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Espersen R, Huang Y, Falco FC, Hägglund P, Gernaey KV, Lange L, Svensson B. Exceptionally rich keratinolytic enzyme profile found in the rare actinomycetes Amycolatopsis keratiniphila D2 T. Appl Microbiol Biotechnol 2021; 105:8129-8138. [PMID: 34605969 DOI: 10.1007/s00253-021-11579-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 09/08/2021] [Accepted: 09/10/2021] [Indexed: 11/25/2022]
Abstract
The non-spore forming Gram-positive actinomycetes Amycolatopsis keratiniphila subsp. keratiniphila D2T (DSM 44,409) has a high potential for keratin valorization as demonstrated by a novel biotechnological microbial conversion process consisting of a bacterial growth phase and a keratinolytic phase, respectively. Compared to the most gifted keratinolytic Bacillus species, a very large number of 621 putative proteases are encoded by the genome of Amycolatopsis keratiniphila subsp. keratiniphila D2T, as predicted by using Peptide Pattern Recognition (PPR) analysis. Proteome analysis by using LC-MS/MS on aliquots of the supernatant of A. keratiniphila subsp. keratiniphila D2T culture on slaughterhouse pig bristle meal, removed at 24, 48, 96 and 120 h of growth, identified 43 proteases. This was supplemented by proteome analysis of specific fractions after enrichment of the supernatant by anion exchange chromatography leading to identification of 50 proteases. Overall 57 different proteases were identified corresponding to 30% of the 186 proteins identified from the culture supernatant and distributed as 17 metalloproteases from 11 families, including an M36 protease, 38 serine proteases from 4 families, and 13 proteolytic enzymes from other families. Notably, M36 keratinolytic proteases are prominent in fungi, but seem not to have been discovered in bacteria previously. Two S01 family peptidases, named T- and C-like proteases, prominent in the culture supernatant, were purified and shown to possess a high azo-keratin/azo-casein hydrolytic activity ratio. The C-like protease revealed excellent thermostability, giving promise for successful applications in biorefinery processes. Notably, the bacterium seems not to secrete enzymes for cleavage of disulfides in the keratinous substrates. KEY POINTS: • A. keratiniphila subsp. keratiniphila D2T is predicted to encode 621 proteases. • This actinomycete efficiently converts bristle meal to a protein hydrolysate. • Proteome analysis identified 57 proteases in its secretome.
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Affiliation(s)
- Roall Espersen
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 224, DK 2800 Kgs., Lyngby, Denmark
- Center for Vaccine Research, Statens Serum Institut, Artillerivej 5 Building 81, DK 2300, Copenhagen S, Denmark
| | - Yuhong Huang
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads Building 227, DK 2800 Kgs., Lyngby, Denmark
- Beijing Key Laboratory of Ionic Liquids Clean Process, Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, 100190, Beijing, People's Republic of China
| | - Francesco C Falco
- Process and Systems Engineering Center, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads Building 228 A, DK 2800 Kgs., Lyngby, Denmark
| | - Per Hägglund
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 224, DK 2800 Kgs., Lyngby, Denmark
- Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3B, DK 2200, Copenhagen N, Denmark
| | - Krist V Gernaey
- Process and Systems Engineering Center, Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads Building 228 A, DK 2800 Kgs., Lyngby, Denmark
| | - Lene Lange
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, Søltofts Plads Building 227, DK 2800 Kgs., Lyngby, Denmark
- Bioeconomy, Research & Advisory, Karensgade 5, DK 2500, Valby, Denmark
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads Building 224, DK 2800 Kgs., Lyngby, Denmark.
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Ran T, Li W, Sun B, Xu M, Qiu S, Xu DQ, He J, Wang W. Crystal structure of mature myroilysin and implication for its activation mechanism. Int J Biol Macromol 2020; 156:1556-1564. [DOI: 10.1016/j.ijbiomac.2019.11.205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 11/23/2019] [Accepted: 11/26/2019] [Indexed: 10/25/2022]
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Huang Y, Łężyk M, Herbst FA, Busk PK, Lange L. Novel keratinolytic enzymes, discovered from a talented and efficient bacterial keratin degrader. Sci Rep 2020; 10:10033. [PMID: 32572051 PMCID: PMC7308268 DOI: 10.1038/s41598-020-66792-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 05/21/2020] [Indexed: 11/30/2022] Open
Abstract
Huge quantities of keratinaceous waste are a substantial and almost totally unexploited protein resource which could be upgraded for use as high value-added products by efficient keratinolytic enzymes. In this study, we found that Bacillus sp. 8A6 can efficiently degrade chicken feather after 24 h growth. According to phylogenetic analysis, the strain (formerly identified as Bacillus pumilus 8A6) belongs to the B. pumilus species clade but it is more closely related to B. safensis. Hotpep predicted 233 putative proteases from Bacillus sp. 8A6 genome. Proteomic analysis of culture broths from Bacillus sp. 8A6 cultured on chicken feathers or on a mixture of bristles and hooves showed high abundance of proteins with functions related to peptidase activity. Five proteases (one from family M12, one from family S01A, two from family S08A and one from family T3) and four oligopeptide and dipeptide binding proteins were highly expressed when Bacillus sp. 8A6 was grown in keratin media compared to LB medium. This study is the first to report that bacterial proteases in families M12, S01A and T3 are involved in keratin degradation together with proteases from family S08.
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Affiliation(s)
- Yuhong Huang
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 224, Søltofts Plads, 2800, Kongens Lyngby, Denmark
- Beijing Key Laboratory of Ionic Liquids Clean Process, Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Mateusz Łężyk
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 224, Søltofts Plads, 2800, Kongens Lyngby, Denmark
- Water Supply and Bioeconomy Division, Faculty of Environmental Engineering and Energy, Poznan University of Technology, Berdychowo 4, 60-965, Poznan, Poland
| | - Florian-Alexander Herbst
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg East, Denmark
| | - Peter Kamp Busk
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 224, Søltofts Plads, 2800, Kongens Lyngby, Denmark
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000, Roskilde, Denmark
| | - Lene Lange
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Building 224, Søltofts Plads, 2800, Kongens Lyngby, Denmark.
- Bioeconomy, Research & Advisory, Karensgade 5, DK-2500, Valby, Denmark.
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Morlighem JÉRL, Radis-Baptista G. The Place for Enzymes and Biologically Active Peptides from Marine Organisms for Application in Industrial and Pharmaceutical Biotechnology. Curr Protein Pept Sci 2019; 20:334-355. [PMID: 30255754 DOI: 10.2174/1389203719666180926121722] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 09/10/2018] [Accepted: 09/15/2018] [Indexed: 01/07/2023]
Abstract
Since the beginning of written history, diverse texts have reported the use of enzymatic preparations in food processing and have described the medicinal properties of crude and fractionated venoms to treat various diseases and injuries. With the biochemical characterization of enzymes from distinct sources and bioactive polypeptides from animal venoms, the last sixty years have testified the advent of industrial enzymology and protein therapeutics, which are currently applicable in a wide variety of industrial processes, household products, and pharmaceuticals. Bioprospecting of novel biocatalysts and bioactive peptides is propelled by their unsurpassed properties that are applicable for current and future green industrial processes, biotechnology, and biomedicine. The demand for both novel enzymes with desired characteristics and novel peptides that lead to drug development, has experienced a steady increase in response to the expanding global market for industrial enzymes and peptidebased drugs. Moreover, although largely unexplored, oceans and marine realms, with their unique ecosystems inhabited by a large variety of species, including a considerable number of venomous animals, are recognized as untapped reservoirs of molecules and macromolecules (enzymes and bioactive venom-derived peptides) that can potentially be converted into highly valuable biopharmaceutical products. In this review, we have focused on enzymes and animal venom (poly)peptides that are presently in biotechnological use, and considering the state of prospection of marine resources, on the discovery of useful industrial biocatalysts and drug leads with novel structures exhibiting selectivity and improved performance.
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Affiliation(s)
- Jean-Étienne R L Morlighem
- Institute for Marine Sciences, Federal University of Ceara, Av da Abolicao 3207. Fortaleza/CE. 60165081, Brazil
| | - Gandhi Radis-Baptista
- Institute for Marine Sciences, Federal University of Ceara, Av da Abolicao 3207. Fortaleza/CE. 60165081, Brazil
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Dumorné K, Severe R. Marine enzymes and their industrial and biotechnological applications. MINERVA BIOTECNOL 2018. [DOI: 10.23736/s1120-4826.18.02442-4] [Citation(s) in RCA: 2] [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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Preparation and functional evaluation of collagen oligopeptide-rich hydrolysate from fish skin with the serine collagenolytic protease from Pseudoalteromonas sp. SM9913. Sci Rep 2017; 7:15716. [PMID: 29146927 PMCID: PMC5691207 DOI: 10.1038/s41598-017-15971-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 11/06/2017] [Indexed: 11/09/2022] Open
Abstract
Although several serine collagenolytic proteases from bacteria were reported, none has been used to prepare bioactive collagen peptides. MCP-01 is the most abundant extracellular protease of deep-sea Pseudoalteromonas sp. SM9913 and is a serine collagenolytic protease with high efficiency on fish collagen hydrolysis. Here, we set up a pilot scale process to ferment SM9913 for extracellular protease production. With SM9913 extracellular protease as a tool, a process to prepare collagen oligopeptide-rich hydrolysate from codfish skin was set up, which was further scaled up to pilot (100 L) and plant (2000 L) levels with yields >66%. The hydrolysates from laboratory-, pilot- and plant-scales had quite similar quality, containing ~95% peptides with molecular weights lower than 3000 Da and approximately 60% lower than 1000 Da, in which collagen oilgopeptides account for approximately 95%. Bioactivity analyses showed that the hydrolysate had moisture-retention ability, antioxidant activity, and promoting effect on cell viability of human dermal fibroblasts. Safety evaluation showed that the hydrolysate was nontoxic and nonirritating to skin. Therefore, SM9913 extracellular protease is a good enzyme to prepare bioactive oligopeptides from fish skin. The results also suggest that the collagen oligopeptides-rich hydrolysate may have potentials in biomedical, functional food, pharmaceutical and cosmetic industries.
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Borchert E, Knobloch S, Dwyer E, Flynn S, Jackson SA, Jóhannsson R, Marteinsson VT, O'Gara F, Dobson ADW. Biotechnological Potential of Cold Adapted Pseudoalteromonas spp. Isolated from 'Deep Sea' Sponges. Mar Drugs 2017. [PMID: 28629190 PMCID: PMC5484134 DOI: 10.3390/md15060184] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The marine genus Pseudoalteromonas is known for its versatile biotechnological potential with respect to the production of antimicrobials and enzymes of industrial interest. We have sequenced the genomes of three Pseudoalteromonas sp. strains isolated from different deep sea sponges on the Illumina MiSeq platform. The isolates have been screened for various industrially important enzymes and comparative genomics has been applied to investigate potential relationships between the isolates and their host organisms, while comparing them to free-living Pseudoalteromonas spp. from shallow and deep sea environments. The genomes of the sponge associated Pseudoalteromonas strains contained much lower levels of potential eukaryotic-like proteins which are known to be enriched in symbiotic sponge associated microorganisms, than might be expected for true sponge symbionts. While all the Pseudoalteromonas shared a large distinct subset of genes, nonetheless the number of unique and accessory genes is quite large and defines the pan-genome as open. Enzymatic screens indicate that a vast array of enzyme activities is expressed by the isolates, including β-galactosidase, β-glucosidase, and protease activities. A β-glucosidase gene from one of the Pseudoalteromonas isolates, strain EB27 was heterologously expressed in Escherichia coli and, following biochemical characterization, the recombinant enzyme was found to be cold-adapted, thermolabile, halotolerant, and alkaline active.
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Affiliation(s)
- Erik Borchert
- School of Microbiology, University College Cork, National University of Ireland, Cork T12 YN60, Ireland.
| | - Stephen Knobloch
- Department of Research and Innovation, Matís ohf., Reykjavik 113, Iceland.
| | - Emilie Dwyer
- School of Microbiology, University College Cork, National University of Ireland, Cork T12 YN60, Ireland.
| | - Sinéad Flynn
- School of Microbiology, University College Cork, National University of Ireland, Cork T12 YN60, Ireland.
| | - Stephen A Jackson
- School of Microbiology, University College Cork, National University of Ireland, Cork T12 YN60, Ireland.
| | - Ragnar Jóhannsson
- Department of Research and Innovation, Matís ohf., Reykjavik 113, Iceland.
| | | | - Fergal O'Gara
- School of Microbiology, University College Cork, National University of Ireland, Cork T12 YN60, Ireland.
- Biomerit Research Centre, University College Cork, National University of Ireland, Cork T12 YN60, Ireland.
- School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth 6102, WA, Australia.
| | - Alan D W Dobson
- School of Microbiology, University College Cork, National University of Ireland, Cork T12 YN60, Ireland.
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Parte S, Sirisha VL, D'Souza JS. Biotechnological Applications of Marine Enzymes From Algae, Bacteria, Fungi, and Sponges. ADVANCES IN FOOD AND NUTRITION RESEARCH 2016; 80:75-106. [PMID: 28215329 DOI: 10.1016/bs.afnr.2016.10.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Diversity is the hallmark of all life forms that inhabit the soil, air, water, and land. All these habitats pose their unique inherent challenges so as to breed the "fittest" creatures. Similarly, the biodiversity from the marine ecosystem has evolved unique properties due to challenging environment. These challenges include permafrost regions to hydrothermal vents, oceanic trenches to abyssal plains, fluctuating saline conditions, pH, temperature, light, atmospheric pressure, and the availability of nutrients. Oceans occupy 75% of the earth's surface and harbor most ancient and diverse forms of organisms (algae, bacteria, fungi, sponges, etc.), serving as an excellent source of natural bioactive molecules, novel therapeutic compounds, and enzymes. In this chapter, we introduce enzyme technology, its current state of the art, unique enzyme properties, and the biocatalytic potential of marine algal, bacterial, fungal, and sponge enzymes that have indeed boosted the Marine Biotechnology Industry. Researchers began exploring marine enzymes, and today they are preferred over the chemical catalysts for biotechnological applications and functions, encompassing various sectors, namely, domestic, industrial, commercial, and healthcare. Next, we summarize the plausible pros and cons: the challenges encountered in the process of discovery of the potent compounds and bioactive metabolites such as biocatalysts/enzymes of biomedical, therapeutic, biotechnological, and industrial significance. The field of Marine Enzyme Technology has recently assumed importance, and if it receives further boost, it could successfully substitute other chemical sources of enzymes useful for industrial and commercial purposes and may prove as a beneficial and ecofriendly option. With appropriate directions and encouragement, marine enzyme technology can sustain the rising demand for enzyme production while maintaining the ecological balance, provided any undesired exploitation of the marine ecosystem is avoided.
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Affiliation(s)
- S Parte
- UM-DAE Centre for Excellence in Basic Sciences, Mumbai, India
| | - V L Sirisha
- UM-DAE Centre for Excellence in Basic Sciences, Mumbai, India
| | - J S D'Souza
- UM-DAE Centre for Excellence in Basic Sciences, Mumbai, India.
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Structure-Based Design and Synthesis of a New Phenylboronic-Modified Affinity Medium for Metalloprotease Purification. Mar Drugs 2016; 15:md15010005. [PMID: 28036010 PMCID: PMC5295225 DOI: 10.3390/md15010005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 12/19/2016] [Accepted: 12/21/2016] [Indexed: 12/16/2022] Open
Abstract
Metalloproteases are emerging as useful agents in the treatment of many diseases including arthritis, cancer, cardiovascular diseases, and fibrosis. Studies that could shed light on the metalloprotease pharmaceutical applications require the pure enzyme. Here, we reported the structure-based design and synthesis of the affinity medium for the efficient purification of metalloprotease using the 4-aminophenylboronic acid (4-APBA) as affinity ligand, which was coupled with Sepharose 6B via cyanuric chloride as spacer. The molecular docking analysis showed that the boron atom was interacting with the hydroxyl group of Ser176 residue, whereas the hydroxyl group of the boronic moiety is oriented toward Leu175 and His177 residues. In addition to the covalent bond between the boron atom and hydroxyl group of Ser176, the spacer between boronic acid derivatives and medium beads contributes to the formation of an enzyme-medium complex. With this synthesized medium, we developed and optimized a one-step purification procedure and applied it for the affinity purification of metalloproteases from three commercial enzyme products. The native metalloproteases were purified to high homogeneity with more than 95% purity. The novel purification method developed in this work provides new opportunities for scientific, industrial and pharmaceutical projects.
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Li S, Wang L, Yang J, Bao J, Liu J, Lin S, Hao J, Sun M. Affinity purification of metalloprotease from marine bacterium using immobilized metal affinity chromatography. J Sep Sci 2016; 39:2050-6. [DOI: 10.1002/jssc.201600104] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/06/2016] [Accepted: 03/21/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Shangyong Li
- Yellow Sea Fisheries Research Institute; Chinese Academy of Fishery Sciences; Qingdao China
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources; Qingdao China
- Ministry of Agriculture, Qingdao Key Laboratory of Marine Enzyme Engineering; Qingdao China
| | - Linna Wang
- Yellow Sea Fisheries Research Institute; Chinese Academy of Fishery Sciences; Qingdao China
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources; Qingdao China
- Ministry of Agriculture, Qingdao Key Laboratory of Marine Enzyme Engineering; Qingdao China
| | - Juan Yang
- Yellow Sea Fisheries Research Institute; Chinese Academy of Fishery Sciences; Qingdao China
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources; Qingdao China
- Ministry of Agriculture, Qingdao Key Laboratory of Marine Enzyme Engineering; Qingdao China
| | - Jing Bao
- Yellow Sea Fisheries Research Institute; Chinese Academy of Fishery Sciences; Qingdao China
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources; Qingdao China
- Ministry of Agriculture, Qingdao Key Laboratory of Marine Enzyme Engineering; Qingdao China
| | - Junzhong Liu
- Yellow Sea Fisheries Research Institute; Chinese Academy of Fishery Sciences; Qingdao China
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources; Qingdao China
- Ministry of Agriculture, Qingdao Key Laboratory of Marine Enzyme Engineering; Qingdao China
| | - Shengxiang Lin
- Laboratory of Oncology and Molecular Endocrinology; CHUL Research Center (CHUQ) and Laval University; Quebec Canada
| | - Jianhua Hao
- Yellow Sea Fisheries Research Institute; Chinese Academy of Fishery Sciences; Qingdao China
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources; Qingdao China
- Ministry of Agriculture, Qingdao Key Laboratory of Marine Enzyme Engineering; Qingdao China
| | - Mi Sun
- Yellow Sea Fisheries Research Institute; Chinese Academy of Fishery Sciences; Qingdao China
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources; Qingdao China
- Ministry of Agriculture, Qingdao Key Laboratory of Marine Enzyme Engineering; Qingdao China
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