| | - Nannan Liu
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, China
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, China
| | - Zhen Wei
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, China
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, China
| | - Zhen Wang
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, China
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, China
| | - Yonghua Wang
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Shujun Wang
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang, China
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Cen X, Zhang R, He L, Tang X, Wu Q, Zhou J, Huang Z. Deletion of the Loop Linking Two Domains of Exo-Inulinase InuAMN8 Diminished the Enzymatic Thermo-Halo-Alcohol Tolerance. Front Microbiol 2022; 13:924447. [PMID: 35814689 PMCID: PMC9260423 DOI: 10.3389/fmicb.2022.924447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/31/2022] [Indexed: 11/27/2022] Open
Abstract
Inulin is the rich water-soluble storage polysaccharide after starch in nature, and utilization of inulin through hydrolysis of exo-inulinases has attracted much attention. Thermo-halo-alcohol tolerance is essential for exo-inulinase applications, while no report reveals the molecular basis involved in halo-alcohol tolerance of exo-inulinases via experimental data. In this study, two loops of exo-inulinase InuAMN8, including the loop built with 360GHVRLGPQP368 linking domains of Glyco_hydro_32N and Glyco_hydro_32C and another loop built with 169GGAG172 in the catalytic domain, were deleted to generate mutants MutG360Δ9 and MutG169Δ4, respectively. After heterologous expression, purification, and dialysis, InuAMN8, MutG169Δ4, and MutG360Δ9 showed half-lives of 144, 151, and 7 min at 50°C, respectively. InuAMN8 and MutG169Δ4 were very stable, while MutG360Δ9 showed a half-life of approximately 60 min in 5.0% (w/v) NaCl, and they showed half-lives of approximately 60 min in 25.0, 25.0, and 5.0% (w/v) ethanol, respectively. Structural analysis indicated that two cation-π bonds, which contributed to thermal properties of InuAMN8 at high temperatures, broke in MutG360Δ9. Four basic amino acid residues were exposed to the structural surface of MutG360Δ9 and formed positive and neutral electrostatic potential that caused detrimental effects on halo-alcohol tolerance. The study may provide a better understanding of the loop-function relationships that are involved in thermo-halo-alcohol adaptation of enzymes in extreme environment.
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Affiliation(s)
- Xiaolong Cen
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, China
- College of Life Sciences, Yunnan Normal University, Kunming, China
- Key Laboratory of Biomass Energy and Environmental Biotechnology, Yunnan Normal University, Kunming, China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Yunnan Normal University, Kunming, China
| | - Rui Zhang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, China
- College of Life Sciences, Yunnan Normal University, Kunming, China
- Key Laboratory of Biomass Energy and Environmental Biotechnology, Yunnan Normal University, Kunming, China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Yunnan Normal University, Kunming, China
| | - Limei He
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, China
- College of Life Sciences, Yunnan Normal University, Kunming, China
- Key Laboratory of Biomass Energy and Environmental Biotechnology, Yunnan Normal University, Kunming, China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Yunnan Normal University, Kunming, China
| | - Xianghua Tang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, China
- College of Life Sciences, Yunnan Normal University, Kunming, China
- Key Laboratory of Biomass Energy and Environmental Biotechnology, Yunnan Normal University, Kunming, China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Yunnan Normal University, Kunming, China
| | - Qian Wu
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, China
- College of Life Sciences, Yunnan Normal University, Kunming, China
- Key Laboratory of Biomass Energy and Environmental Biotechnology, Yunnan Normal University, Kunming, China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Yunnan Normal University, Kunming, China
| | - Junpei Zhou
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, China
- College of Life Sciences, Yunnan Normal University, Kunming, China
- Key Laboratory of Biomass Energy and Environmental Biotechnology, Yunnan Normal University, Kunming, China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Yunnan Normal University, Kunming, China
- *Correspondence: Junpei Zhou, ,
| | - Zunxi Huang
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming, China
- College of Life Sciences, Yunnan Normal University, Kunming, China
- Key Laboratory of Biomass Energy and Environmental Biotechnology, Yunnan Normal University, Kunming, China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Yunnan Normal University, Kunming, China
- Zunxi Huang,
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