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Quan Y, Jiang H, Hamouda HI, Li J, Tang H, Mao X. A Novel Thermostable Laminarinase with High Activity from Streptomyces albus and Its Catalytic Characteristics in Laminarin Degradation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2025; 73:3056-3068. [PMID: 39591591 DOI: 10.1021/acs.jafc.4c09109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2024]
Abstract
Laminarin oligosaccharides (LOSs) degraded from laminarin present nutritional functions. Laminarinases with high activity and good stability are significant tools for LOS production. OUC-SaLam66, a novel GH128 laminarinase from Streptomyces albus, was heterologously expressed. OUC-SaLam66 harbored a significant activity advantage up to 2294.80 U/mg at 45 °C and pH 4.0; meanwhile, it could preserve 80% activity at 45 °C for 12 h, indicating good stability. Significantly, its residual activity was over 75% after incubating at 100 °C for 1 h. Differential scanning calorimetry and molecular dynamic modeling revealed that its melting point and RMSD average point were 114.83 °C and 0.125 nm at 100 °C, respectively, which further proved its superior stability. Its apparent Km and Vmax against laminarin were 6.437 mM and 2.5 μg/min/mg, respectively. Hydrolysis products were mainly composed of laminaritriose and laminaribiose. The high activity and thermostability of OUC-SaLam66 make it a promising candidate for LOS preparation.
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Affiliation(s)
- Yongyi Quan
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, PR China
- Qingdao Key Laboratory of Food Biotechnology, Qingdao 266404, PR China
- Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, Qingdao 266404, PR China
| | - Hong Jiang
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, PR China
- Qingdao Key Laboratory of Food Biotechnology, Qingdao 266404, PR China
- Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, Qingdao 266404, PR China
| | - Hamed I Hamouda
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, PR China
- Qingdao Key Laboratory of Food Biotechnology, Qingdao 266404, PR China
- Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, Qingdao 266404, PR China
| | - Jiayu Li
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, PR China
- Qingdao Key Laboratory of Food Biotechnology, Qingdao 266404, PR China
- Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, Qingdao 266404, PR China
| | - Hengxin Tang
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, PR China
- Qingdao Key Laboratory of Food Biotechnology, Qingdao 266404, PR China
- Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, Qingdao 266404, PR China
| | - Xiangzhao Mao
- State Key Laboratory of Marine Food Processing and Safety Control, College of Food Science and Engineering, Ocean University of China, Qingdao 266404, PR China
- Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, Qingdao 266237, PR China
- Qingdao Key Laboratory of Food Biotechnology, Qingdao 266404, PR China
- Key Laboratory of Biological Processing of Aquatic Products, China National Light Industry, Qingdao 266404, PR China
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Feng J, Xu S, Feng R, Kovalevsky A, Zhang X, Liu D, Wan Q. Identification and structural analysis of a thermophilic β-1,3-glucanase from compost. BIORESOUR BIOPROCESS 2021; 8:102. [PMID: 38650272 PMCID: PMC10992293 DOI: 10.1186/s40643-021-00449-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 09/24/2021] [Indexed: 11/10/2022] Open
Abstract
β-1,3-glucanase can specifically hydrolyze glucans to oligosaccharides and has potential applications in biotechnology. We used the metatranscriptomic technology to discover a thermophilic β-1,3-glucanase from compost. The phylogenetic study shows that it belongs to the family 16 glycoside hydrolase (GH16) and is most homologous with an enzyme from Streptomyces sioyaensis, an actinobacterium. It has the activity of 146.9 U/mg in the optimal reaction condition (75 °C and pH 5.5). Its catalytic domain was crystallized and diffracted to 1.14 Å resolution. The crystal structure shows a sandwich-like β-jelly-roll fold with two disulfide bonds. After analyzing the occurring frequencies of these cysteine residues, we designed two mutants (C160G and C180I) to study the role of these disulfide bonds. Both mutants have decreased their optimal temperature from 75 to 70 °C, which indicate that the disulfide bonds are important to maintain thermostability. Interestingly, the activity of C160G has increased ~ 17% to reach 171.4 U/mg. We speculate that the increased activity of C160G mutant is due to increased dynamics near the active site. Our studies give a good example of balancing the rigidity and flexibility for enzyme activity, which is helpful for protein engineering.
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Affiliation(s)
- Jianwei Feng
- College of Science, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Shenyuan Xu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
| | - Ruirui Feng
- College of Science, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Xia Zhang
- Department of Molecular Biology, Qingdao Vland Biotech Group Inc., Qingdao, Shandong, 266000, People's Republic of China
| | - Dongyang Liu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Qun Wan
- College of Science, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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Comparative Analysis of Carbohydrate Active Enzymes in the Flammulina velutipes var. lupinicola Genome. Microorganisms 2020; 9:microorganisms9010020. [PMID: 33374587 PMCID: PMC7822412 DOI: 10.3390/microorganisms9010020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/17/2020] [Accepted: 12/18/2020] [Indexed: 11/17/2022] Open
Abstract
The purpose of this study was to determine the genome sequence of Flammulina velutipes var. lupinicola based on next-generation sequencing (NGS) and to identify the genes encoding carbohydrate-active enzymes (CAZymes) in the genome. The optimal assembly (71 kmer) based on ABySS de novo assembly revealed a total length of 33,223,357 bp (49.53% GC content). A total of 15,337 gene structures were identified in the F. velutipes var. lupinicola genome using ab initio gene prediction method with Funannotate pipeline. Analysis of the orthologs revealed that 11,966 (96.6%) out of the 15,337 predicted genes belonged to the orthogroups and 170 genes were specific for F. velutipes var. lupinicola. CAZymes are divided into six classes: auxiliary activities (AAs), glycosyltransferases (GTs), carbohydrate esterases (CEs), polysaccharide lyases (PLs), glycoside hydrolases (GHs), and carbohydrate-binding modules (CBMs). A total of 551 genes encoding CAZymes were identified in the F. velutipes var. lupinicola genome by analyzing the dbCAN meta server database (HMMER, Hotpep, and DIAMOND searches), which consisted of 54-95 AAs, 145-188 GHs, 55-73 GTs, 6-19 PLs, 13-59 CEs, and 7-67 CBMs. CAZymes can be widely used to produce bio-based products (food, paper, textiles, animal feed, and biofuels). Therefore, information about the CAZyme repertoire of the F. velutipes var. lupinicola genome will help in understanding the lignocellulosic machinery and in-depth studies will provide opportunities for using this fungus for biotechnological and industrial applications.
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Park YJ, Lee CS, Kong WS. Genomic Insights into the Fungal Lignocellulolytic Machinery of Flammulina rossica. Microorganisms 2019; 7:microorganisms7100421. [PMID: 31597238 PMCID: PMC6843371 DOI: 10.3390/microorganisms7100421] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/27/2019] [Accepted: 09/28/2019] [Indexed: 11/16/2022] Open
Abstract
Next-generation sequencing (NGS) of the Flammulina rossica (wood-rotting basidiomycete) genome was performed to identify its carbohydrate-active enzymes (CAZymes). De novo genome assembly (31 kmer) revealed a total length of 35,646,506 bp (49.79% GC content). In total, 12,588 gene models of F. rossica were predicted using an ab initio gene prediction tool (AUGUSTUS). Orthologous analysis with other fungal species revealed that 7433 groups contained at least one F. rossica gene. Additionally, 12,033 (95.6%) of 12,588 genes for F. rossica proteins had orthologs among the Dikarya, and F. rossica contained 12 species-specific genes. CAZyme annotation in the F. rossica genome revealed 511 genes predicted to encode CAZymes including 102 auxiliary activities, 236 glycoside hydrolases, 94 glycosyltransferases, 19 polysaccharide lyases, 56 carbohydrate esterases, and 21 carbohydrate binding-modules. Among the 511 genes, several genes were predicted to simultaneously encode two different CAZymes such as glycoside hydrolases (GH) as well as carbohydrate-binding module (CBM). The genome information of F. rossica offers opportunities to understand the wood-degrading machinery of this fungus and will be useful for biotechnological and industrial applications.
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Affiliation(s)
- Young-Jin Park
- Department of Biomedical Chemistry, Research Institute for Biomedical & Health Science, College of Biomedical and Health Science, Konkuk University, 268 Chungwon-daero, Chungju-si 27478, Korea.
| | - Chang-Soo Lee
- Department of Biomedical Chemistry, Research Institute for Biomedical & Health Science, College of Biomedical and Health Science, Konkuk University, 268 Chungwon-daero, Chungju-si 27478, Korea.
| | - Won-Sik Kong
- Mushroom Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, 92, Bisan-ro, Eumseong-gun 27709, Korea.
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Comparative Analysis and Biochemical Characterization of Two Endo-β-1,3-Glucanases from the Thermophilic Bacterium Fervidobacterium sp. Catalysts 2019. [DOI: 10.3390/catal9100830] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Laminarinases exhibit potential in a wide range of industrial applications including the production of biofuels and pharmaceuticals. In this study, we present the genetic and biochemical characteristics of FLamA and FLamB, two laminarinases derived from a metagenomic sample from a hot spring in the Azores. Sequence comparison revealed that both genes had high similarities to genes from Fervidobacterium nodosum Rt17-B1. The two proteins showed sequence similarities of 62% to each other and belong to the glycoside hydrolase (GH) family 16. For biochemical characterization, both laminarinases were heterologously produced in Escherichia coli and purified to homogeneity. FLamA and FLamB exhibited similar properties and both showed highest activity towards laminarin at 90 °C and pH 6.5. The two enzymes were thermostable but differed in their half-life at 80 °C with 5 h and 1 h for FLamA and FLamB, respectively. In contrast to other laminarinases, both enzymes prefer β-1,3-glucans and mixed-linked glucans as substrates. However, FLamA and FLamB differ in their catalytic efficiency towards laminarin. Structure predictions were made and showed minor differences particularly in a kink adjacent to the active site cleft. The high specific activities and resistance to elevated temperatures and various additives make both enzymes suitable candidates for application in biomass conversion.
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Park YJ, Kong WS. Genome-Wide Comparison of Carbohydrate-Active Enzymes (CAZymes) Repertoire of Flammulina ononidis. MYCOBIOLOGY 2018; 46:349-360. [PMID: 30637143 PMCID: PMC6319455 DOI: 10.1080/12298093.2018.1537585] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/09/2018] [Accepted: 10/12/2018] [Indexed: 06/09/2023]
Abstract
Whole-genome sequencing of Flammulina ononidis, a wood-rotting basidiomycete, was performed to identify genes associated with carbohydrate-active enzymes (CAZymes). A total of 12,586 gene structures with an average length of 2009 bp were predicted by the AUGUSTUS tool from a total 35,524,258 bp length of de novo genome assembly (49.76% GC). Orthologous analysis with other fungal species revealed that 7051 groups contained at least one F. ononidis gene. In addition, 11,252 (89.5%) of 12,586 genes for F. ononidis proteins had orthologs among the Dikarya, and F. ononidis contained 8 species-specific genes, of which 5 genes were paralogous. CAZyme prediction revealed 524 CAZyme genes, including 228 for glycoside hydrolases, 21 for polysaccharide lyases, 87 for glycosyltransferases, 61 for carbohydrate esterases, 87 with auxiliary activities, and 40 for carbohydrate-binding modules in the F. ononidis genome. This genome information including CAZyme repertoire will be useful to understand lignocellulolytic machinery of this white rot fungus F. ononidis.
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Affiliation(s)
- Young-Jin Park
- Department of Integrated Biosciences, Research Institute for Biomedical & Health Science, College of Biomedical and Health Science, Konkuk University, Chungju-si, Korea
| | - Won-Sik Kong
- Mushroom Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong-gun, Korea
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Genome Sequencing and Carbohydrate-Active Enzyme (CAZyme) Repertoire of the White Rot Fungus Flammulina elastica. Int J Mol Sci 2018; 19:ijms19082379. [PMID: 30104475 PMCID: PMC6121412 DOI: 10.3390/ijms19082379] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 07/30/2018] [Accepted: 08/07/2018] [Indexed: 11/25/2022] Open
Abstract
Next-generation sequencing (NGS) of the Flammulina elastica (wood-rotting basidiomycete) genome was performed to identify carbohydrate-active enzymes (CAZymes). The resulting assembly (31 kmer) revealed a total length of 35,045,521 bp (49.7% GC content). Using the AUGUSTUS tool, 12,536 total gene structures were predicted by ab initio gene prediction. An analysis of orthologs revealed that 6806 groups contained at least one F. elastica protein. Among the 12,536 predicted genes, F. elastica contained 24 species-specific genes, of which 17 genes were paralogous. CAZymes are divided into five classes: glycoside hydrolases (GHs), carbohydrate esterases (CEs), polysaccharide lyases (PLs), glycosyltransferases (GTs), and auxiliary activities (AA). In the present study, annotation of the predicted amino acid sequences from F. elastica genes using the dbCAN CAZyme database revealed 508 CAZymes, including 82 AAs, 218 GHs, 89 GTs, 18 PLs, 59 CEs, and 42 carbohydrate binding modules in the F. elastica genome. Although the CAZyme repertoire of F. elastica was similar to those of other fungal species, the total number of GTs in F. elastica was larger than those of other basidiomycetes. This genome information elucidates newly identified wood-degrading machinery in F. elastica, offers opportunities to better understand this fungus, and presents possibilities for more detailed studies on lignocellulosic biomass degradation that may lead to future biotechnological and industrial applications.
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Wu Q, Dou X, Wang Q, Guan Z, Cai Y, Liao X. Isolation of β-1,3-Glucanase-Producing Microorganisms from Poria cocos Cultivation Soil via Molecular Biology. Molecules 2018; 23:molecules23071555. [PMID: 29954113 PMCID: PMC6100237 DOI: 10.3390/molecules23071555] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 06/25/2018] [Accepted: 06/26/2018] [Indexed: 11/26/2022] Open
Abstract
β-1,3-Glucanase is considered as a useful enzymatic tool for β-1,3-glucan degradation to produce (1→3)-linked β-glucan oligosaccharides with pharmacological activity properties. To validly isolate β-1,3-glucanase-producing microorganisms, the soil of Wolfiporia extensa, considered an environment rich in β-1,3-glucan-degrading microorganisms, was subjected to high throughput sequencing. The results demonstrated that the genera Streptomyces (1.90%) and Arthrobacter (0.78%) belonging to the order Actinomycetales (8.64%) in the phylum Actinobacteria (18.64%) were observed in soil for P. cocos cultivation (FTL1). Actinomycetes were considered as the candidates for isolation of glucan-degrading microorganisms. Out of 58 isolates, only 11 exhibited β-1,3-glucan-degrading activity. The isolate SYBCQL belonging to the genus Kitasatospora with β-1,3-glucan-degrading activity was found and reported for the first time and the isolate SYBC17 displayed the highest yield (1.02 U/mg) among the isolates. To check the β-1,3-glucanase contribution to β-1,3-glucan-degrading activity, two genes, 17-W and 17-Q, encoding β-1,3-glucanase in SYBC17 and one gene QLK1 in SYBCQL were cloned and expressed for verification at the molecular level. Our findings collectively showed that the isolates able to secrete β-1,3-glucanase could be obtained with the assistance of high-throughput sequencing and genes expression analysis. These methods provided technical support for isolating β-1,3-glucanase-producing microorganisms.
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Affiliation(s)
- Qiulan Wu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
| | - Xin Dou
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
| | - Qi Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
| | - Zhengbing Guan
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
| | - Xiangru Liao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
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Mitsuya D, Sugiyama T, Zhang S, Takeuchi Y, Okai M, Urano N, Ishida M. Enzymatic properties and the gene structure of a cold-adapted laminarinase from Pseudoalteromonas species LA. J Biosci Bioeng 2018; 126:169-175. [PMID: 29627318 DOI: 10.1016/j.jbiosc.2018.02.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 02/17/2018] [Accepted: 02/22/2018] [Indexed: 11/18/2022]
Abstract
We isolated a laminarin-degrading cold-adapted bacterium strain LA from coastal seawater in Sagami Bay, Japan and identified it as a Pseudoalteromonas species. We named the extracellular laminarinase LA-Lam, and purified and characterized it. LA-Lam showed high degradation activity for Laminaria digitata laminarin in the ranges of 15-50°C and pH 5.0-9.0. The major terminal products degraded from L. digitata laminarin with LA-Lam were glucose, laminaribiose, and laminaritriose. The degradation profile of laminarioligosaccharides with LA-Lam suggested that the enzyme has a high substrate binding ability toward tetrameric or larger saccharides. Our results of the gene sequence and the SDS-PAGE analyses revealed that the major part of mature LA-Lam is a catalytic domain that belongs to the GH16 family, although its precursor is composed of a signal peptide, the catalytic domain, and three-repeated unknown regions.
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Affiliation(s)
- Daisuke Mitsuya
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo 108-8477, Japan
| | - Takuya Sugiyama
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo 108-8477, Japan
| | - Shuo Zhang
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo 108-8477, Japan
| | - Yo Takeuchi
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo 108-8477, Japan
| | - Masahiko Okai
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo 108-8477, Japan
| | - Naoto Urano
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo 108-8477, Japan
| | - Masami Ishida
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato, Tokyo 108-8477, Japan.
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A first glycoside hydrolase family 50 endo-β-1,3-d-glucanase from Pseudomonas aeruginosa. Enzyme Microb Technol 2018; 108:34-41. [DOI: 10.1016/j.enzmictec.2017.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/26/2017] [Accepted: 09/02/2017] [Indexed: 01/18/2023]
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Qin HM, Miyakawa T, Inoue A, Nakamura A, Nishiyama R, Ojima T, Tanokura M. Laminarinase from Flavobacterium sp. reveals the structural basis of thermostability and substrate specificity. Sci Rep 2017; 7:11425. [PMID: 28900273 PMCID: PMC5595797 DOI: 10.1038/s41598-017-11542-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 08/29/2017] [Indexed: 12/28/2022] Open
Abstract
Laminarinase from Flavobacterium sp. strain UMI-01, a new member of the glycosyl hydrolase 16 family of a marine bacterium associated with seaweeds, mainly degrades β-1,3-glucosyl linkages of β-glucan (such as laminarin) through the hydrolysis of glycosidic bonds. We determined the crystal structure of ULam111 at 1.60-Å resolution to understand the structural basis for its thermostability and substrate specificity. A calcium-binding motif located on the opposite side of the β-sheet from catalytic cleft increased its degrading activity and thermostability. The disulfide bridge Cys31-Cys34, located on the β2-β3 loop near the substrate-binding site, is responsible for the thermostability of ULam111. The substrates of β-1,3-linked laminarin and β-1,3-1,4-linked glucan bound to the catalytic cleft in a completely different mode at subsite -3. Asn33 and Trp113, together with Phe212, formed hydrogen bonds with preferred substrates to degrade β-1,3-linked laminarin based on the structural comparisons. Our structural information provides new insights concerning thermostability and substrate recognition that will enable the design of industrial biocatalysts.
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Affiliation(s)
- Hui-Min Qin
- Laboratory of Basic Science on Healthy Longevity, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, Tianjin, 300457, China
| | - Takuya Miyakawa
- Laboratory of Basic Science on Healthy Longevity, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Akira Inoue
- Laboratory of Marine Biotechnology and Microbiology, Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate, 041-8611, Japan
| | - Akira Nakamura
- Laboratory of Basic Science on Healthy Longevity, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Ryuji Nishiyama
- Laboratory of Marine Biotechnology and Microbiology, Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate, 041-8611, Japan
| | - Takao Ojima
- Laboratory of Marine Biotechnology and Microbiology, Graduate School of Fisheries Sciences, Hokkaido University, 3-1-1 Minato-cho, Hakodate, 041-8611, Japan
| | - Masaru Tanokura
- Laboratory of Basic Science on Healthy Longevity, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan. .,College of Biotechnology, Tianjin University of Science and Technology, No. 29, 13th Avenue, Tianjin, 300457, China.
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Alvarez TM, Liberato MV, Cairo JPLF, Paixão DAA, Campos BM, Ferreira MR, Almeida RF, Pereira IO, Bernardes A, Ematsu GCG, Chinaglia M, Polikarpov I, de Oliveira Neto M, Squina FM. A Novel Member of GH16 Family Derived from Sugarcane Soil Metagenome. Appl Biochem Biotechnol 2015; 177:304-17. [DOI: 10.1007/s12010-015-1743-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 07/03/2015] [Indexed: 10/23/2022]
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Bennur T, Kumar AR, Zinjarde S, Javdekar V. Nocardiopsis species: Incidence, ecological roles and adaptations. Microbiol Res 2015; 174:33-47. [PMID: 25946327 DOI: 10.1016/j.micres.2015.03.010] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 03/13/2015] [Accepted: 03/16/2015] [Indexed: 12/23/2022]
Abstract
Members of the genus Nocardiopsis are ecologically versatile and biotechnologically important. They produce a variety of bioactive compounds such as antimicrobial agents, anticancer substances, tumor inducers, toxins and immunomodulators. They also secrete novel extracellular enzymes such as amylases, chitinases, cellulases, β-glucanases, inulinases, xylanases and proteases. Nocardiopsis species are aerobic, Gram-positive, non-acid-fast, catalase-positive actinomycetes with nocardioform substrate mycelia and their aerial mycelia bear long chains of spores. Their DNA possesses high contents of guanine and cytosine. There is a marked variation in properties of the isolates obtained from different ecological niches and their products. An important feature of several species is their halophilic or halotolerant nature. They are associated with a variety of marine and terrestrial biological forms wherein they produce antibiotics and toxins that help their hosts in evading pathogens and predators. Two Nocardiopsis species, namely, N. dassonvillei and N. synnemataformans (among the thirty nine reported ones) are opportunistic human pathogens and cause mycetoma, suppurative infections and abscesses. Nocardiopsis species are present in some plants (as endophytes or surface microflora) and their rhizospheres. Here, they are reported to produce enzymes such as α-amylases and antifungal agents that are effective in warding-off plant pathogens. They are prevalent as free-living entities in terrestrial locales, indoor locations, marine ecosystems and hypersaline habitats on account of their salt-, alkali- and desiccation-resistant behavior. In such natural locations, Nocardiopsis species mainly help in recycling organic compounds. Survival under these diverse conditions is mediated by the production of extracellular enzymes, antibiotics, surfactants, and the accumulation of compatible solutes. The accommodative genomic features of Nocardiopsis species support their existence under the diverse conditions where they prevail.
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Affiliation(s)
- Tahsin Bennur
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune 411007, India
| | - Ameeta Ravi Kumar
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune 411007, India
| | - Smita Zinjarde
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune 411007, India.
| | - Vaishali Javdekar
- Department of Biotechnology, Abasaheb Garware College, Pune 411004, India.
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14
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Bennur T, Kumar AR, Zinjarde S, Javdekar V. Nocardiopsis species as potential sources of diverse and novel extracellular enzymes. Appl Microbiol Biotechnol 2014; 98:9173-85. [PMID: 25269602 DOI: 10.1007/s00253-014-6111-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 09/18/2014] [Accepted: 09/19/2014] [Indexed: 01/10/2023]
Abstract
Members of the genus Nocardiopsis are generally encountered in locations that are inherently extreme. They are present in frozen soils, desert sand, compost, saline or hypersaline habitats (marine systems, salterns and soils) and alkaline places (slag dumps, lake soils and sediments). In order to survive under these severe conditions, they produce novel and diverse enzymes that allow them to utilize the available nutrients and to thrive. The members of this genus are multifaceted and release an assortment of extracellular hydrolytic enzymes. They produce enzymes that are cold-adapted (α-amylases), thermotolerant (α-amylases and xylanases), thermoalkalotolerant (cellulases, β-1,3-glucanases), alkali-tolerant thermostable (inulinases), acid-stable (keratinase) and alkalophilic (serine proteases). Some of the enzymes derived from Nocardiopsis species act on insoluble polymers such as glucans (pachyman and curdlan), keratin (feathers and prion proteins) and polyhydroxyalkanoates. Extreme tolerance exhibited by proteases has been attributed to the presence of some amino acids (Asn and Pro) in loop structures, relocation of multiple salt bridges to outer regions of the protein or the presence of a distinct polyproline II helix. The range of novel enzymes is projected to increase in the forthcoming years, as new isolates are being continually reported, and the development of processes involving such enzymes is envisaged in the future.
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Affiliation(s)
- Tahsin Bennur
- Institute of Bioinformatics and Biotechnology, University of Pune, Pune, 411007, India
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15
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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: 10] [Impact Index Per Article: 0.9] [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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16
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Additional Carbohydrate-Binding Modules Enhance the Insoluble Substrate-Hydrolytic Activity of β-1,3-Glucanase from AlkaliphilicNocardiopsissp. F96. Biosci Biotechnol Biochem 2014; 73:1078-82. [DOI: 10.1271/bbb.80846] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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17
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Pesentseva MS, Kovalchuk SN, Anastyuk SD, Kusaykin MI, Sova VV, Rasskazov VA, Zvyagintseva TN. Endo-(1→3)-β-d-glucanase GI from marine mollusk Littorina sitkana: Amino acid sequence and ESIMS/MS-estimated features of transglycosylation and hydrolysis reactions in comparison to analogous enzyme LIV from Pseudocardium sachalinensis. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.molcatb.2011.11.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Mo X, Ma J, Huang H, Wang B, Song Y, Zhang S, Zhang C, Ju J. Δ11,12 Double Bond Formation in Tirandamycin Biosynthesis is Atypically Catalyzed by TrdE, a Glycoside Hydrolase Family Enzyme. J Am Chem Soc 2012; 134:2844-7. [PMID: 22280373 DOI: 10.1021/ja206713a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xuhua Mo
- CAS Key Laboratory of Marine
Bio-resources Sustainable Utilization, Guangdong Key Laboratory of
Marine Materia Medica, RNAM Center for Marine Microbiology, South
China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- Graduate University of the Chinese Academy of Sciences, 19 Yuquan Road,
Beijing 110039, China
| | - Junying Ma
- CAS Key Laboratory of Marine
Bio-resources Sustainable Utilization, Guangdong Key Laboratory of
Marine Materia Medica, RNAM Center for Marine Microbiology, South
China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Hongbo Huang
- CAS Key Laboratory of Marine
Bio-resources Sustainable Utilization, Guangdong Key Laboratory of
Marine Materia Medica, RNAM Center for Marine Microbiology, South
China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Bo Wang
- CAS Key Laboratory of Marine
Bio-resources Sustainable Utilization, Guangdong Key Laboratory of
Marine Materia Medica, RNAM Center for Marine Microbiology, South
China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Yongxiang Song
- CAS Key Laboratory of Marine
Bio-resources Sustainable Utilization, Guangdong Key Laboratory of
Marine Materia Medica, RNAM Center for Marine Microbiology, South
China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Si Zhang
- CAS Key Laboratory of Marine
Bio-resources Sustainable Utilization, Guangdong Key Laboratory of
Marine Materia Medica, RNAM Center for Marine Microbiology, South
China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Changsheng Zhang
- CAS Key Laboratory of Marine
Bio-resources Sustainable Utilization, Guangdong Key Laboratory of
Marine Materia Medica, RNAM Center for Marine Microbiology, South
China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Jianhua Ju
- CAS Key Laboratory of Marine
Bio-resources Sustainable Utilization, Guangdong Key Laboratory of
Marine Materia Medica, RNAM Center for Marine Microbiology, South
China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
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19
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Nocardiopsis yanglingensis sp. nov., a thermophilic strain isolated from a compost of button mushrooms. Antonie van Leeuwenhoek 2011; 100:415-9. [DOI: 10.1007/s10482-011-9597-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Accepted: 05/27/2011] [Indexed: 10/18/2022]
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20
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Kotake T, Hirata N, Degi Y, Ishiguro M, Kitazawa K, Takata R, Ichinose H, Kaneko S, Igarashi K, Samejima M, Tsumuraya Y. Endo-beta-1,3-galactanase from winter mushroom Flammulina velutipes. J Biol Chem 2011; 286:27848-54. [PMID: 21653698 DOI: 10.1074/jbc.m111.251736] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Arabinogalactan proteins are proteoglycans found on the cell surface and in the cell walls of higher plants. The carbohydrate moieties of most arabinogalactan proteins are composed of β-1,3-galactan main chains and β-1,6-galactan side chains, to which other auxiliary sugars are attached. For the present study, an endo-β-1,3-galactanase, designated FvEn3GAL, was first purified and cloned from winter mushroom Flammulina velutipes. The enzyme specifically hydrolyzed β-1,3-galactan, but did not act on β-1,3-glucan, β-1,3:1,4-glucan, xyloglucan, and agarose. It released various β-1,3-galactooligosaccharides together with Gal from β-1,3-galactohexaose in the early phase of the reaction, demonstrating that it acts on β-1,3-galactan in an endo-fashion. Phylogenetic analysis revealed that FvEn3GAL is member of a novel subgroup distinct from known glycoside hydrolases such as endo-β-1,3-glucanase and endo-β-1,3:1,4-glucanase in glycoside hydrolase family 16. Point mutations replacing the putative catalytic Glu residues conserved for enzymes in this family with Asp abolished activity. These results indicate that FvEn3GAL is a highly specific glycoside hydrolase 16 endo-β-1,3-galactanase.
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Affiliation(s)
- Toshihisa Kotake
- Division of Life Science, Graduate School of Science and Engineering, Faculty of Science, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama 338-8570, Japan.
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21
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Song JM, Nam K, Sun YU, Kang MH, Kim CG, Kwon ST, Lee J, Lee YH. Molecular and biochemical characterizations of a novel arthropod endo-β-1,3-glucanase from the Antarctic springtail, Cryptopygus antarcticus, horizontally acquired from bacteria. Comp Biochem Physiol B Biochem Mol Biol 2010; 155:403-12. [DOI: 10.1016/j.cbpb.2010.01.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Revised: 01/06/2010] [Accepted: 01/07/2010] [Indexed: 10/20/2022]
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22
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Cloning, characterization, and antifungal activity of an endo-1,3-β-d-glucanase from Streptomyces sp. S27. Appl Microbiol Biotechnol 2009; 85:1483-90. [DOI: 10.1007/s00253-009-2187-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2009] [Revised: 07/17/2009] [Accepted: 08/05/2009] [Indexed: 10/20/2022]
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23
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Mertz B, Gu X, Reilly PJ. Analysis of functional divergence within two structurally related glycoside hydrolase families. Biopolymers 2009; 91:478-95. [DOI: 10.1002/bip.21154] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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24
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Ilari A, Fiorillo A, Angelaccio S, Florio R, Chiaraluce R, van der Oost J, Consalvi V. Crystal structure of a family 16 endoglucanase from the hyperthermophile Pyrococcus furiosus--structural basis of substrate recognition. FEBS J 2008; 276:1048-58. [PMID: 19154353 DOI: 10.1111/j.1742-4658.2008.06848.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bacterial and archaeal endo-beta-1,3-glucanases that belong to glycoside hydrolase family 16 share a beta-jelly-roll fold, but differ significantly in sequence and in substrate specificity. The crystal structure of the laminarinase (EC 3.2.1.39) from the hyperthermophilic archaeon Pyrococcus furiosus (pfLamA) has been determined at 2.1 A resolution by molecular replacement. The pfLamA structure reveals a kink of six residues (72-77) at the entrance of the catalytic cleft. This peptide is absent in the endoglucanases from alkaliphilic Nocardiopsis sp. strain F96 and Bacillus macerans, two proteins displaying an overall fold similar to that of pfLamA, but with different substrate specificity. A deletion mutant of pfLamA, lacking residues 72-75, hydrolyses the mixed-linkage beta-1,3-1,4-glucan lichenan 10 times more efficiently than the wild-type protein, indicating the importance of the kink in substrate preference.
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Affiliation(s)
- Andrea Ilari
- CNR Institute of Molecular Biology and Pathology, Italy.
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25
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Fibriansah G, Masuda S, Koizumi N, Nakamura S, Kumasaka T. The 1.3 Å crystal structure of a novel endo-β-1,3-glucanase of glycoside hydrolase family 16 from alkaliphilic Nocardiopsis sp. strain F96. Proteins 2007; 69:683-90. [PMID: 17879342 DOI: 10.1002/prot.21589] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Guntur Fibriansah
- Department of Life Science, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
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26
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Ferrer M, Golyshina O, Beloqui A, Golyshin PN. Mining enzymes from extreme environments. Curr Opin Microbiol 2007; 10:207-14. [PMID: 17548239 DOI: 10.1016/j.mib.2007.05.004] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2007] [Revised: 04/09/2007] [Accepted: 05/17/2007] [Indexed: 11/21/2022]
Abstract
Current advances in metagenomics have revolutionized the research in fields of microbial ecology and biotechnology, enabling not only a glimpse into the uncultured microbial population and mechanistic understanding of possible biogeochemical cycles and lifestyles of extreme organisms but also the high-throughput discovery of new enzymes for industrial bioconversions. Nowadays, the genetic and enzymatic differences across the gradients from 'neutral and pristine' to 'extreme and polluted' environments are well documented. Yet, extremophilic organisms are possibly the least well understood because our ability to study and understand their metabolic potential has been hampered by our inability to isolate pure cultures. There are at least two obstacles for reaping the fruit of the microbial diversity of extremophiles: first, in spite of the recent progress in development of new culturing techniques most extremophiles cannot be cultured using traditional culturing technologies; and second, the problem of the very low biomass densities often occurs under the conditions hostile for life, which often do not yield enough DNA and reduces the effectiveness of cloning.
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Affiliation(s)
- Manuel Ferrer
- Division of Applied Biocatalysis, Institute of Catalysis, CSIC, Cantoblanco, 28049 Madrid, Spain.
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