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Li X, Yang M, Mo K, Hu Y, Gu H, Sun D, Bao S, Huang H. Genome Analysis of Multiple Polysaccharide-Degrading Bacterium Microbulbifer thermotolerans HB226069: Determination of Alginate Lyase Activity. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:488-499. [PMID: 38668917 DOI: 10.1007/s10126-024-10311-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 04/05/2024] [Indexed: 06/15/2024]
Abstract
Polysaccharide-degrading bacteria are key participants in the global carbon cycle and algal biomass recycling. Herein, a polysaccharide lyase-producing strain HB226069 was isolated from Sargassum sp. from Qingge Port, Hainan, China. Results of the phylogenetic of the 16S rRNA gene and genotypic analysis indicated that the isolate should be classified as Microbulbifer thermotolerans. The whole genome is a 4,021,337 bp circular chromosome with a G+C content of 56.5%. Analysis of the predicted genes indicated that strain HB226069 encoded 161 carbohydrate-active enzymes (CAZymes), and abundant putative enzymes involved in polysaccharide degradation were predicted, including alginate lyase, fucosidase, agarase, xylanase, cellulase, pectate lyase, amylase, and chitinase. Three of the putative polysaccharide lyases from PL7 and PL17 families were involved in alginate degradation. The alginate lyases of strain HB226069 showed the maximum activity of 117.4 U/mL at 50 °C, pH 7.0, and 0.05 M FeCl3, while exhibiting the best stability at 30 °C and pH 7.0. The Thin Layer Chromatography (TLC) and Electrospray Ionization Mass Spectrometry (ESI-MS) analyses indicated that the alginate oligosaccharides (AOSs) degraded by the partially purified alginate lyases contained oligosaccharides of DP2-DP5 and monosaccharide while reacting for 36 h. The complete genome of M. thermotolerans HB226069 enriches our understanding of the mechanism of polysaccharide lyase production and supports its potential application in polysaccharide degradation.
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Affiliation(s)
- Xue Li
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163000, Heilongjiang, China
| | - Miao Yang
- Institute of Tropical Bioscience and Biotechnology, Hainan Institute for Tropical Agricultural Resources, CATAS, Haikou, 571101, Hainan, China
- College of Life Science and Technology, Huazhong Agricultural University, CATAS, Wuhan, 430070, Hubei, China
| | - Kunlian Mo
- Institute of Tropical Bioscience and Biotechnology, Hainan Institute for Tropical Agricultural Resources, CATAS, Haikou, 571101, Hainan, China
- Zhanjiang Experimental Station, CATAS, Zhanjiang, 524013, Guangdong, China
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bioresources, Haikou, 571101, Hainan, China
| | - Yonghua Hu
- Institute of Tropical Bioscience and Biotechnology, Hainan Institute for Tropical Agricultural Resources, CATAS, Haikou, 571101, Hainan, China
- Zhanjiang Experimental Station, CATAS, Zhanjiang, 524013, Guangdong, China
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bioresources, Haikou, 571101, Hainan, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266071, Shandong, China
| | - Hanjie Gu
- Institute of Tropical Bioscience and Biotechnology, Hainan Institute for Tropical Agricultural Resources, CATAS, Haikou, 571101, Hainan, China
- Zhanjiang Experimental Station, CATAS, Zhanjiang, 524013, Guangdong, China
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bioresources, Haikou, 571101, Hainan, China
| | - Dongmei Sun
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, 163000, Heilongjiang, China.
| | - Shixiang Bao
- Institute of Tropical Bioscience and Biotechnology, Hainan Institute for Tropical Agricultural Resources, CATAS, Haikou, 571101, Hainan, China.
- Zhanjiang Experimental Station, CATAS, Zhanjiang, 524013, Guangdong, China.
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bioresources, Haikou, 571101, Hainan, China.
| | - Huiqin Huang
- Institute of Tropical Bioscience and Biotechnology, Hainan Institute for Tropical Agricultural Resources, CATAS, Haikou, 571101, Hainan, China.
- Zhanjiang Experimental Station, CATAS, Zhanjiang, 524013, Guangdong, China.
- Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bioresources, Haikou, 571101, Hainan, China.
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Xu H, Gao Q, Li L, Su T, Ming D. How alginate lyase produces quasi-monodisperse oligosaccharides: A normal-mode-based docking and molecular dynamics simulation study. Carbohydr Res 2024; 536:109022. [PMID: 38242069 DOI: 10.1016/j.carres.2024.109022] [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: 09/24/2023] [Revised: 12/12/2023] [Accepted: 01/04/2024] [Indexed: 01/21/2024]
Abstract
Oligosaccharide degradation products of alginate (AOS) hold significant potential in diverse fields, including pharmaceuticals, health foods, textiles, and agricultural production. Enzymatic alginate degradation is appealing due to its mild conditions, predictable activity, high yields, and controllability. However, the alginate degradation often results in a complex mixture of oligosaccharides, necessitating costly purification to isolate highly active oligosaccharides with a specific degree of polymerization (DP). Addressing this, our study centers on the alginate lyase AlyB from Vibrio Splendidus OU02, which uniquely breaks down alginate into mono-distributed trisaccharides. This enzyme features a polysaccharide lyase family 7 domain (PL-7) and a CBM32 carbohydrate-binding module connected by a helical structure. Through normal-mode-based docking and all-atom molecular simulations, we demonstrate that AlyB's substrate and product specificities are influenced by the spatial conformation of the catalytic pocket and the flexibility of its structure. The helically attached CBM is pivotal in releasing trisaccharides, which is crucial for avoiding further degradation. This study sheds light on AlyB's specificity and efficiency and contributes to the evolving field of enzyme design for producing targeted oligosaccharides, with significant implications for various bioindustries.
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Affiliation(s)
- Hengyue Xu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 South Puzhu Road, Jiangbei New District, Nanjing City, Jiangsu, 211816, PR China; Now Studying in the State Key Laboratory of Chemical Oncogenomics, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, PR China
| | - Qi Gao
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 South Puzhu Road, Jiangbei New District, Nanjing City, Jiangsu, 211816, PR China
| | - Lu Li
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 South Puzhu Road, Jiangbei New District, Nanjing City, Jiangsu, 211816, PR China
| | - Ting Su
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 South Puzhu Road, Jiangbei New District, Nanjing City, Jiangsu, 211816, PR China
| | - Dengming Ming
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 South Puzhu Road, Jiangbei New District, Nanjing City, Jiangsu, 211816, PR China.
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3
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Du M, Li X, Qi W, Li Y, Wang L. Identification and characterization of a critical loop for the high activity of alginate lyase VaAly2 from the PL7_5 subfamily. Front Microbiol 2024; 14:1333597. [PMID: 38282736 PMCID: PMC10811132 DOI: 10.3389/fmicb.2023.1333597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 12/27/2023] [Indexed: 01/30/2024] Open
Abstract
As the major component in the cell wall of brown algae, alginates are degradable by alginate lyases via β-elimination. Alginate lyases can be categorized into various polysaccharide lyase (PL) families, and PL7 family alginate lyases are the largest group and can be divided into six subfamilies. However, the major difference among different PL7 subfamilies is not fully understood. In this work, a marine alginate lyase, VaAly2, from Vibrio alginolyticus ATCC 17749 belonging to the PL7_5 subfamily was identified and characterized. It displayed comparatively high alginolytic activities toward different alginate substrates and functions as a bifunctional lyase. Molecular docking and biochemical analysis suggested that VaAly2 not only contains a key catalyzing motif (HQY) conserved in the PL7 family but also exhibits some specific characters limited in the PL7_5 subfamily members, such as the key residues and a long loop1 structure around the active center. Our work provides insight into a loop structure around the center site which plays an important role in the activity and substrate binding of alginate lyases belonging to the PL7_5 subfamily.
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Affiliation(s)
- Muxuan Du
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- School of Life Sciences, Shandong University, Qingdao, China
| | - Xue Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Weipeng Qi
- Foshan Haitian (Gaoming) Flavoring & Food Co., Ltd., Foshan, China
| | - Yingjie Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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Xiao Z, Li K, Li T, Zhang F, Xue J, Zhao M, Yin H. Characterization and Mechanism Study of a Novel PL7 Family Exolytic Alginate Lyase from Marine Bacteria Vibrio sp. W13. Appl Biochem Biotechnol 2024; 196:68-84. [PMID: 37099125 DOI: 10.1007/s12010-023-04483-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2023] [Indexed: 04/27/2023]
Abstract
Alginate lyase can degrade alginate into oligosaccharides through β-elimination for various biological, biorefinery, and agricultural purposes. Here, we report a novel PL7 family exolytic alginate lyase VwAlg7A from marine bacteria Vibrio sp. W13 and achieve the heterologous expression in E. coli BL21 (DE3). VwAlg7A is 348aa with a calculated molecular weight of 36 kDa, containing an alginate lyase 2 domain. VwAlg7A exhibits specificity towards poly-guluronate. The optimal temperature and pH of VwAlg7A are 30 °C and 7.0, respectively. The activity of VwAlg7A can be significantly inhibited by the Ni2+, Zn2+, and NaCl. The Km and Vmax of VwAlg7A are 36.9 mg/ml and 395.6 μM/min, respectively. The ESI and HPAEC-PAD results indicate that VwAlg7A cleaves the sugar bond in an exolytic mode. Based on the molecular docking and mutagenesis results, we further confirmed that R98, H169, and Y303 are important catalytic residues.
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Affiliation(s)
- Zhongbin Xiao
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Dalian Technology Innovation Center for Green Agriculture, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Department of Materials and Chemicals, Dalian Polytechnic University, Dalian, 116023, China
| | - Kuikui Li
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Dalian Technology Innovation Center for Green Agriculture, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Tang Li
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Dalian Technology Innovation Center for Green Agriculture, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Fanxing Zhang
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Dalian Technology Innovation Center for Green Agriculture, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Department of Materials and Chemicals, Dalian Polytechnic University, Dalian, 116023, China
| | - Jiayi Xue
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Dalian Technology Innovation Center for Green Agriculture, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
- Department of Materials and Chemicals, Dalian Polytechnic University, Dalian, 116023, China
| | - Miao Zhao
- Department of Materials and Chemicals, Dalian Polytechnic University, Dalian, 116023, China
| | - Heng Yin
- Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Dalian Technology Innovation Center for Green Agriculture, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
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Lozano-Andrade CN, Nogueira CG, Henriksen NNSE, Wibowo M, Jarmusch SA, Kovács ÁT. Establishment of a transparent soil system to study Bacillus subtilis chemical ecology. ISME COMMUNICATIONS 2023; 3:110. [PMID: 37838789 PMCID: PMC10576751 DOI: 10.1038/s43705-023-00318-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/21/2023] [Accepted: 10/05/2023] [Indexed: 10/16/2023]
Abstract
Bacterial secondary metabolites are structurally diverse molecules that drive microbial interaction by altering growth, cell differentiation, and signaling. Bacillus subtilis, a Gram-positive soil-dwelling bacterium, produces a wealth of secondary metabolites, among them, lipopeptides have been vastly studied by their antimicrobial, antitumor, and surfactant activities. However, the natural functions of secondary metabolites in the lifestyles of the producing organism remain less explored under natural conditions, i.e. in soil. Here, we describe a hydrogel-based transparent soil system to investigate B. subtilis chemical ecology under controllable soil-like conditions. The transparent soil matrix allows the growth of B. subtilis and other isolates gnotobiotically and under nutrient-controlled conditions. Additionally, we show that transparent soil allows the detection of lipopeptides production and dynamics by HPLC-MS, and MALDI-MS imaging, along with fluorescence imaging of 3-dimensional bacterial assemblages. We anticipate that this affordable and highly controllable system will promote bacterial chemical ecology research and help to elucidate microbial interactions driven by secondary metabolites.
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Affiliation(s)
| | - Carla G Nogueira
- DTU Bioengineering, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | | | - Mario Wibowo
- DTU Bioengineering, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Scott A Jarmusch
- DTU Bioengineering, Technical University of Denmark, 2800, Kgs Lyngby, Denmark
| | - Ákos T Kovács
- DTU Bioengineering, Technical University of Denmark, 2800, Kgs Lyngby, Denmark.
- Institute of Biology, Leiden University, 2333 BE, Leiden, The Netherlands.
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6
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Cloning, Expression and Characterization of an Alginate Lyase in Bacillus subtilis WB600. FERMENTATION 2023. [DOI: 10.3390/fermentation9020144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The aim of this study was to further broaden the heterologous expression of alginate lyase from Vibrio alginolyticus in a Bacillus subtilis expression vector. A B. subtilis WB600/pP43NMK-alg62 strain was constructed. (NH4)2SO4 precipitation and Ni-affinity chromatography were performed to purify the enzyme. We then characterized the enzyme. Its molecular weight was 57.64 kDa, and it worked optimally at 30 °C with a pH of 8.0. Ca2+ markedly enhanced the enzymatic activity of Alg62 while Cu2+ and Ni2+ inhibited its activity. Alg62 had a wide range of substrate specificity, showing high activity toward sodium alginate and polyG. Following optimization of the fermentation process, the optimal conditions for the recombinant expression of Alg62 were as follows: temperature of 37 °C, pH of 7.0, medium consisting of glycerol 15 g/L, yeast powder 25 g/L and K+ 1.5 mmol/L. At these optimal conditions, enzyme activity reached 318.21 U/mL, which was 1.54 times higher than the initial enzyme activity.
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Ghosh D, Ghorai P, Sarkar S, Maiti KS, Hansda SR, Das P. Microbial assemblage for solid waste bioremediation and valorization with an essence of bioengineering. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:16797-16816. [PMID: 36595166 DOI: 10.1007/s11356-022-24849-x] [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: 04/19/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
Environmental solid waste bioremediation is a method of treating contaminated solid waste that involves changing ecological conditions to foster the growth of a broad spectrum of microorganisms and the destruction of the target contaminants. A wide range of microorganisms creates metabolites that may break down and change solid waste-based pollution to various value-added molecules. Diverse bioremediation technologies, their limitations, and the procedure involve recycling solid waste materials from the environment. The existing environmental solid waste disposal services are insufficient and must be upgraded with more lucrative recovery, recycling, and reuse technologies to decrease the enormous expenditures in treatment procedures. Bioremediation of solid waste eliminates the toxic components. It restores the site with the advent of potential microbial communities towards solid waste valorization utilizing agriculture solid waste, organic food waste, plastic solid waste, and multiple industrial solid wastes.Bioengineering on diverse ranges of microbial regimes has accelerated to provide extra momentum toward solid waste recycling and valorization. This approach increases the activity of bioremediating microbes in the commercial development of waste treatment techniques and increases the cost-effective valuable product generation. This framework facilitates collaboration between solid waste and utilities. It can aid in establishing a long-term management strategy for recycling development with the advent of a broad spectrum of potential microbial assemblages, increasing solid waste contamination tolerance efficiency and solid waste degradability. The current literature survey extensively summarises solid waste remediation valorization using a broad spectrum of microbial assemblages with special emphasis on bioengineering-based acceleration. This approach is to attain sustainable environmental management and value-added biomolecule generation.
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Affiliation(s)
- Dipankar Ghosh
- Microbial Engineering & Algal Biotechnology Laboratory, Department of Biosciences, JIS University, Kolkata, 700109, India.
| | - Palash Ghorai
- Microbial Engineering & Algal Biotechnology Laboratory, Department of Biosciences, JIS University, Kolkata, 700109, India
| | - Soumita Sarkar
- Microbial Engineering & Algal Biotechnology Laboratory, Department of Biosciences, JIS University, Kolkata, 700109, India
| | - Kumar Sagar Maiti
- Microbial Engineering & Algal Biotechnology Laboratory, Department of Biosciences, JIS University, Kolkata, 700109, India
| | - Serma Rimil Hansda
- Microbial Engineering & Algal Biotechnology Laboratory, Department of Biosciences, JIS University, Kolkata, 700109, India
| | - Parna Das
- Microbial Engineering & Algal Biotechnology Laboratory, Department of Biosciences, JIS University, Kolkata, 700109, India
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Determination of oligosaccharide product distributions of PL7 alginate lyases by their structural elements. Commun Biol 2022; 5:782. [PMID: 35918517 PMCID: PMC9345997 DOI: 10.1038/s42003-022-03721-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 07/14/2022] [Indexed: 11/17/2022] Open
Abstract
Alginate lyases can be used to produce well-defined alginate oligosaccharides (AOSs) because of their specificities for AOS products. A large number of alginate lyases have been recorded in the CAZy database; however, the majority are annotated-only alginate lyases that include little information on their products, thus limiting their applications. Here, we establish a simple and experiment-saving approach to predict product distributions for PL7 alginate lyases through extensive structural biology, bioinformatics and biochemical studies. Structural study on several PL7 alginate lyases reveals that two loops around the substrate binding cleft determine product distribution. Furthermore, a database containing the loop information of all annotated-only single-domain PL7 alginate lyases is constructed, enabling systematic exploration of the association between loop and product distribution. Based on these results, a simplified loop/product distribution relationship is proposed, giving us information on product distribution directly from the amino acid sequence. Characterization of PL7 alginate lyase structure and products enables a bioinformatics approach to predict product distribution from the amino acid sequence.
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Barzkar N, Sheng R, Sohail M, Jahromi ST, Babich O, Sukhikh S, Nahavandi R. Alginate Lyases from Marine Bacteria: An Enzyme Ocean for Sustainable Future. Molecules 2022; 27:3375. [PMID: 35684316 PMCID: PMC9181867 DOI: 10.3390/molecules27113375] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/11/2022] [Accepted: 05/16/2022] [Indexed: 12/13/2022] Open
Abstract
The cell wall of brown algae contains alginate as a major constituent. This anionic polymer is a composite of β-d-mannuronate (M) and α-l-guluronate (G). Alginate can be degraded into oligosaccharides; both the polymer and its products exhibit antioxidative, antimicrobial, and immunomodulatory activities and, hence, find many commercial applications. Alginate is attacked by various enzymes, collectively termed alginate lyases, that degrade glycosidic bonds through β-elimination. Considering the abundance of brown algae in marine ecosystems, alginate is an important source of nutrients for marine organisms, and therefore, alginate lyases play a significant role in marine carbon recycling. Various marine microorganisms, particularly those that thrive in association with brown algae, have been reported as producers of alginate lyases. Conceivably, the marine-derived alginate lyases demonstrate salt tolerance, and many are activated in the presence of salts and, therefore, find applications in the food industry. Therefore, this review summarizes the structural and biochemical features of marine bacterial alginate lyases along with their applications. This comprehensive information can aid in the expansion of future prospects of alginate lyases.
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Affiliation(s)
- Noora Barzkar
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas 3995, Iran
| | - Ruilong Sheng
- CQM—Centro de Química da Madeira, Campus da Penteada, Universidade da Madeira, 9000-390 Funchal, Portugal;
- Department of Radiology, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai 200072, China
| | - Muhammad Sohail
- Department of Microbiology, University of Karachi, Karachi 75270, Pakistan;
| | - Saeid Tamadoni Jahromi
- Persian Gulf and Oman Sea Ecology Research Center, Iranian Fisheries Sciences Research Institute, Agricultural Research Education and Extension Organization (AREEO), Bandar Abbas 9145, Iran;
| | - Olga Babich
- Institute of Living Systems, Immanuel Kant Baltic Federal University, A. Nevskogo Street 14, Kaliningrad 236016, Russia; (O.B.); (S.S.)
| | - Stanislav Sukhikh
- Institute of Living Systems, Immanuel Kant Baltic Federal University, A. Nevskogo Street 14, Kaliningrad 236016, Russia; (O.B.); (S.S.)
| | - Reza Nahavandi
- Animal Science Research Institute of Iran (ASRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj 8361, Iran;
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Lu S, Na K, Wei J, Zhang L, Guo X. Alginate oligosaccharides: The structure-function relationships and the directional preparation for application. Carbohydr Polym 2022; 284:119225. [PMID: 35287920 DOI: 10.1016/j.carbpol.2022.119225] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/20/2022] [Accepted: 02/02/2022] [Indexed: 01/02/2023]
Abstract
Alginate oligosaccharides (AOS) are degradation products of alginate extracted from brown algae. With low molecular weight, high water solubility, and good biological activity, AOS present anti-inflammatory, antimicrobial, antioxidant, and antitumor properties. They also exert growth-promoting effects in animals and plants. Three types of AOS, mannuronate oligosaccharides (MAOS), guluronate oligosaccharides (GAOS), and heterozygous mannuronate and guluronate oligosaccharides (HAOS), can be produced from alginate by enzymatic hydrolysis. Thus far, most studies on the applications and biological activities of AOS have been based mainly on a hybrid form of HAOS. To improve the directional production of AOS for practical applications, systematic studies on the structures and related biological activities of AOS are needed. This review provides a summary of current understanding of structure-function relationships and advances in the production of AOS. The current challenges and opportunities in the application of AOS is suggested to guide the precise application of AOS in practice.
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Affiliation(s)
- Shuang Lu
- College of Life Science, South-Central University for Nationalities, No. 182, Minyuan Road, Hongshan District, Wuhan City, Hubei Province 430074, China
| | - Kai Na
- College of Life Science, South-Central University for Nationalities, No. 182, Minyuan Road, Hongshan District, Wuhan City, Hubei Province 430074, China
| | - Jiani Wei
- College of Life Science, South-Central University for Nationalities, No. 182, Minyuan Road, Hongshan District, Wuhan City, Hubei Province 430074, China
| | - Li Zhang
- College of Life Science, South-Central University for Nationalities, No. 182, Minyuan Road, Hongshan District, Wuhan City, Hubei Province 430074, China
| | - Xiaohua Guo
- College of Life Science, South-Central University for Nationalities, No. 182, Minyuan Road, Hongshan District, Wuhan City, Hubei Province 430074, China.
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Ibrahim SRM, Choudhry H, Asseri AH, Elfaky MA, Mohamed SGA, Mohamed GA. Stachybotrys chartarum-A Hidden Treasure: Secondary Metabolites, Bioactivities, and Biotechnological Relevance. J Fungi (Basel) 2022; 8:504. [PMID: 35628759 PMCID: PMC9144806 DOI: 10.3390/jof8050504] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 02/04/2023] Open
Abstract
Fungi are renowned as a fountainhead of bio-metabolites that could be employed for producing novel therapeutic agents, as well as enzymes with wide biotechnological and industrial applications. Stachybotrys chartarum (black mold) (Stachybotriaceae) is a toxigenic fungus that is commonly found in damp environments. This fungus has the capacity to produce various classes of bio-metabolites with unrivaled structural features, including cyclosporins, cochlioquinones, atranones, trichothecenes, dolabellanes, phenylspirodrimanes, xanthones, and isoindoline and chromene derivatives. Moreover, it is a source of various enzymes that could have variable biotechnological and industrial relevance. The current review highlights the formerly published data on S. chartarum, including its metabolites and their bioactivities, as well as industrial and biotechnological relevance dated from 1973 to the beginning of 2022. In this work, 215 metabolites have been listed and 138 references have been cited.
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Affiliation(s)
- Sabrin R. M. Ibrahim
- Department of Chemistry, Preparatory Year Program, Batterjee Medical College, Jeddah 21442, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | - Hani Choudhry
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (H.C.); (A.H.A.)
- Center for Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Amer H. Asseri
- Biochemistry Department, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; (H.C.); (A.H.A.)
- Center for Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Mahmoud A. Elfaky
- Center for Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Shaimaa G. A. Mohamed
- Faculty of Dentistry, British University, El Sherouk City, Suez Desert Road, Cairo 11837, Egypt;
| | - Gamal A. Mohamed
- Department of Natural Products and Alternative Medicine, Faculty of Pharmacy, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
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Gut microbiota analysis of Blenniidae fishes including an algae-eating fish and clear boundary formation among isolated Vibrio strains. Sci Rep 2022; 12:4642. [PMID: 35301363 PMCID: PMC8930983 DOI: 10.1038/s41598-022-08511-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 03/07/2022] [Indexed: 12/29/2022] Open
Abstract
Some marine fishes are algae-feeding, and the microorganisms in their digestive tracts produce carbohydrate hydrolyzing enzymes such as agarose and fucosidase, which are potentially interesting resource for new functional enzymes. The purpose of this study was to establish a method for identifying and utilizing characteristic bacteria from the intestines of two algae-eating fish species: Andamia tetradactylus, which exclusively eats algae on the rock surface, and stellar rockskipper Entomacrodus stellifer, which feeds on both algae and invertebrates. We tested the species composition of the intestinal bacterial flora and found that Proteobacteria were commonly found both in species as in the common gut communities of marine fish, whereas Spirochaetes and Tenericutes occupied the flora of A. tetradactylus. We then performed anaerobic and aerobic cultures and isolated 34 and 44 strains including 48 strains belonged to Vibrio species from A. tetradactylus and E. stellifer. We observed that some Vibrio strains formed a clear boundary to avoid contacting other strains of bacteria. Whole-genome sequencing of such two Vibrio alginolyticus strains revealed two cyclic chromosomes commonly found in the genome of Vibrio species, and some unique genes encoding alginate lyase, chitinases, and type I-F CRISPR-associated endoribonuclease for the first time in Vibrio alginolyticus.
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13
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Li J, He Z, Liang Y, Peng T, Hu Z. Insights into Algal Polysaccharides: A Review of Their Structure, Depolymerases, and Metabolic Pathways. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:1749-1765. [PMID: 35124966 DOI: 10.1021/acs.jafc.1c05365] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In recent years, marine macroalgae with extensive biomass have attracted the attention of researchers worldwide. Furthermore, algal polysaccharides have been widely studied in the food, pharmaceutical, and cosmetic fields because of their various kinds of bioactivities. However, there are immense barriers to their application as a result of their high molecular size, poor solubility, hydrocolloid nature, and low physiological activities. Unique polysaccharides, such as laminarin, alginate, fucoidan, agar, carrageenan, porphyran, ulvan, and other complex structural polysaccharides, can be digested by marine bacteria with many carbohydrate-active enzymes (CAZymes) by breaking down the limitation of glycosidic bonds. However, structural elucidation of algal polysaccharides, metabolic pathways, and identification of potential polysaccharide hydrolases that participate in different metabolic pathways remain major obstacles restricting the efficient utilization of algal oligosaccharides. This review focuses on the structure, hydrolase families, metabolic pathways, and potential applications of seven macroalgae polysaccharides. These results will contribute to progressing our understanding of the structure of algal polysaccharides and their metabolic pathways and will be valuable for clearing the way for the compelling utilization of bioactive oligosaccharides.
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Affiliation(s)
- Jin Li
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong 515063, People's Republic of China
| | - Zhixiao He
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong 515063, People's Republic of China
| | - Yumei Liang
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong 515063, People's Republic of China
| | - Tao Peng
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong 515063, People's Republic of China
| | - Zhong Hu
- Department of Biology, College of Science, Shantou University, Shantou, Guangdong 515063, People's Republic of China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, Guangdong 511458, People's Republic of China
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14
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Kawai S, Hashimoto W. 4-Deoxy-l- erythro-5-hexoseulose Uronate (DEH) and DEH Reductase: Key Molecule and Enzyme for the Metabolism and Utilization of Alginate. Molecules 2022; 27:338. [PMID: 35056653 PMCID: PMC8778563 DOI: 10.3390/molecules27020338] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/29/2021] [Accepted: 01/04/2022] [Indexed: 12/31/2022] Open
Abstract
4-Deoxy-l-erythro-5-hexoseulose uronate (DEH), DEH reductase, and alginate lyase have key roles in the metabolism of alginate, a promising carbon source in brown macroalgae for biorefinery. In contrast to the widely reviewed alginate lyase, DEH and DEH reductase have not been previously reviewed. Here, we summarize the current understanding of DEH and DEH reductase, with emphasis on (i) the non-enzymatic and enzymatic formation and structure of DEH and its reactivity to specific amino groups, (ii) the molecular identification, classification, function, and structure, as well as the structural determinants for coenzyme specificity of DEH reductase, and (iii) the significance of DEH for biorefinery. Improved understanding of this and related fields should lead to the practical utilization of alginate for biorefinery.
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Affiliation(s)
- Shigeyuki Kawai
- Laboratory for Environmental Biotechnology, Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi 921-8836, Ishikawa, Japan
| | - Wataru Hashimoto
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji 611-0011, Kyoto, Japan
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15
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Jeong DW, Hyeon JE, Lee ME, Ko YJ, Kim M, Han SO. Efficient utilization of brown algae for the production of Polyhydroxybutyrate (PHB) by using an enzyme complex immobilized on Ralstonia eutropha. Int J Biol Macromol 2021; 189:819-825. [PMID: 34453982 DOI: 10.1016/j.ijbiomac.2021.08.149] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/28/2021] [Accepted: 08/18/2021] [Indexed: 11/22/2022]
Abstract
Marine macroalgae are potential renewable feedstocks for valuable biomaterials. Among them, alginate is a primary component in brown algae that can be nonenzymatically converted and enzymatically degraded by alginate lyases to 4-deoxy-l-erythro-5-hexoseulose uronic acid (DEH). Here, we constructed alginolytic enzyme complexes comprising two different alginate lyases for synergistic alginate degradation. The complexes showed good thermostability with 60% of the residual activity at high temperature (60 °C). Furthermore, they produced 0.85 and 0.18 mg/mL DEH from alginate and natural brown algae as substrates, respectively. The enzyme complex successfully decomposed brown algal biomass, resulting in a 3.15-fold improvement in DEH when compared to free enzymes. The Ralstonia eutropha strain with alginolytic enzyme complexes on the cell surface showed higher Polyhydroxybutyrate (PHB) production and produced 2.58 g/L PHB from alginate. After the use of alginate, remaining biomass such as fucoidan and laminaran can also be used in the future for high value ingredients in nutritional, medical device, skincare and dermatological products. These results demonstrate that it is possible to create more efficient strategies for producing biodegradable PHB and functional polysaccharides from brown algal substrates.
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Affiliation(s)
- Da Woon Jeong
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Jeong Eun Hyeon
- 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
| | - Myeong-Eun Lee
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Young Jin Ko
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Minhye Kim
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Sung Ok Han
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea.
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16
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Mrudulakumari Vasudevan U, Lee OK, Lee EY. Alginate derived functional oligosaccharides: Recent developments, barriers, and future outlooks. Carbohydr Polym 2021; 267:118158. [PMID: 34119132 DOI: 10.1016/j.carbpol.2021.118158] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 04/14/2021] [Accepted: 04/14/2021] [Indexed: 02/07/2023]
Abstract
Alginate is a biopolymer used extensively in the food, pharmaceutical, and chemical industries. Alginate oligosaccharides (AOS) derived from alginate exhibit superior biological activities and therapeutic potential. Alginate lyases with characteristic substrate specificity can facilitate the production of a broad array of AOS with precise structure and functionality. By adopting innovative analytical tools in conjunction with focused clinical studies, the structure-bioactivity relationship of a number of AOS has been brought to light. This review covers fundamental aspects and recent developments in AOS research. Enzymatic and microbial processes involved in AOS production from brown algae and sequential steps involved in AOS structure elucidation are outlined. Biological mechanisms underlying the health benefits of AOS and their potential industrial and therapeutic applications are elaborated. Withal, various challenges in AOS research are traced out, and future directions, specifically on recombinant systems for AOS preparation, are delineated to further widen the horizon of these exceptional oligosaccharides.
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Affiliation(s)
- Ushasree Mrudulakumari Vasudevan
- Department of Chemical Engineering (Integrated Engineering), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Ok Kyung Lee
- Department of Chemical Engineering (Integrated Engineering), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering (Integrated Engineering), Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea.
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