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Li J, Sun M, Liu G, Zhou J, Chang Y, Xue C. Characterization and elucidation of a novel M-specific alginate lyase Aly7Aq with strict recognition at subsites ±2. Int J Biol Macromol 2024; 277:133972. [PMID: 39029836 DOI: 10.1016/j.ijbiomac.2024.133972] [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: 04/21/2024] [Revised: 05/23/2024] [Accepted: 07/16/2024] [Indexed: 07/21/2024]
Abstract
A novel alginate lyase Aly7Aq was cloned and heterologous expressed by a combination of bioinformatics and molecular biology. Aly7Aq was an M-specific alginate lyase, exhibiting optimum reaction conditions at 50 °C and pH 10.0. Aly7Aq was determined to degrade polysaccharides in a random endo-acting manner. The minimum reaction substrate was tetrasaccharide, and Aly7Aq mainly attacked the third glycosidic linkage from the reducing end of oligosaccharide substrates. The disaccharide product of Aly7Aq was ΔM and the trisaccharide products were ΔMM and ΔMG, which differed from all previously characterized M-specific alginate lyases. The degradation products demonstrated that the ±2 subsites of Aly7Aq strictly recognized M units, while the -1 subsite accommodated both M and G units. Therefore, the substrate specificity of Aly7Aq was derived from the specificity of ±2 subsites. This is the first report on the specificity at subsite ±2 of M-specific alginate lyase. The novel M-specific Aly7Aq could serve as a potential tool in the specific degradation of alginate and targeted preparation of oligosaccharide.
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Affiliation(s)
- Jiajing Li
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Menghui Sun
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Guanchen Liu
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Jinhang Zhou
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
| | - Yaoguang Chang
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China.
| | - Changhu Xue
- State Key Laboratory of Marine Food Processing & Safety Control, College of Food Science and Engineering, Ocean University of China, 1299 Sansha Road, Qingdao 266404, China
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Wang X, Xu W, Dai Q, Liu X, Guang C, Zhang W, Mu W. Characterization of a thermostable PL-31 family alginate lyase from Paenibacillus ehimensis and its application for alginate oligosaccharides bioproduction. Enzyme Microb Technol 2023; 166:110221. [PMID: 36906979 DOI: 10.1016/j.enzmictec.2023.110221] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 02/26/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023]
Abstract
Currently, people pay more attention to marine sugars, because of their unique physiological effects. Alginate oligosaccharides (AOS) are the degradation products of alginate and have been used in food, cosmetic, and medicine fields. AOS display good physical characteristics (low relative molecular weight, good solubility, high safety, and high stability) and excellent physiological functions (immunomodulatory, antioxidant, antidiabetic, and prebiotic activities). Alginate lyase plays a key role in the AOS bioproduction. In this study, a novel PL-31 family alginate lyase from Paenibacillus ehimensis (paeh-aly) was identified and characterized. It was extracellularly secreted in E. coli and exhibited a preference for the substrate poly β-D-mannuronate. Using sodium alginate as the substrate, it showed the maximum catalytic activity (125.7 U/mg) at pH 7.5 and 55 °C with 50 mM NaCl. Compared with other alginate lyases, paeh-aly exhibited good stability. About 86.6% and 61.0% residual activity could be maintained after 5 h incubation at 50 and 55 °C respectively, and its Tm value was 61.5 °C. The degradation products were AOS with DP 2-4. Paeh-aly demonstrated strong promise for AOS industrial production because of its excellent thermostability and efficiency.
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Affiliation(s)
- Xinxiu Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wei Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; Shandong Haizhibao Ocean Technology Co., Ltd, Weihai, Shandong 264333, China
| | - Quanyu Dai
- China Rural Technology Development Center, Beijing 100045, China
| | - Xiaoyong Liu
- Shandong Haizhibao Ocean Technology Co., Ltd, Weihai, Shandong 264333, China
| | - Cuie Guang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; Shandong Haizhibao Ocean Technology Co., Ltd, Weihai, Shandong 264333, China.
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
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Yan F, Chen J, Cai T, Zhong J, Zhang S. Cloning, expression, and characterization of a novel endo-type alginate lyase from Microbulbifer sp. BY17. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:4522-4531. [PMID: 35137421 DOI: 10.1002/jsfa.11807] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/27/2022] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Alginate oligosaccharides (AOS), with various physiological effects, have been widely used in the food, agricultural, and pharmaceutical industries. The biological enzymatic method of preparing AOS, using alginate lyase, has more advantages compared with physical and chemical methods. Cloning and heterologously expressing alginate lyase are therefore very important. RESULTS A novel alginate lyase, BY17PV7, from Microbulbifer sp. BY17, isolated from Gracilaria, was cloned and expressed in Escherichia coli BL21(DE3). BY17PV7 was about 27 KDa. BY17PV7 showed the greatest activity (150.42 ± 3.32 U/mg) at 43 °C and pH 8.9. It could be activated by Ca2+ , Mn2+ , Co2+ , Fe3+ , Na+ , and inhibited by Mg2+ , Zn2+ , Ba2+ , Cu2+ , sodium dodecyl sulfate (SDS), ethylene diamine tetraacetic acid (EDTA). BY17PV7 had a wide range of substrate specificity and good degradation effects for poly β-D-mannuronate (polyM) and poly α-L-guluronate (polyG), demonstrating that it is a bifunctional alginate lyase. The kinetic parameters showed that BY17PV7 had a greater affinity for polyG. BY17PV7 released AOS with a degree of polymerization (DP) of 3-4 in an endolytic manner from sodium alginate. Alginate oligosaccharides showed strong antioxidant ability of reducing Fe3+ and scavenging radicals such as hydroxyl, 2,2-azion-bia (3-ethylbenzo-thiazoline-6-sulfonic acid diammonium salt) (ABTS) and 2,2-diphenyl-1-picrylhydrazyl (DPPH). CONCLUSION A novel bifunctional alginate lyase, BY17PV7, was expressed and characterized in Escherichia coli BL21(DE3). The results were helpful for the analysis of the molecular mechanisms of degrading patterns in the polysaccharide lyase (PL) family. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Fen Yan
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian, China
| | - Junying Chen
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian, China
| | - Ting Cai
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian, China
| | - Jinfu Zhong
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian, China
| | - Shaolong Zhang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian, China
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Inoue A, Kudo M, Werner E, Ojima T. Identification and characterization of cellouronate (β-1,4-linked polyglucuronic acid) lyase from the scallop Mizuhopecten yessoensis. Carbohydr Polym 2021; 254:117306. [PMID: 33357872 DOI: 10.1016/j.carbpol.2020.117306] [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: 07/28/2020] [Revised: 10/11/2020] [Accepted: 10/20/2020] [Indexed: 10/23/2022]
Abstract
The semisynthetic polysaccharide cellouronate is a β-1,4-linked polyglucuronic acid prepared from regenerated cellulose by chemical oxidation. Here, we isolated a novel enzyme, MyAly, as a cellouronate lyase from a scallop Mizuhopecten yessoensis. Its optimum temperature, pH, and NaCl concentration for cellouronate degradation were determined to be 30 °C, 6.9, and 200-500 mM, respectively. MyAly endolytically degraded cellouronate into unsaturated di-, tri-, and tetrasaccharides with kcat of 31.1 s-1. MyAly also showed an alginate-degradation activity with a kcat value of 0.58 s-1. However, there was no significant difference in Km values between cellouronate and alginate. MyAly consisted of 280 amino acids and shared 36.5-44.1 % identity with known marine gastropod alginate lyases belonging to the polysaccharide lyase family 14. This is the first study to identify and characterize a cellouronate-degrading lyase from a marine organism, providing a better understanding of the biodegradability of the industrially important polysaccharide, cellouronate, in marine environments.
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Affiliation(s)
- Akira Inoue
- Laboratory of Marine Biotechnology and Microbiology, Division of Marine Life Science, Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate, Hokkaido, 041-8611, Japan.
| | - Masataka Kudo
- Laboratory of Marine Biotechnology and Microbiology, Division of Marine Life Science, Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate, Hokkaido, 041-8611, Japan
| | - Elisa Werner
- Section of Organic Chemistry and Biochemistry, Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, D-85748, Garching, Germany
| | - Takao Ojima
- Laboratory of Marine Biotechnology and Microbiology, Division of Marine Life Science, Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate, Hokkaido, 041-8611, Japan
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Cheng D, Jiang C, Xu J, Liu Z, Mao X. Characteristics and applications of alginate lyases: A review. Int J Biol Macromol 2020; 164:1304-1320. [PMID: 32745554 DOI: 10.1016/j.ijbiomac.2020.07.199] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/09/2020] [Accepted: 07/22/2020] [Indexed: 12/26/2022]
Abstract
Brown algae, as the main source of alginate, are a type of marine biomass with a very high output. Alginate, a polysaccharide composed of β-D-mannuronic acid (M) and α-L-guluronic acid (G), has great potential for applications in the food, cosmetic and pharmaceutical industries. Alginate lyases (Alys) can degrade alginate polymers into oligosaccharides or monosaccharides, resulting in a broad application field. Alys can be used for both the production of alginate oligosaccharides and the biorefinery of brown algae. In view of their important functions, an increasing number of Alys have been isolated and characterized. For better application, a comprehensive understanding of Alys is essential. Therefore, in this paper, we summarized recently discovered Alys, discussed their characteristics, and introduced their structural properties, degradation patterns and biological roles in alginate-degrading organisms. In addition, applications of Alys have been illustrated with examples. This paper provides a relatively comprehensive description of Alys, which is significant for Alys exploration and application.
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Affiliation(s)
- Danyang Cheng
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Chengcheng Jiang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Jiachao Xu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Zhen Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China.
| | - Xiangzhao Mao
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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Dudek M, Dieudonné A, Jouanneau D, Rochat T, Michel G, Sarels B, Thomas F. Regulation of alginate catabolism involves a GntR family repressor in the marine flavobacterium Zobellia galactanivorans DsijT. Nucleic Acids Res 2020; 48:7786-7800. [PMID: 32585009 PMCID: PMC7641319 DOI: 10.1093/nar/gkaa533] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/02/2020] [Accepted: 06/10/2020] [Indexed: 12/19/2022] Open
Abstract
Marine flavobacteria possess dedicated Polysaccharide Utilization Loci (PULs) enabling efficient degradation of a variety of algal polysaccharides. The expression of these PULs is tightly controlled by the presence of the substrate, yet details on the regulatory mechanisms are still lacking. The marine flavobacterium Zobellia galactanivorans DsijT digests many algal polysaccharides, including alginate from brown algae. Its complex Alginate Utilization System (AUS) comprises a PUL and several other loci. Here, we showed that the expression of the AUS is strongly and rapidly (<30 min) induced upon addition of alginate, leading to biphasic substrate utilization. Polymeric alginate is first degraded into smaller oligosaccharides that accumulate in the extracellular medium before being assimilated. We found that AusR, a GntR family protein encoded within the PUL, regulates alginate catabolism by repressing the transcription of most AUS genes. Based on our genetic, genomic, transcriptomic and biochemical results, we propose the first model of regulation for a PUL in marine bacteria. AusR binds to promoters of AUS genes via single, double or triple copies of operator. Upon addition of alginate, secreted enzymes expressed at a basal level catalyze the initial breakdown of the polymer. Metabolic intermediates produced during degradation act as effectors of AusR and inhibit the formation of AusR/DNA complexes, thus lifting transcriptional repression.
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Affiliation(s)
- Magda Dudek
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Anissa Dieudonné
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Diane Jouanneau
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Tatiana Rochat
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
| | - Gurvan Michel
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Benoit Sarels
- Sorbonne Université, CNRS, Laboratoire Jacques-Louis Lions, Université de Paris, 75252 Paris, France
| | - François Thomas
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
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Huang Z, Petersen JM, Martijn J, Ettema TJG, Shao Z. A novel alphaproteobacterium with a small genome identified from the digestive gland of multiple species of abalone. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:387-395. [PMID: 32307920 DOI: 10.1111/1758-2229.12845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 04/01/2020] [Accepted: 04/15/2020] [Indexed: 06/11/2023]
Abstract
We identified an alphaproteobacterium in the digestive gland of the abalone species Haliotis discus hannai. This phylotype dominated our 16S rRNA clone libraries from the digestive gland of H. discus hannai. Diversity surveys revealed that this phylotype was associated with H. discus hannai and also in another host species, H. gigantea. Whole genome phylogenies placed this bacterium as a new member affiliated with the family Rhodospirillaceae in Alphaproteobacteria. Gene annotation revealed a nearly complete glycolysis pathway but no TCA cycle, but the presence of anaerobic ribonucleoside-triphosphate reductase and oxygen-insensitive NAD(P)H-dependent nitroreductase, which show the genomic potential for anaerobic metabolism. A large cluster of genes encoding ankyrin repeat proteins (ANK) of eukaryotic-like repeat domains and a large gene set for the flagellar system were also detected. Alginate-binding periplasmic proteins and key genes responsible for alginate assimilation were found in the genome, which could potentially contribute to the breakdown of the host's alginate-rich macroalgal diet. These results raise the possibility that this novel alphaproteobacterium is a widespread member of the abalone microbiome that may use polysaccharides derived from its host's macroalgal diet.
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Affiliation(s)
- Zhaobin Huang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
| | - Jillian M Petersen
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Joran Martijn
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Thijs J G Ettema
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, the Netherlands
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, China
- State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, China
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Elucidation of a Unique Pattern and the Role of Carbohydrate Binding Module of an Alginate Lyase. Mar Drugs 2019; 18:md18010032. [PMID: 31905894 PMCID: PMC7024192 DOI: 10.3390/md18010032] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 12/12/2019] [Accepted: 12/13/2019] [Indexed: 02/06/2023] Open
Abstract
Alginate oligosaccharides with different degrees of polymerization (DPs) possess diverse physiological activities. Therefore, in recent years, increasing attention has been drawn to the use of enzymes for the preparation of alginate oligosaccharides for food and industrial applications. Previously, we identified and characterized a novel bifunctional alginate lyase Aly7A, which can specifically release trisaccharide from three different substrate types with a unique degradation pattern. Herein, we investigated its degradation pattern by modular truncation and molecular docking. The results suggested that Aly7A adopted a unique action mode towards different substrates with the substrate chain sliding into the binding pocket of the catalytic domain to position the next trisaccharide for cleavage. Deletion of the Aly7A carbohydrate binding module (CBM) domain resulted in a complex distribution of degradation products and no preference for trisaccharide formation, indicating that the CBM may act as a “controller” during the trisaccharide release process. This study further testifies CBM as a regulator of product distribution and provides new insights into well-defined generation of alginate oligosaccharides with associated CBMs.
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Zhu B, Li K, Wang W, Ning L, Tan H, Zhao X, Yin H. Preparation of trisaccharides from alginate by a novel alginate lyase Alg7A from marine bacterium Vibrio sp. W13. Int J Biol Macromol 2019; 139:879-885. [DOI: 10.1016/j.ijbiomac.2019.08.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 06/24/2019] [Accepted: 08/01/2019] [Indexed: 01/18/2023]
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10
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Liu J, Yang S, Li X, Yan Q, Reaney MJT, Jiang Z. Alginate Oligosaccharides: Production, Biological Activities, and Potential Applications. Compr Rev Food Sci Food Saf 2019; 18:1859-1881. [DOI: 10.1111/1541-4337.12494] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 07/09/2019] [Accepted: 07/29/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Jun Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthCollege of Food Science and Nutritional EngineeringChina Agricultural Univ. Beijing 100083 China
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthBeijing Technology and Business Univ. Beijing 100048 China
| | - Shaoqing Yang
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthCollege of Food Science and Nutritional EngineeringChina Agricultural Univ. Beijing 100083 China
| | - Xiuting Li
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthBeijing Technology and Business Univ. Beijing 100048 China
| | - Qiaojuan Yan
- Bioresource Utilization LaboratoryCollege of EngineeringChina Agricultural Univ. Beijing 100083 China
| | - Martin J. T. Reaney
- Dept. of Plant SciencesUniv. of Saskatchewan Saskatoon SK S7N 5A8 Canada
- Guangdong Saskatchewan Oilseed Joint Laboratory (GUSTO)Dept. of Food Science and EngineeringJinan Univ. Guangzhou 510632 China
| | - Zhengqiang Jiang
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthCollege of Food Science and Nutritional EngineeringChina Agricultural Univ. Beijing 100083 China
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11
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Nam BH, Jang J, Caetano-Anolles K, Kim YO, Park JY, Sohn H, Yoon SH, Kim H, Kwak W. Microbial community and functions associated with digestion of algal polysaccharides in the visceral tract of Haliotis discus hannai: Insights from metagenome and metatranscriptome analysis. PLoS One 2018; 13:e0205594. [PMID: 30308038 PMCID: PMC6181387 DOI: 10.1371/journal.pone.0205594] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 09/27/2018] [Indexed: 02/01/2023] Open
Abstract
Haliotis discus hannai, a species of Pacific abalone, is a highly valuable food source throughout Northeast Asia. As H. discus hannai primarily feed on brown algae and largely extract their energy from algal polysaccharides, understanding the mechanisms by which they digest algal polysaccharides is essential for elucidating their energy metabolism. Gut microbes, as well as the host animal, are involved in the process of polysaccharide degradation. To identify algal polysaccharide-digestion mechanisms and their origin, we analyzed the metagenome and metatranscriptome of abalone visceral extracts. Microbial communities were characterized using the 16S rRNA gene sequences in the metagenome and our results differed significantly from those of previous studies using traditional microbiological methods such as bacterial cultivation and cloning. A greater diversity of bacterial taxa was identified here than was previously identified using cultivation methods. Furthermore, the most abundant bacterial taxa also differed from previous studies, which is not common when comparing the results of bacterial culturing with those of molecular methodologies. Based on the metatranscriptome, overall functions were identified and additional analyses were performed on the coding sequences of algal polysaccharide-digestive enzymes, including alginate lyase. Results of the transcriptomic analyses suggest that alginate lyase in the visceral extracts of H. discus hannai was produced by the host itself, not by visceral bacteria. This is the first next-generation sequencing study performed on abalone to characterize the visceral microbiota and the source of the ability to digest algal polysaccharides by analyzing the metagenome and metatranscriptome together.
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Affiliation(s)
- Bo-Hye Nam
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Jisung Jang
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
- C&K Genomics, Seoul, Republic of Korea
| | - Kelsey Caetano-Anolles
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Young-Ok Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Jung Youn Park
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Hawsun Sohn
- Cetacean Research Institute, National Institute of Fisheries Science, Nam-gu, Ulsan, Republic of Korea
| | - Sook Hee Yoon
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Heebal Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
- C&K Genomics, Seoul, Republic of Korea
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
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12
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He M, Guo M, Zhang X, Chen K, Yan J, Irbis C. Purification and characterization of alginate lyase from Sphingomonas sp. ZH0. J Biosci Bioeng 2018; 126:310-316. [PMID: 29680368 DOI: 10.1016/j.jbiosc.2018.01.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 01/09/2018] [Accepted: 01/25/2018] [Indexed: 11/15/2022]
Abstract
Alginate lyases degrade alginate in a beta-elimination reaction to produce oligosaccharides. Thus, alginate lyases are widely used in the food/pharmaceutical industries and are commercially valuable. In this study, four alginate lyase encoding genes were successfully cloned from Sphingomonas sp. ZH0. The expression systems of these alginate lyases were then constructed in Escherichia coli cells. The recombinant ZH0-I, ZH0-II, ZH0-III and ZH0-IV were purified from E. coli cells and were confirmed to be monomeric enzymes with molecular weights of approximately 91, 52, 67, and 113 kDa, respectively. The conditions for enzymes to have the highest specific lyase activities were 53.2 U/mg, 42 °C, pH 7.0 for ZH0-I, 103.9 U/mg, 47 °C, pH 6.5 for ZH0-II, 13.7 U/mg, 52 °C, pH 7.5 for ZH0-III, and 12.3 U/mg, 37 °C, pH 7.0 for ZH0-IV, respectively. These recombinant enzymes were stable over a pH range. Moreover, the enzymes were active in the absence of salt ions, and their activities were substantially reduced by the addition of HgCl2. ZH0-I, ZH0-II and ZH0-III belong to endotype alginate lyases, while ZH0-IV is an exotype alginate lyase. All types could degrade both poly-β-d-mannuronate and poly-α-l-guluronate blocks, yielding alginate oligosaccharides as the main product. The Km and Vmax values were 0.51 mg/ml and 56.18 U/ml for ZH0-I, 0.47 mg/ml and 27.5 U/ml for ZH0-II, 0.55 mg/ml and 60.24 U/ml for ZH0-III, and 0.41 mg/ml and 5.53 U/ml for ZH0-IV, respectively. These features indicate that these alginate lyases are promising candidates for producing antioxidants from alginates in industrial applications.
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Affiliation(s)
- Manman He
- Laboratory of Bioconversion, Life Science and Technology College, Kunming University of Science and Technology, Jingming South Road, Kunming 650500, PR China; Kunming Jida Pharmaceutical Co., Ltd., Kexin Road, Kunming 650106, PR China
| | - Min Guo
- Laboratory of Bioconversion, Life Science and Technology College, Kunming University of Science and Technology, Jingming South Road, Kunming 650500, PR China
| | - Xu Zhang
- Laboratory of Bioconversion, Life Science and Technology College, Kunming University of Science and Technology, Jingming South Road, Kunming 650500, PR China
| | - Keke Chen
- Laboratory of Bioconversion, Life Science and Technology College, Kunming University of Science and Technology, Jingming South Road, Kunming 650500, PR China
| | - Jinping Yan
- Laboratory of Bioconversion, Life Science and Technology College, Kunming University of Science and Technology, Jingming South Road, Kunming 650500, PR China
| | - Chagan Irbis
- Laboratory of Bioconversion, Life Science and Technology College, Kunming University of Science and Technology, Jingming South Road, Kunming 650500, PR China.
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14
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Nishiyama R, Inoue A, Ojima T. Identification of 2-keto-3-deoxy-d-Gluconate Kinase and 2-keto-3-deoxy-d-Phosphogluconate Aldolase in an Alginate-Assimilating Bacterium, Flavobacterium sp. Strain UMI-01. Mar Drugs 2017; 15:md15020037. [PMID: 28216576 PMCID: PMC5334617 DOI: 10.3390/md15020037] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 01/26/2017] [Accepted: 02/08/2017] [Indexed: 01/21/2023] Open
Abstract
Recently, we identified an alginate-assimilating gene cluster in the genome of Flavobacterium sp. strain UMI-01, a member of Bacteroidetes. Alginate lyase genes and a 4-deoxy-l-erythro-5-hexoseulose uronic acid (DEH) reductase gene in the cluster have already been characterized; however, 2-keto-3-deoxy-d-gluconate (KDG) kinase and 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase genes, i.e., flkin and flald, still remained uncharacterized. The amino acid sequences deduced from flkin and flald showed low identities with those of corresponding enzymes of Saccharophagus degradans 2-40T, a member of Proteobacteria (Kim et al., Process Biochem., 2016). This led us to consider that the DEH-assimilating enzymes of Bacteroidetes species are somewhat deviated from those of Proteobacteria species. Thus, in the present study, we first assessed the characteristics in the primary structures of KDG kinase and KDG aldolase of the strain UMI-01, and then investigated the enzymatic properties of recombinant enzymes, recFlKin and recFlAld, expressed by an Escherichia coli expression system. Multiple-sequence alignment among KDG kinases and KDG aldolases from several Proteobacteria and Bacteroidetes species indicated that the strain UMI-01 enzymes showed considerably low sequence identities (15%-25%) with the Proteobacteria enzymes, while they showed relatively high identities (47%-68%) with the Bacteroidetes enzymes. Phylogenetic analyses for these enzymes indicated the distant relationship between the Proteobacteria enzymes and the Bacteroidetes enzymes, i.e., they formed distinct clusters in the phylogenetic tree. recFlKin and recFlAld produced with the genes flkin and flald, respectively, were confirmed to show KDG kinase and KDPG aldolase activities. Namely, recFlKin produced 1.7 mM KDPG in a reaction mixture containing 2.5 mM KDG and 2.5 mM ATP in a 90-min reaction, while recFlAld produced 1.2 mM pyruvate in the reaction mixture containing 5 mM KDPG at the equilibrium state. An in vitro alginate-metabolizing system constructed from recFlKin, recFlAld, and previously reported alginate lyases and DEH reductase of the strain UMI-01 could convert alginate to pyruvate and glyceraldehyde-3-phosphate with an efficiency of 38%.
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Affiliation(s)
- Ryuji Nishiyama
- Laboratory of Marine Biotechnology and Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan.
| | - Akira Inoue
- Laboratory of Marine Biotechnology and Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan.
| | - Takao Ojima
- Laboratory of Marine Biotechnology and Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan.
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15
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Qin HM, Miyakawa T, Inoue A, Nishiyama R, Nakamura A, Asano A, Sawano Y, Ojima T, Tanokura M. Structure and Polymannuronate Specificity of a Eukaryotic Member of Polysaccharide Lyase Family 14. J Biol Chem 2017; 292:2182-2190. [PMID: 28011642 PMCID: PMC5313092 DOI: 10.1074/jbc.m116.749929] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 12/13/2016] [Indexed: 11/06/2022] Open
Abstract
Alginate is an abundant algal polysaccharide, composed of β-d-mannuronate and its C5 epimer α-l-guluronate, that is a useful biomaterial in cell biology and tissue engineering, with applications in cancer and aging research. The alginate lyase (EC 4.2.2.3) from Aplysia kurodai, AkAly30, is a eukaryotic member of the polysaccharide lyase 14 (PL-14) family and degrades alginate by cleaving the glycosidic bond through a β-elimination reaction. Here, we present the structural basis for the substrate specificity, with a preference for polymannuronate, of AkAly30. The crystal structure of AkAly30 at a 1.77 Å resolution and the putative substrate-binding model show that the enzyme adopts a β-jelly roll fold at the core of the structure and that Lys-99, Tyr-140, and Tyr-142 form catalytic residues in the active site. Their arrangements allow the carboxyl group of mannuronate residues at subsite +1 to form ionic bonds with Lys-99. The coupled tyrosine forms a hydrogen bond network with the glycosidic bond, and the hydroxy group of Tyr-140 is located near the C5 atom of the mannuronate residue. These interactions could promote the β-elimination of the mannuronate residue at subsite +1. More interestingly, Gly-118 and the disulfide bond formed by Cys-115 and Cys-124 control the conformation of an active-site loop, which makes the space suitable for substrate entry into subsite -1. The cleavage efficiency of AkAly30 is enhanced relative to that of mutants lacking either Gly-118 or the Cys-115-Cys-124 disulfide bond. The putative binding model and mutagenesis studies provide a novel substrate recognition mode explaining the polymannuronate specificity of PL-14 alginate lyases.
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Affiliation(s)
- Hui-Min Qin
- From the Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- the College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, Tianjin 300457, China
| | - Takuya Miyakawa
- From the Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Akira Inoue
- the Laboratory of Marine Biotechnology and Microbiology, Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate 041-8611, Japan, and
| | - Ryuji Nishiyama
- the Laboratory of Marine Biotechnology and Microbiology, Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate 041-8611, Japan, and
| | - Akira Nakamura
- From the Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Atsuko Asano
- From the Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yoriko Sawano
- From the Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
- the Laboratory of Chemistry, College of Liberal Arts and Sciences, Tokyo Medical and Dental University, 2-8-30 Kounodai, Ichikawa-shi, Chiba 272-0827, Japan
| | - Takao Ojima
- the Laboratory of Marine Biotechnology and Microbiology, Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate 041-8611, Japan, and
| | - Masaru Tanokura
- From the Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan,
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16
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Yue MM, Gong WW, Qiao Y, Ding H. A method for efficient expression of Pseudomonas aeruginosa alginate lyase in Pichia pastoris. Prep Biochem Biotechnol 2016; 46:165-70. [PMID: 25569244 DOI: 10.1080/10826068.2014.996233] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
As an eco-friendly biocatalyst for alginate hydrolysis, bacteria-derived alginate lyase (AlgL) has been widely used in research and industries to produce oligosaccharides. However, the cost of AlgL enzyme production remains high due to the low expression and difficulty in purification from bacterial cells. In this study we report an effective method to overexpress the Pseudomonas aeruginosa AlgL (paAlgL) enzyme in Pichia pastoris. Fused with a secretory peptide, the recombinant paAlgL was expressed extracellularly and purified from the culture supernatant through a simple process. The purified recombinant enzyme is highly specific for alginate sodium with a maximal activity of 2,440 U/mg. The enzymatic activity remained stable below 45°C and at pH between 4 and 10. The recombinant paAlgL was inhibited by Zn(2+), Cu(2+), and Fe(2+) and promoted by Co(2+) and Ca(2+). Interestingly, we also found that the recombinant paAlgL significantly enhanced the antimicrobial activity of antibiotics ampicillin and kanamycin against Pseudomonas aeruginosa. Our results introduce a method for efficient AlgL production, the characterization, and a new feature of the recombinant paAlgL as an enhancer of antibiotics against Pseudomonas aeruginosa.
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Affiliation(s)
- Michael M Yue
- a Feed Research Institute , Chinese Academy of Agricultural Sciences , Beijing , China
| | - Wendy W Gong
- b Institute of Plant Protection , Chinese Academy of Agricultural Sciences , Beijing , China
| | - Yu Qiao
- a Feed Research Institute , Chinese Academy of Agricultural Sciences , Beijing , China
| | - Hongbiao Ding
- a Feed Research Institute , Chinese Academy of Agricultural Sciences , Beijing , China
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Inoue A, Mashino C, Uji T, Saga N, Mikami K, Ojima T. Characterization of an Eukaryotic PL-7 Alginate Lyase in the Marine Red Alga Pyropia yezoensis. ACTA ACUST UNITED AC 2015; 4:240-248. [PMID: 28553576 PMCID: PMC5436490 DOI: 10.2174/2211550104666150915210434] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 09/02/2015] [Accepted: 09/09/2015] [Indexed: 11/22/2022]
Abstract
BACKGROUND Alginate lyases belonging to polysaccharide lyase family-7 (PL-7) are the most well studied on their structures and functions among whole alginate lyases. However, all characterized PL-7 alginate lyases are from prokaryotic bacteria cells. Here we report the first identification of eukaryotic PL-7 alginate lyase from marine red alga Pyropia yezoensis. METHODS The cDNA encoding an alginate lyase PyAly was cloned and was used for the construction of recombinant PyAly (rPyAly) expression system in Escherichia coli. Purified rPyAly was assayed to identify its enzymatic properties. Its expression pattern in P. yessoensis was also investigated. RESULTS PyAly is likely a secreted protein consisting of an N-terminal signal peptide of 25 residues and a catalytic domain of 216 residues. The amino-acid sequence of the catalytic domain showed 19-29% identities to those of bacterial characterized alginate lyases classified into family PL-7. Recombinant PyAly protein, rPyAly, which was produced with E. coli BL21(DE3) by cold-inducible expression system, drastically decreased the viscosity of alginate solution in the early stage of reaction. The most preferable substrate for rPyAly was the poly(M) of alginate with an optimal temperature and pH at 35oC and 8.0, respectively. After reaction, unsaturated tri- and tetra-saccharides were produced from poly(M) as major end products. These enzymatic properties indicated that PyAly is an endolytic alginate lyase belonging to PL-7. Moreover, we found that the PyAly gene is split into 4 exons with 3 introns. PyAly was also specifically expressed in the gametophytic haplopid stage. CONCLUSION This study demonstrates that PyAly in marine red alga P. yezoensis is a novel PL-7 alginate lyase with an endolytic manner. PyAly is a gametophyte-specifically expressed protein and its structural gene is composed of four exons and three introns. Thus, PyAly is the first enzymatically characterized eukaryotic PL-7 alginate lyase.
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Affiliation(s)
- Akira Inoue
- Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho Hakodate, Hokkaido 041-8611, Japan
| | - Chieco Mashino
- Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho Hakodate, Hokkaido 041-8611, Japan
| | - Toshiki Uji
- Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho Hakodate, Hokkaido 041-8611, Japan
| | - Naotsune Saga
- Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho Hakodate, Hokkaido 041-8611, Japan
| | - Koji Mikami
- Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho Hakodate, Hokkaido 041-8611, Japan
| | - Takao Ojima
- Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho Hakodate, Hokkaido 041-8611, Japan
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18
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Masuda Y, Okuyama M, Iizuka T, Nakai H, Saburi W, Fukukawa T, Maneesan J, Tagami T, Naraoka T, Mori H, Kimura A. Purification and characterization of a chloride ion-dependent α-glucosidase from the midgut gland of Japanese scallop (Patinopecten yessoensis). Biosci Biotechnol Biochem 2015; 80:479-85. [PMID: 26645800 DOI: 10.1080/09168451.2015.1116926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Marine glycoside hydrolases hold enormous potential due to their habitat-related characteristics such as salt tolerance, barophilicity, and cold tolerance. We purified an α-glucosidase (PYG) from the midgut gland of the Japanese scallop (Patinopecten yessoensis) and found that this enzyme has unique characteristics. The use of acarbose affinity chromatography during the purification was particularly effective, increasing the specific activity 570-fold. PYG is an interesting chloride ion-dependent enzyme. Chloride ion causes distinctive changes in its enzymatic properties, increasing its hydrolysis rate, changing the pH profile of its enzyme activity, shifting the range of its pH stability to the alkaline region, and raising its optimal temperature from 37 to 55 °C. Furthermore, chloride ion altered PYG's substrate specificity. PYG exhibited the highest Vmax/Km value toward maltooctaose in the absence of chloride ion and toward maltotriose in the presence of chloride ion.
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Affiliation(s)
- Yasushi Masuda
- a Research Faculty of Agriculture , Hokkaido University , Sapporo , Japan
| | - Masayuki Okuyama
- a Research Faculty of Agriculture , Hokkaido University , Sapporo , Japan
| | - Takahisa Iizuka
- a Research Faculty of Agriculture , Hokkaido University , Sapporo , Japan
| | - Hiroyuki Nakai
- a Research Faculty of Agriculture , Hokkaido University , Sapporo , Japan
| | - Wataru Saburi
- a Research Faculty of Agriculture , Hokkaido University , Sapporo , Japan
| | - Taro Fukukawa
- a Research Faculty of Agriculture , Hokkaido University , Sapporo , Japan
| | - Janjira Maneesan
- a Research Faculty of Agriculture , Hokkaido University , Sapporo , Japan
| | - Takayoshi Tagami
- a Research Faculty of Agriculture , Hokkaido University , Sapporo , Japan
| | | | - Haruhide Mori
- a Research Faculty of Agriculture , Hokkaido University , Sapporo , Japan
| | - Atsuo Kimura
- a Research Faculty of Agriculture , Hokkaido University , Sapporo , Japan
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Mochizuki S, Nishiyama R, Inoue A, Ojima T. A Novel Aldo-Keto Reductase, HdRed, from the Pacific Abalone Haliotis discus hannai, Which Reduces Alginate-derived 4-Deoxy-L-erythro-5-hexoseulose Uronic Acid to 2-Keto-3-deoxy-D-gluconate. J Biol Chem 2015; 290:30962-74. [PMID: 26555267 DOI: 10.1074/jbc.m115.686725] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Indexed: 11/06/2022] Open
Abstract
Abalone feeds on brown seaweeds and digests seaweeds' alginate with alginate lyases (EC 4.2.2.3). However, it has been unclear whether the end product of alginate lyases (i.e. unsaturated monouronate-derived 4-deoxy-L-erythro-5-hexoseulose uronic acid (DEH)) is assimilated by abalone itself, because DEH cannot be metabolized via the Embden-Meyerhof pathway of animals. Under these circumstances, we recently noticed the occurrence of an NADPH-dependent reductase, which reduced DEH to 2-keto-3-deoxy-D-gluconate, in hepatopancreas extract of the pacific abalone Haliotis discus hannai. In the present study, we characterized this enzyme to some extent. The DEH reductase, named HdRed in the present study, could be purified from the acetone-dried powder of hepatopancreas by ammonium sulfate fractionation followed by conventional column chromatographies. HdRed showed a single band of ∼ 40 kDa on SDS-PAGE and reduced DEH to 2-keto-3-deoxy-D-gluconate with an optimal temperature and pH at around 50 °C and 7.0, respectively. HdRed exhibited no appreciable activity toward 28 authentic compounds, including aldehyde, aldose, ketose, α-keto-acid, uronic acid, deoxy sugar, sugar alcohol, carboxylic acid, ketone, and ester. The amino acid sequence of 371 residues of HdRed deduced from the cDNA showed 18-60% identities to those of aldo-keto reductase (AKR) superfamily enzymes, such as human aldose reductase, halophilic bacterium reductase, and sea hare norsolorinic acid (a polyketide derivative) reductase-like protein. Catalytic residues and cofactor binding residues known in AKR superfamily enzymes were fairly well conserved in HdRed. Phylogenetic analysis for HdRed and AKR superfamily enzymes indicated that HdRed is an AKR belonging to a novel family.
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Affiliation(s)
- Shogo Mochizuki
- From the Laboratory of Marine Biotechnology and Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan
| | - Ryuji Nishiyama
- From the Laboratory of Marine Biotechnology and Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan
| | - Akira Inoue
- From the Laboratory of Marine Biotechnology and Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan
| | - Takao Ojima
- From the Laboratory of Marine Biotechnology and Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan
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20
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Inoue A, Takadono K, Nishiyama R, Tajima K, Kobayashi T, Ojima T. Characterization of an alginate lyase, FlAlyA, from Flavobacterium sp. strain UMI-01 and its expression in Escherichia coli. Mar Drugs 2014; 12:4693-712. [PMID: 25153766 PMCID: PMC4145338 DOI: 10.3390/md12084693] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 06/27/2014] [Accepted: 07/31/2014] [Indexed: 11/16/2022] Open
Abstract
A major alginate lyase, FlAlyA, was purified from the periplasmic fraction of an alginate-assimilating bacterium, Flavobacterium sp. strain UMI-01. FlAlyA showed a single band of ~30 kDa on SDS-PAGE and exhibited the optimal temperature and pH at 55 °C and pH 7.7, respectively. Analyses for substrate preference and reaction products indicated that FlAlyA was an endolytic poly(mannuronate) lyase (EC 4.2.2.3). A gene fragment encoding the amino-acid sequence of 288 residues for FlAlyA was amplified by inverse PCR. The N-terminal region of 21 residues except for the initiation Met in the deduced sequence was predicted as the signal peptide and the following region of six residues was regarded as propeptide, while the C-terminal region of 260 residues was regarded as the polysaccharide-lyase-family-7-type catalytic domain. The entire coding region for FlAlyA was subjected to the pCold I—Escherichia coli BL21(DE3) expression system and ~eight times higher yield of recombinant FlAlyA (recFlAlyA) than that of native FlAlyA was achieved. The recFlAlyA recovered in the periplasmic fraction of E. coli had lost the signal peptide region along with the N-terminal 3 residues of propeptide region. This suggested that the signal peptide of FlAlyA could function in part in E. coli.
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Affiliation(s)
- Akira Inoue
- Laboratory of Marine Biotechnology and Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan.
| | - Kohei Takadono
- Laboratory of Marine Biotechnology and Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan.
| | - Ryuji Nishiyama
- Laboratory of Marine Biotechnology and Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan.
| | - Kenji Tajima
- Laboratory of Molecular Materials Chemistry, Faculty of Engineering, Hokkaido University, Sapporo, Hokkaido 060-8626, Japan.
| | - Takanori Kobayashi
- Hokkaido Industrial Technology Center, Kikyou, Hakodate, Hokkaido 041-0801, Japan.
| | - Takao Ojima
- Laboratory of Marine Biotechnology and Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041-8611, Japan.
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21
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Rahman MM, Inoue A, Ojima T. Characterization of a GHF45 cellulase, AkEG21, from the common sea hare Aplysia kurodai. Front Chem 2014; 2:60. [PMID: 25147784 PMCID: PMC4123733 DOI: 10.3389/fchem.2014.00060] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 07/15/2014] [Indexed: 11/18/2022] Open
Abstract
The common sea hare Aplysia kurodai is known to be a good source for the enzymes degrading seaweed polysaccharides. Recently four cellulases, i.e., 95, 66, 45, and 21 kDa enzymes, were isolated from A. kurodai (Tsuji et al., 2013). The former three cellulases were regarded as glycosyl-hydrolase-family 9 (GHF9) enzymes, while the 21 kDa cellulase was suggested to be a GHF45 enzyme. The 21 kDa cellulase was significantly heat stable, and appeared to be advantageous in performing heterogeneous expression and protein-engineering study. In the present study, we determined some enzymatic properties of the 21 kDa cellulase and cloned its cDNA to provide the basis for the protein engineering study of this cellulase. The purified 21 kDa enzyme, termed AkEG21 in the present study, hydrolyzed carboxymethyl cellulose with an optimal pH and temperature at 4.5 and 40°C, respectively. AkEG21 was considerably heat-stable, i.e., it was not inactivated by the incubation at 55°C for 30 min. AkEG21 degraded phosphoric-acid-swollen cellulose producing cellotriose and cellobiose as major end products but hardly degraded oligosaccharides smaller than tetrasaccharide. This indicated that AkEG21 is an endolytic β-1,4-glucanase (EC 3.2.1.4). A cDNA of 1013 bp encoding AkEG21 was amplified by PCR and the amino-acid sequence of 197 residues was deduced. The sequence comprised the initiation Met, the putative signal peptide of 16 residues for secretion and the catalytic domain of 180 residues, which lined from the N-terminus in this order. The sequence of the catalytic domain showed 47–62% amino-acid identities to those of GHF45 cellulases reported in other mollusks. Both the catalytic residues and the N-glycosylation residues known in other GHF45 cellulases were conserved in AkEG21. Phylogenetic analysis for the amino-acid sequences suggested the close relation between AkEG21 and fungal GHF45 cellulases.
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Affiliation(s)
- Mohammad M Rahman
- Laboratory of Marine Biotechnology and Microbiology, Division of Applied Marine Life Science, Graduate School of Fisheries Sciences, Hokkaido University Hakodate, Japan ; Department of Fisheries Biology and Genetics, Bangladesh Agricultural University Mymensingh, Bangladesh
| | - Akira Inoue
- Laboratory of Marine Biotechnology and Microbiology, Division of Applied Marine Life Science, Graduate School of Fisheries Sciences, Hokkaido University Hakodate, Japan
| | - Takao Ojima
- Laboratory of Marine Biotechnology and Microbiology, Division of Applied Marine Life Science, Graduate School of Fisheries Sciences, Hokkaido University Hakodate, Japan
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Kumagai Y, Satoh T, Inoue A, Ojima T. A laminaribiose-hydrolyzing enzyme, AkLab, from the common sea hare Aplysia kurodai and its transglycosylation activity. Comp Biochem Physiol B Biochem Mol Biol 2014; 167:1-7. [DOI: 10.1016/j.cbpb.2013.07.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 07/19/2013] [Accepted: 07/24/2013] [Indexed: 10/26/2022]
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23
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Satoh T, Inoue A, Ojima T. Characterization of an α-glucosidase, HdAgl, from the digestive fluid of Haliotis discus hannai. Comp Biochem Physiol B Biochem Mol Biol 2013; 166:15-22. [DOI: 10.1016/j.cbpb.2013.06.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 06/07/2013] [Accepted: 06/07/2013] [Indexed: 10/26/2022]
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Transcriptomic and cellular response to bacterial challenge (pathogenic Vibrio parahaemolyticus) in farmed juvenile Haliotis rufescens fed with or without probiotic diet. J Invertebr Pathol 2013; 113:163-76. [DOI: 10.1016/j.jip.2013.03.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2012] [Revised: 02/11/2013] [Accepted: 03/12/2013] [Indexed: 11/24/2022]
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25
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Enzymatic properties and primary structures of two α-amylase isozymes from the Pacific abalone Haliotis discus hannai. Comp Biochem Physiol B Biochem Mol Biol 2013; 164:80-8. [DOI: 10.1016/j.cbpb.2012.11.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2012] [Revised: 10/27/2012] [Accepted: 11/01/2012] [Indexed: 11/21/2022]
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26
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SNP discovery and High Resolution Melting Analysis from massive transcriptome sequencing in the California red abalone Haliotis rufescens. Mar Genomics 2013; 10:11-6. [PMID: 23353006 DOI: 10.1016/j.margen.2012.12.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Revised: 12/27/2012] [Accepted: 12/28/2012] [Indexed: 11/22/2022]
Abstract
The California red abalone, Haliotis rufescens that belongs to the Haliotidae family, is the largest species of abalone in the world that has sustained the major fishery and aquaculture production in the USA and Mexico. This native mollusk has not been evaluated or assigned a conservation category even though in the last few decades it was heavily exploited until it disappeared in some areas along the California coast. In Chile, the red abalone was introduced in the 1970s from California wild abalone stocks for the purposes of aquaculture. Considering the number of years that the red abalone has been cultivated in Chile crucial genetic information is scarce and critical issues remain unresolved. This study reports and validates novel single nucleotide polymorphisms (SNP) markers for the red abalone H. rufescens using cDNA pyrosequencing. A total of 622 high quality SNPs were identified in 146 sequences with an estimated frequency of 1 SNP each 1000bp. Forty-five SNPs markers with functional information for gene ontology were selected. Of these, 8 were polymorphic among the individuals screened: Heat shock protein 70 (HSP70), vitellogenin (VTG), lysin, alginate lyase enzyme (AL), Glucose-regulated protein 94 (GRP94), fructose-bisphosphate aldolase (FBA), sulfatase 1A precursor (S1AP) and ornithine decarboxylase antizyme (ODC). Two additional sequences were also identified with polymorphisms but no similarities with known proteins were achieved. To validate the putative SNP markers, High Resolution Melting Analysis (HRMA) was conducted in a wild and hatchery-bred population. Additionally, SNP cross-amplifications were tested in two further native abalone species, Haliotis fulgens and Haliotis corrugata. This study provides novel candidate genes that could be used to evaluate loss of genetic diversity due to hatchery selection or inbreeding effects.
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Rahman MM, Wang L, Inoue A, Ojima T. cDNA cloning and bacterial expression of a PL-14 alginate lyase from a herbivorous marine snail Littorina brevicula. Carbohydr Res 2012; 360:69-77. [PMID: 22940178 DOI: 10.1016/j.carres.2012.05.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 05/07/2012] [Accepted: 05/16/2012] [Indexed: 10/28/2022]
Abstract
Herbivorous marine snails like Littorina species are known to possess alginate lyases in their digestive tracts. The Littorina enzymes have been identified as endolytic polymannuronate (poly(M)) lyases (EC 4.2.2.3); however, it is still unclear which polysaccharide-lyase family (PL) the Littorina enzymes belong to, since no complete primary structure of Littorina enzymes has been determined. Thus, in the present study, we analyzed the primary structure of LbAly28, a 28kDa alginate lyase isozyme of Littorina brevicula, by the cDNA method. LbAly28 cDNAs were amplified by PCR followed by 5'- and 3'-RACE PCRs from the L. brevicula hepatopancreas cDNA. A cDNA covering entire coding region of LbAly28 consisted of 1129bp and encoded an amino-acid sequence of 291 residues. The deduced amino-acid sequence comprised an initiation methionine, a putative signal peptide of 14 residues, a propeptide-like region of 16 residues, and a mature LbAly28 domain of 260 residues. The mature LbAly28 domain showed 43-53% amino-acid identities with other molluscan PL-14 enzymes. The catalytically important residues in PL-14 enzymes, which were identified in the Chlorella virus glucuronate-specific lyase vAL-1 and Aplysia poly(M) lyase AkAly30, were also conserved in LbAly28. Site-directed mutagenesis regarding these residues, that is, replacements of Lys94, Lys97, Thr121, Arg 123, Tyr135, and Tyr137 to Ala, decreased the activity of recombinant LbAly28 to various degrees. From these results we concluded that LbAly28 is a member of PL-14 alginate lyases. Besides the effects of above mutations, we noticed that the replacement of T121 by Ala changed the substrate preference of LbAly28. Namely, the activities toward sodium alginate and poly(MG)-block substrate increased and became comparable with the activity toward poly(M)-block substrate. This suggests that the region including T121 of LbAly28 closely relates to the recognition of poly(MG) region of alginate.
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Affiliation(s)
- Mohammad Matiur Rahman
- Laboratory of Marine Biotechnology and Microbiology, Graduate School of Fisheries Sciences, Hokkaido University, Minato-cho 3-1-1, Hakodate 041-8611, Japan
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Sim SJ, Baik KS, Park SC, Choe HN, Seong CN, Shin TS, Woo HC, Cho JY, Kim D. Characterization of alginate lyase gene using a metagenomic library constructed from the gut microflora of abalone. ACTA ACUST UNITED AC 2012; 39:585-93. [DOI: 10.1007/s10295-011-1054-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2011] [Accepted: 10/28/2011] [Indexed: 10/15/2022]
Abstract
Abstract
A metagenomic fosmid library was constructed using a genomic DNA mixture extracted from the gut microflora of abalone. The library gave an alginate lyase positive clone (AlyDW) harboring a 31.7-kbp insert. The AlyDW insert consisted of 22 open reading frames (ORFs). The deduced amino acid sequences of ORFs 11–13 were similar to those of known alginate lyase genes, which are found adjacent in the genome of Klebsiella pneumoniae subsp. aerogenes, Vibrio splendidus, and Vibrio sp. belonging to the phylum Gammaproteobacteria. Among the three recombinant proteins expressed from the three ORFs, alginate lyase activity was only observed in the recombinant protein (AlyDW11) coded by ORF 11. The expressed protein (AlyDW11) had the highest alginate lyase activity at pH 7.0 and 45°C in the presence of 1 mM AgNO3. The alginate lyase activity of ORF 11 was confirmed to be endolytic by thin-layer chromatography. AlyDW11 preferred poly(β-d-mannuronate) as a substrate over poly(α-l-guluronate). AlyDW11 contained three highly conserved regions, RSEL, QIH, and YFKAGVYNQ, which may act to stabilize the three-dimensional conformation and function of the alginate lyase.
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Affiliation(s)
- Su-Jung Sim
- grid.14005.30 0000000103569399 Department of Food Science and Technology and Functional Food Research Center Chonnam National University 500-757 Gwangju Republic of Korea
| | - Keun Sik Baik
- grid.412871.9 0000000085435345 Department of Biology Sunchon National University 540-742 Suncheon Jeonnam Republic of Korea
| | - Seong Chan Park
- grid.412871.9 0000000085435345 Department of Biology Sunchon National University 540-742 Suncheon Jeonnam Republic of Korea
| | - Han Na Choe
- grid.412871.9 0000000085435345 Department of Biology Sunchon National University 540-742 Suncheon Jeonnam Republic of Korea
| | - Chi Nam Seong
- grid.412871.9 0000000085435345 Department of Biology Sunchon National University 540-742 Suncheon Jeonnam Republic of Korea
| | - Tai-Sun Shin
- grid.14005.30 0000000103569399 Department of Food Science and Nutrition Chonnam National University 550-757 Yeosu Republic of Korea
| | - Hee Chul Woo
- grid.412576.3 0000 0001 0719 8994 Department of Chemical Engineering Pukyung National University 608-739 Busan Republic of Korea
| | - Jeong-Yong Cho
- grid.14005.30 0000000103569399 Department of Food Science and Technology and Functional Food Research Center Chonnam National University 500-757 Gwangju Republic of Korea
| | - Duwoon Kim
- grid.14005.30 0000000103569399 Department of Food Science and Technology and Functional Food Research Center Chonnam National University 500-757 Gwangju Republic of Korea
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Silva-Aciares F, Zapata M, Tournois J, Moraga D, Riquelme C. Identification of genes expressed in juvenile Haliotis rufescens in response to different copper concentrations in the north of Chile under controlled conditions. MARINE POLLUTION BULLETIN 2011; 62:2671-2680. [PMID: 22001298 DOI: 10.1016/j.marpolbul.2011.09.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2011] [Revised: 09/13/2011] [Accepted: 09/20/2011] [Indexed: 05/31/2023]
Abstract
This study reports molecular markers potentially associated with resistance or sensitivity to the impact of copper in juvenile red abalone, Haliotis rufescens, in the north of Chile under experimental conditions. Genomic analysis was made applying subtractive hybridization libraries (SSH) to identify genes up-and down regulated during cooper exposure in abalone over periods of 12 and 168 h exposed to 2.5 and 10 μg/L of Cu(+2). Results obtained from the SSH library revealed 368 different sequences regulated by copper, that correspond to eight major physiological functions. The validation of these sequences obtained by SSH as well as their expression kinetics were made by PCR in real time on 14 potential genes regulated by metal stress. This study provides information for the characterization of potential genomic markers that may be used in future environmental monitoring and to investigate new mechanisms of stress to copper in this commercially important marine species.
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Rahman MM, Inoue A, Tanaka H, Ojima T. cDNA cloning of an alginate lyase from a marine gastropod Aplysia kurodai and assessment of catalytically important residues of this enzyme. Biochimie 2011; 93:1720-30. [PMID: 21689718 DOI: 10.1016/j.biochi.2011.06.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 06/06/2011] [Indexed: 10/18/2022]
Abstract
Herbivorous marine gastropods such as abalone and sea hare ingest brown algae as a major diet and degrade the dietary alginate with alginate lyase (EC 4.2.2.3) in their digestive fluid. To date alginate lyases from Haliotidae species such as abalone have been well characterized and the primary structure analyses have classified abalone enzymes into polysaccharide-lyase-family 14 (PL-14). However, other gastropod enzymes have not been so well investigated and only partial amino-acid sequences are currently available. To improve the knowledge for primary structure and catalytic residues of gastropod alginate lyases, we cloned the cDNA encoding an alginate lyase, AkAly30, from an Aplysiidae species Aplysia kurodai and assessed its catalytically important residues by site-directed mutagenesis. Alginate lyase cDNA fragments were amplified by PCR followed by 5'- and 3'-RACE from A. kurodai hepatopancreas cDNA. The finally cloned cDNA comprised 1313 bp which encoded an amino-acid sequence of 295 residues of AkAly30. The deduced sequence comprised an initiation methionine, a putative signal peptide for secretion (18 residues), a propeptide-like region (9 residues), and a mature AkAly30 domain (267 residues) which showed ∼40% amino-acid identity with abalone alginate lyases. An Escherichia coli BL21(DE3)-pCold I expression system for recombinant AkAly30 (recAkAly30) was constructed and site-directed mutagenesis was performed to assess catalytically important amino-acid residues which had been suggested in abalone and Chlorella virus PL-14 enzymes. Replacements of K99, S126, R128, Y140 and Y142 of recAkAly30 by Ala and/or Phe greatly decreased its activity as in the case of abalone and/or Chlorella virus enzymes. Whereas, H213 that was essential for Chlorella virus enzyme to exhibit the activity at pH 10.0 was originally replaced by N120 in AkAly30. The reverse replacement of N120 by His in recAkAly30 increased the activity at pH 10.0 from 8 U/mg to 93 U/mg; however, the activity level at pH 7.0, i.e., 774.8 U/mg, was still much higher than that at pH 10.0. This indicates that N120 is not directly related to the pH dependence of AkAly30 unlike H213 of vAL-1.
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Affiliation(s)
- Mohammad Matiur Rahman
- Laboratory of Marine Biotechnology and Microbiology, Graduate School of Fisheries Sciences, Hokkaido University, Minato-cho 3-1-1, Hakodate 041-8611, Japan
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Inoue A, Mashino C, Kodama T, Ojima T. Protoplast preparation from Laminaria japonica with recombinant alginate lyase and cellulase. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2011; 13:256-63. [PMID: 20393774 DOI: 10.1007/s10126-010-9290-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2009] [Accepted: 03/21/2010] [Indexed: 05/27/2023]
Abstract
Functional recombinant abalone alginate lyase (rHdAly) and β-1,4-endoglucanase (rHdEG66) were expressed as secreted proteins with baculoviral expression systems. The specific activity of each recombinant enzyme, 2,490 and 18.2 U/mg for rHdAly and rHdEG66, respectively, was comparable to its native form at 30°C. Purified rHdAly and rHdEG66 showed the highest specific activity both at 35°C and optimum pH 8.7 and 5.9, respectively. These properties were also comparable to those of the native enzymes. Protoplast isolation was attempted from Laminaria japonica using both rHdAly and rHdEG66. When L. japonica blades were incubated in artificial seawater containing rHdAly and rHdEG66, very low numbers of protoplasts (<1 × 10(3) protoplasts/g fresh weight) resulted. However, using blades pretreated with proteinase K, the protoplast was increased up to 5 × 10(6) protoplasts/g fresh weight. Since the average diameter of isolated protoplasts was 11.6 μm, these cells were mostly derived from the epidermal layer rather than the cortical layer. Our results suggest that at least three enzymes, alginate lyase, cellulase, and protease, are essential for effective protoplast isolation from L. japonica. The protoplast isolation method in this study is more useful than earlier methods because it preferentially yielded protoplasts of the epidermal layer, which are known to be able to be regenerated.
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Affiliation(s)
- Akira Inoue
- Laboratory of Marine Biotechnology and Microbiology, Graduate School of Fisheries Sciences, Hokkaido University, Hakodate Hokkaido, 041-8611, Japan
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Rahman MM, Inoue A, Tanaka H, Ojima T. Isolation and characterization of two alginate lyase isozymes, AkAly28 and AkAly33, from the common sea hare Aplysia kurodai. Comp Biochem Physiol B Biochem Mol Biol 2010; 157:317-25. [DOI: 10.1016/j.cbpb.2010.07.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Revised: 07/30/2010] [Accepted: 07/30/2010] [Indexed: 10/19/2022]
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Zahura UA, Rahman MM, Inoue A, Tanaka H, Ojima T. An endo-β-1,4-mannanase, AkMan, from the common sea hare Aplysia kurodai. Comp Biochem Physiol B Biochem Mol Biol 2010; 157:137-43. [DOI: 10.1016/j.cbpb.2010.05.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Revised: 05/26/2010] [Accepted: 05/27/2010] [Indexed: 10/19/2022]
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Isolation and characterization of two types of β-1,3-glucanases from the common sea hare Aplysia kurodai. Comp Biochem Physiol B Biochem Mol Biol 2010; 155:138-44. [DOI: 10.1016/j.cbpb.2009.10.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Revised: 10/19/2009] [Accepted: 10/26/2009] [Indexed: 11/21/2022]
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Ogura K, Yamasaki M, Yamada T, Mikami B, Hashimoto W, Murata K. Crystal structure of family 14 polysaccharide lyase with pH-dependent modes of action. J Biol Chem 2010; 284:35572-9. [PMID: 19846561 DOI: 10.1074/jbc.m109.068056] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Chlorella virus enzyme vAL-1 (38 kDa), a member of polysaccharide lyase family 14, degrades the Chlorella cell wall by cleaving the glycoside bond of the glucuronate residue (GlcA) through a beta-elimination reaction. The enzyme consists of an N-terminal cell wall-attaching domain (11 kDa) and a C-terminal catalytic module (27 kDa). Here, we show the enzyme characteristics of vAL-1, especially its pH-dependent modes of action, and determine the structure of the catalytic module. vAL-1 also exhibited alginate lyase activity at alkaline pH, and truncation of the N-terminal domain increased the lyase activity by 50-fold at pH 7.0. The truncated form vAL-1(S) released di- to hexasaccharides from alginate at pH 7.0, whereas disaccharides were preferentially generated at pH 10.0. This indicates that vAL-1(S) shows two pH-dependent modes of action: endo- and exotypes. The x-ray crystal structure of vAL-1(S) at 1.2 A resolution showed two antiparallel beta-sheets with a deep cleft showing a beta-jelly roll fold. The structure of GlcA-bound vAL-1(S) at pH 7.0 and 10.0 was determined: GlcA was found to be bound outside and inside the cleft at pH 7.0 and 10.0, respectively. This suggests that the electric charges at the active site greatly influence the binding mode of substrates and regulate endo/exo activity. Site-directed mutagenesis demonstrated that vAL-1(S) has a specific amino acid arrangement distinct from other alginate lyases crucial for catalysis. This is, to our knowledge, the first study in which the structure of a family 14 polysaccharide lyase with two different modes of action has been determined.
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Affiliation(s)
- Kohei Ogura
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Gokasho, Uji 611-0011 , Japan
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Kumagai Y, Ojima T. Enzymatic properties and the primary structure of a β-1,3-glucanase from the digestive fluid of the Pacific abalone Haliotis discus hannai. Comp Biochem Physiol B Biochem Mol Biol 2009; 154:113-20. [DOI: 10.1016/j.cbpb.2009.05.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Revised: 05/11/2009] [Accepted: 05/11/2009] [Indexed: 11/16/2022]
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An QD, Zhang GL, Wu HT, Zhang ZC, Zheng GS, Luan L, Murata Y, Li X. Alginate-deriving oligosaccharide production by alginase from newly isolated Flavobacterium sp. LXA and its potential application in protection against pathogens. J Appl Microbiol 2009; 106:161-70. [PMID: 19054241 DOI: 10.1111/j.1365-2672.2008.03988.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
AIMS To examine algino-oligosaccharide production by alginase from newly isolated Flavobacterium sp. LXA and its elicitor and antibacterial activity. METHODS AND RESULTS Algino-oligosaccharide production from alginate was carried out using alginase obtained from a newly isolated Flavobacterium sp. LXA. When alginase was partially purified by dual ammonium sulfate precipitation and used for alginate degradation, the viscosity loss correlated well with the release of reducing terminals. The optimal temperature and pH for alginate degradation was 40 degrees C and pH 7.0, respectively. When alginate was added at an initial concentration of more than 0.8%, the maximal degradation rate of alginate was obtained. Under these optimal reaction conditions and with partially purified alginase, the average degrees of polymerization (DP) of alginate-degraded products was about 6.0, which favoured algino-oligosaccharide production. The algino-oligosaccharides showed an elicitor activity stimulating the accumulation of phytoalexin and inducing phenylalanine ammonia lyase in soybean cotyledon, and antimicrobial activity on Pseudomonas aeruginosa. CONCLUSIONS Algino-oligosaccharide could be degraded from alginate by the partially purified alginase and its maximal bioactivity occurred on the oligosaccharide with average DP 6.8. SIGNIFICANCE AND IMPACT OF THE STUDY Algino-oligosaccharide was first reported to have elicitor and antibacterial activity and have potential as a biological agent for protection against plant or human disease.
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Affiliation(s)
- Q-D An
- Department of Chemical and Material Engineering, Dalian College of Light Industry, Dalian, PR China
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Catalytically important amino-acid residues of abalone alginate lyase HdAly assessed by site-directed mutagenesis. Enzyme Microb Technol 2008. [DOI: 10.1016/j.enzmictec.2008.06.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Ootsuka S, Saga N, Suzuki KI, Inoue A, Ojima T. Isolation and cloning of an endo-β-1,4-mannanase from Pacific abalone Haliotis discus hannai. J Biotechnol 2006; 125:269-80. [PMID: 16621092 DOI: 10.1016/j.jbiotec.2006.03.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2005] [Revised: 02/09/2006] [Accepted: 03/03/2006] [Indexed: 10/24/2022]
Abstract
An endo-beta-1,4-mannanase was isolated from digestive fluid of Pacific abalone, Haliotis discus hannai, by successive chromatographies on TOYPEARL CM-650M, hydroxyapatite, and TOYOPEARL HW50F. The abalone mannanase, named HdMan in the present paper, showed a molecular mass of approximately 39,000 Da on SDS-PAGE, and exhibited high hydrolyic activity on both galactomannan from locust bean gum and glucomannan from konjac at an optimal pH and temperature of 7.5 and 45 degrees C, respectively. HdMan could degrade either beta-1,4-mannan or beta-1,4-mannooligosaccharides to mannotriose and mannobiose similarly to beta-1,4-mannanases from Pomacea, Littorina, and Mytilus. In addition, HdMan could disperse the fronds of a red alga Porphyra yezoensis into cell masses consisting of 10-20 cells that are available for cell engineering of this alga. cDNAs encoding HdMan were amplified by polymerase chain reaction from an abalone-hepatopancreas cDNA library. From the nucleotide sequences of the cDNAs, the sequence of 1232 bp in total was determined and the amino-acid sequence of 377 residues was deduced from the translational region of 1134 bp locating at nucleotide positions 15-1148. The N-terminal region of 17 residues except for the initiation Met, was regarded as the signal peptide of HdMan because it was absent in the HdMan protein and showed high similarity to the consensus sequence for signal peptides of eukaryote secretory proteins. Accordingly, mature HdMan was considered to consist of 359 residues with the calculated molecular mass of 39,627.2 Da. HdMan is classified into glycoside hydrolase family 5 (GHF5) on the basis of sequence homology to GHF5 enzymes.
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Affiliation(s)
- Shuuji Ootsuka
- Laboratory of Breeding Sciences, Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido, Japan
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Wang YH, Yu GL, Wang XM, Lv ZH, Zhao X, Wu ZH, Ji WS. Purification and characterization of alginate lyase from marine Vibrio sp. YWA. Acta Biochim Biophys Sin (Shanghai) 2006; 38:633-8. [PMID: 16953302 DOI: 10.1111/j.1745-7270.2006.00210.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Extracellular alginate lyase secreted by marine Vibrio sp. YWA, isolated from decayed Laminaria japonica, was purified by a combination of ammonium sulfate precipitation and diethylaminoethyl-Sephacel column chromatography. The results show that the molecular mass of alginate lyase was approximately 62.5 kDa, with an optimal pH and temperature at pH 7.0 and 25 degrees C, respectively. K(m) was approximately 72.73 g/L. The activity of the enzyme was enhanced by EDTA and Zn(2+), but inhibited by Ba(2+). The substrates specificity analysis shows that it was specific for hydrolyzing poly-beta-D-1,4-mannuronate in alginate.
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Affiliation(s)
- Yuan-Hong Wang
- Marine Drug and Food Institute, Key Laboratory of Marine Drugs of Shandong Province, Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao 266003, China.
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Suzuki H, Suzuki KI, Inoue A, Ojima T. A novel oligoalginate lyase from abalone, Haliotis discus hannai, that releases disaccharide from alginate polymer in an exolytic manner. Carbohydr Res 2006; 341:1809-19. [PMID: 16697989 DOI: 10.1016/j.carres.2006.04.032] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2006] [Revised: 04/05/2006] [Accepted: 04/13/2006] [Indexed: 11/22/2022]
Abstract
We previously reported the isolation and cDNA cloning of an endolytic alginate lyase, HdAly, from abalone Haliotis discus hannai [Carbohydr. Res.2003, 338, 2841-2852]. Although HdAly preferentially degraded mannuronate-rich substrates, it was incapable of degrading unsaturated oligomannuronates smaller than tetrasaccharide. In the present study, we used conventional chromatographic techniques to isolate a novel unsaturated-trisaccharide-degrading enzyme, named HdAlex, from the digestive fluid of the abalone. The HdAlex showed a molecular weight of 32,000 on SDS-PAGE and could degrade not only unsaturated trisaccharide but also alginate and mannuronate-rich polymers at an optimal pH and temperature of 7.1 and 42 degrees C, respectively. Upon digestion of alginate polymer, HdAlex decreased the viscosity of the alginate at a slower rate than did HdAly, producing only unsaturated disaccharide without any intermediate oligosaccharides. These results indicate that HdAlex degrades the alginate polymer in an exolytic manner. Because HdAlex split saturated trisaccharide producing unsaturated disaccharide, we considered that this enzyme cleaved the alginate at the second glycoside linkage from the reducing terminus. The primary structure of HdAlex was deduced with cDNAs amplified from an abalone hepatopancreas cDNA library by the polymerase chain reaction. The translational region of 822 bp in the total 887-bp sequence of HdAlex cDNA encoded an amino-acid sequence of 273 residues. The N-terminal sequence of 16 residues, excluding the initiation methionine, was regarded as the signal peptide of this enzyme. The amino-acid sequence of the remaining 256 residues shared 62-67% identities with those of the polysaccharide lyase family-14 (PL14) enzymes such as HdAly and turban-shell alginate lyase SP2. To our knowledge, HdAlex is the first exolytic oligoalginate lyase belonging to PL14.
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Affiliation(s)
- Harumasa Suzuki
- Laboratory of Marine Biotechnology and Microbiology, Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Japan
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Ochiai A, Hashimoto W, Murata K. A biosystem for alginate metabolism in Agrobacterium tumefaciens strain C58: molecular identification of Atu3025 as an exotype family PL-15 alginate lyase. Res Microbiol 2006; 157:642-9. [PMID: 16545947 DOI: 10.1016/j.resmic.2006.02.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2005] [Revised: 02/01/2006] [Accepted: 02/09/2006] [Indexed: 11/30/2022]
Abstract
The Gram-negative bacterium Sphingomonas sp. strain A1 (strain A1) has a peculiar biosystem to directly import and depolymerize a macromolecule, alginate, which is encoded by a cluster of genes on the genome. We identified five clustered ORFs homologous to some genes of the strain A1 cluster in the genome of Agrobacterium tumefaciens strain C58 (strain C58). These ORFs are Atu3021, Atu3022, Atu3023, and Atu3024, encoding a putative sugar ABC transporter system and Atu3025, which encodes a putative alginate lyase. We analyzed the involvement of this gene cluster in alginate metabolism. Strain C58 cells grew significantly on low-molecular-weight (LMW) alginate (average molecular weight, 1000), and we detected specific alginate-induced expression of Atu3024 and Atu3025. This strain does not grow on alginate (average molecular weight, 25,600), suggesting that the strain C58 gene cluster is involved in importing and degrading LMW alginate. One protein, Atu3025, purified from strain C58, was identified as an alginate lyase, and the enzyme overexpressed in Escherichia coli was further characterized. Atu3025 released monosaccharides specifically from alginate most efficiently at pH 7.3 and 30 degrees C through a beta-elimination reaction, indicating that Atu3025 is an exotype alginate lyase potentially involved in the assimilation of LMW alginate in strain C58.
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Affiliation(s)
- Akihito Ochiai
- Laboratory of Basic and Applied Molecular Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
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Hashimoto W, Miyake O, Ochiai A, Murata K. Molecular identification of Sphingomonas sp. A1 Alginate lyase (A1-IV′) as a member of novel polysaccharide lyase family 15 and implications in alginate lyase evolution. J Biosci Bioeng 2005; 99:48-54. [PMID: 16233753 DOI: 10.1263/jbb.99.48] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2004] [Accepted: 10/14/2004] [Indexed: 11/17/2022]
Abstract
Sphingomonas sp. A1 (strain A1) produces three endotypes (A1-I [65 kDa], A1-II [25 kDa], and A1-III [40 kDa]) and an exotype (A1-IV [86 kDa]) alginate lyases in cytoplasm. These four enzymes cooperatively depolymerize alginate into constituent monosaccharides. In addition to the genes for these lyases, novel genes encoding hypothetical proteins homologous with A1-IV were found in the genomes of many bacteria including strain A1. One such protein, A1-IV' (90 kDa) of strain A1, was overexpressed in Escherichia coli cells, purified, and characterized. A1-IV' catalyzed the cleavage of glycosidic bonds in alginate through a beta-elimination reaction and released unsaturated di- and trisaccharides as main products, thus indicating that the enzyme is an endotype alginate lyase. A1-IV', which differed from A1-IV in some enzymatic properties, was not expressed in strain A1, suggesting that A1-IV' has no significant role in alginate metabolism. A1-IV' and other A1-IV homologs facilitate the creation of novel polysaccharide lyase family 15 based on their primary structures, implying the evolution route of alginate lyases in family PL-15.
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Affiliation(s)
- Wataru Hashimoto
- Laboratory of Basic and Applied Molecular Biotechnology, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
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