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Akram F, Ul Haq I, Mir AS. Gene cloning, IPTG-independent auto-induction and characterization of a novel hyperstable S9 prolyl oligopeptidase having lipolytic activity from Thermotoga naphthophila RKU-10 T with applications. Int J Biol Macromol 2024; 279:135107. [PMID: 39197610 DOI: 10.1016/j.ijbiomac.2024.135107] [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: 07/07/2024] [Revised: 08/25/2024] [Accepted: 08/25/2024] [Indexed: 09/01/2024]
Abstract
A hyperstable lipase from Thermotoga naphthophila (TnLip) was cloned and overexpressed as a soluble and active monomeric protein in an effectual mesophilic host system. Sequence study revealed that TnLip is a peptidase S9 prolyl oligopeptidase domain (acetyl esterase/lipase-like protein), belongs to alpha/beta (α/β)-hydrolase superfamily containing a well-conserved α/β-hydrolase fold and penta-peptide (GLSAG) motif. Various cultivation and induction strategies were applied to improve the heterologous expression and bacterial biomass, but TnLip intracellular activity was enhanced by 14.25- fold with IPTG-independent auto-induction approach after 16 h (26 °C, 150 rev min-1) incubation. Purified TnLip (35 kDa) showed peak activity at 85 °C in McIlvaine buffer (pH 7.0-8.0), and has great stability over a broad range of pH (5.0-10.0), and temperature (40-85 °C) for 8 h. TnLip exhibited prodigious resistance toward various commercial detergents, chemical additives, and salt. TnLip activity was improved by 170.51 %, 130.67 %, 127.42 %, 126.54 %, 126.61 %, 120.32 %, and 116.31 % with 50 % (v/v) of methanol, ethanol, n-butanol, isopropanol, acetone, glycerol, and acetic acid, respectively. Moreover, with 3.0 M of NaCl, and 10 mM of Ca2+, Mn2+, and Mg2+ TnLip activity was augmented by 210 %, 185.64 %, 152.03 %, and 116.26 %, respectively. TnLip has an affinity with various substrates (p-nitrophenyl ester and natural oils) but maximal hydrolytic activity was perceived with p-nitrophenyl palmitate (pNPP, 3600 U mg-1) and olive oil (1182.05 U mg-1). The values of Km (0.576 mM), Vmax (4216 μmol mg-1 min-1), VmaxKm-1 (7319.44 min-1), kcat (1106.74 s-1), and kcatKm-1 (1921.42 mM-1 s-1) were calculated using pNPP substrate. Additionally, TnLip degraded animals' fats and removed oil stains within 3 h and 5 min, respectively. All these features make halo-alkali-thermophilic TnLip as an auspicious contender for laundry detergents (cleaning bio-additive), fat degradation, wastewater treatment and endorse eco-friendly stewardship along with various other biotechnological applications.
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Affiliation(s)
- Fatima Akram
- Dr. Ikram ul Haq Institute of Industrial Biotechnology, Government College University, Lahore, Pakistan; Department of Biology, Saint Louis University, St. Louis, MO, USA.
| | - Ikram Ul Haq
- Dr. Ikram ul Haq Institute of Industrial Biotechnology, Government College University, Lahore, Pakistan; Pakistan Academy of Sciences, Islamabad, Pakistan
| | - Azka Shahzad Mir
- Dr. Ikram ul Haq Institute of Industrial Biotechnology, Government College University, Lahore, Pakistan
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2
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Yuan SF, Yue XJ, Hu WF, Wang Y, Li YZ. Genome-wide analysis of lipolytic enzymes and characterization of a high-tolerant carboxylesterase from Sorangium cellulosum. Front Microbiol 2023; 14:1304233. [PMID: 38111649 PMCID: PMC10725956 DOI: 10.3389/fmicb.2023.1304233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 11/17/2023] [Indexed: 12/20/2023] Open
Abstract
Microorganisms are important sources of lipolytic enzymes with characteristics for wide promising usages in the specific industrial biotechnology. The cellulolytic myxobacterium Sorangium cellulosum is rich of lipolytic enzymes in the genome, but little has been investigated. Here, we discerned 406 potential lipolytic enzymes in 13 sequenced S. cellulosum genomes. These lipolytic enzymes belonged to 12 families, and most are novel with low identities (14-37%) to those reported. We characterized a new carboxylesterase, LipB, from the alkaline-adaptive So0157-2. This enzyme, belonging to family VIII, hydrolyzed glyceryl tributyrate and p-nitrophenyl esters with short chain fatty acids (≤C12), and exhibited the highest activity against p-nitrophenyl butyrate. It retained over 50% of the activities in a broad temperature range (from 20°C to 60°C), alkaline conditions (pH 8.0-9.5), and the enzymatic activity was stable with methanol, ethanol and isopropanol, and stimulated significantly in the presence of 5 mM Ni2+. LipB also exhibited β-lactamase activity on nitrocefin, but not ampicillin, cefotaxime and imipenem. The bioinformatic analysis and specific enzymatic characteristics indicate that S. cellulosum is a promising resource to explore lipolytic enzymes for industrial adaptations.
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Affiliation(s)
| | - Xin-Jing Yue
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | | | | | - Yue-Zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
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3
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Ariaeenejad S, Kavousi K, Han JL, Ding XZ, Hosseini Salekdeh G. Efficiency of an alkaline, thermostable, detergent compatible, and organic solvent tolerant lipase with hydrolytic potential in biotreatment of wastewater. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 866:161066. [PMID: 36565882 DOI: 10.1016/j.scitotenv.2022.161066] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Discharging the tannery wastewater into the environment is a serious challenge worldwide due to the release of severe recalcitrant pollutants such as oil compounds and organic materials. The biological treatment through enzymatic hydrolysis is a cheap and eco-friendly method for eliminating fatty substances from wastewater. In this context, lipases can be utilized for bio-treatment of wastewater in multifaceted industrial applications. To overcome the limitations in removing pollutants in the effluent, we aimed to identify a novel robust stable lipase (PersiLipase1) from metagenomic data of tannery wastewater for effective bio-degradation of the oily wastewater pollution. The lipase displayed remarkable thermostability and maintained over 81 % of its activity at 60 °C.After prolonged incubation for 35 days at 60°C, the PersiLipase1 still maintained 53.9 % of its activity. The enzyme also retained over 67 % of its activity in a wide range of pH (4.0 to 9.0). In addition, PersiLipase1 demonstrated considerable tolerance toward metal ions and organic solvents (e.g., retaining >70% activity after the addition of 100 mM of chemicals). Hydrolysis of olive oil and sheep fat by this enzyme showed 100 % efficiency. Furthermore, the PersiLipase1 proved to be efficient for biotreatment of oil and grease from tannery wastewater with the hydrolysis efficiency of 90.76 % ± 0.88. These results demonstrated that the metagenome-derived PersiLipase1 from tannery wastewater has a promising potential for the biodegradation and management of oily wastewater pollution.
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Affiliation(s)
- Shohreh Ariaeenejad
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran.
| | - Kaveh Kavousi
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Department of Bioinformatics, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Jian-Lin Han
- Livestock Genetics Program, International Livestock Research Institute (ILRI), 00100 Nairobi, Kenya; CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Xue-Zhi Ding
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou 730050, China
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Devkar HU, Thakur NL, Kaur P. Marine-derived antimicrobial molecules from the sponges and their associated bacteria. Can J Microbiol 2023; 69:1-16. [PMID: 36288610 DOI: 10.1139/cjm-2022-0147] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Antimicrobial resistance (AMR) is one of the leading global health issues that demand urgent attention. Very soon the world will have to bear the consequences of increased drug resistance if new anti-infectives are not pumped into the clinical pipeline in a short period. This presses on the need for novel chemical entities, and the marine environment is one such hotspot to look for. The Ocean harbours a variety of organisms, of which from this aspect, "Sponges (Phylum Porifera)" are of particular interest. To tackle the stresses faced due to their sessile and filter-feeding lifestyle, sponges produce various bioactive compounds, which can be tapped for human use. The sponges harbour several microorganisms of different types and in most cases; the microbial symbionts are the actual producers of the bioactive compounds. This review describes the alarming need for the development of new antimicrobials and how marine sponges can contribute to this. Selected antimicrobial compounds from the marine sponges and their associated bacteria have been described. Additionally, measures to tackle the supply problem have been covered, which is the primary obstacle in marine natural product drug discovery.
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Affiliation(s)
- Heena U Devkar
- CSIR- National Institute of Oceanography, Dona Paula 403004, Goa, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Narsinh L Thakur
- CSIR- National Institute of Oceanography, Dona Paula 403004, Goa, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Parvinder Kaur
- Foundation for Neglected Disease Research, Bangalore 561203, Karnataka, India
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Singh J, Mehta A. The main Aflatoxin B1 degrading enzyme in Pseudomonas putida is thermostable lipase. Heliyon 2022; 8:e10809. [PMID: 36217476 PMCID: PMC9547207 DOI: 10.1016/j.heliyon.2022.e10809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 07/11/2022] [Accepted: 09/23/2022] [Indexed: 12/03/2022] Open
Abstract
Aflatoxin B1 is a carcinogenic and mutagenic mycotoxin mainly produced by Aspergillus flavus and A. parasiticus, and prevalent in food and feed. Microbial degradation is a promising strategy which can be performed in mild and environmental friendly condition. This work is a step towards identifying the enzyme responsible for biodegradation of AFB1 by P. putida. Experiments were performed with P. putida lysate and compared with commercial lipase to see the degradation efficiency and the temperature stability. The cell free lysate of P. putida efficiently degraded AFB1 in a range of temperature from 20 to 90 °C. The lysate is thermostable and could retain its activity on pre-incubation up to 90 °C. Highest rate of degradation was observed at 70 °C. These observations show that the P. putida lysate is not only stable at higher temperatures but its enzymatic activity increases after incubation. Similarly, the commercial lipase degraded AFB1 efficiently. However, both, the P. putida lysate and lipase ceased degradation in presence of a lipase inhibitor, HgCl2. The Hill function accurately predicted enzyme activity at various times and temperatures. Like lipase, the lysate also hydrolyses the p-nitrophenyl palmitate to p-nitrophenol. Kinetic parameters such as Vmax, Km and n values are good measures to characterize the lysate response with respect to changing paranitro phenyl palmitate levels. The substrate specificity test of lipase showed linear correlation between the absorbance at 410 nm vs amount of product paranitro phenol. The value of Km, Vmax and n are 0.62 mM, 355.7 μmol min−1 and 1.29, respectively. The lipase gene presence in P. putida was confirmed using PCR technique. These observations indicate that the main enzyme responsible for AFB1 degradation by P. putida is lipase. Thus, lipase as a multifunctional biocatalyst provides a promising future for a variety of industries and may also help to ensure the food safety by degrading the mycotoxins.
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Jackson SA, Duan M, Zhang P, Ihua MW, Stengel DB, Duan D, Dobson ADW. Isolation, identification, and biochemical characterization of a novel bifunctional phosphomannomutase/phosphoglucomutase from the metagenome of the brown alga Laminaria digitata. Front Microbiol 2022; 13:1000634. [PMID: 36212884 PMCID: PMC9537760 DOI: 10.3389/fmicb.2022.1000634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022] Open
Abstract
Macroalgae host diverse epiphytic bacterial communities with potential symbiotic roles including important roles influencing morphogenesis and growth of the host, nutrient exchange, and protection of the host from pathogens. Macroalgal cell wall structures, exudates, and intra-cellular environments possess numerous complex and valuable carbohydrates such as cellulose, hemi-cellulose, mannans, alginates, fucoidans, and laminarin. Bacterial colonizers of macroalgae are important carbon cyclers, acquiring nutrition from living macroalgae and also from decaying macroalgae. Seaweed epiphytic communities are a rich source of diverse carbohydrate-active enzymes which may have useful applications in industrial bioprocessing. With this in mind, we constructed a large insert fosmid clone library from the metagenome of Laminaria digitata (Ochrophyta) in which decay was induced. Subsequent sequencing of a fosmid clone insert revealed the presence of a gene encoding a bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM) enzyme 10L6AlgC, closely related to a protein from the halophilic marine bacterium, Cobetia sp. 10L6AlgC was subsequently heterologously expressed in Escherichia coli and biochemically characterized. The enzyme was found to possess both PMM and PGM activity, which had temperature and pH optima of 45°C and 8.0, respectively; for both activities. The PMM activity had a K m of 2.229 mM and V max of 29.35 mM min-1 mg-1, while the PGM activity had a K m of 0.5314 mM and a V max of 644.7 mM min-1 mg-1. Overall characterization of the enzyme including the above parameters as well as the influence of various divalent cations on these activities revealed that 10L6AlgC has a unique biochemical profile when compared to previously characterized PMM/PGM bifunctional enzymes. Thus 10L6AlgC may find utility in enzyme-based production of biochemicals with different potential industrial applications, in which other bacterial PMM/PGMs have previously been used such as in the production of low-calorie sweeteners in the food industry.
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Affiliation(s)
- Stephen A. Jackson
- School of Microbiology, University College Cork, Cork, Ireland
- Environmental Research Institute, University College Cork, Cork, Ireland
| | - Maohang Duan
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Pengyan Zhang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Maureen W. Ihua
- School of Microbiology, University College Cork, Cork, Ireland
| | - Dagmar B. Stengel
- Botany and Plant Science, School of Natural Sciences, Ryan Institute for Environmental, Marine and Energy Research, University of Galway, Galway, Ireland
| | - Delin Duan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Alan D. W. Dobson
- School of Microbiology, University College Cork, Cork, Ireland
- Environmental Research Institute, University College Cork, Cork, Ireland
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Xu Y, Du X, Yu X, Jiang Q, Zheng K, Xu J, Wang P. Recent Advances in the Heterologous Expression of Biosynthetic Gene Clusters for Marine Natural Products. Mar Drugs 2022; 20:341. [PMID: 35736144 PMCID: PMC9225448 DOI: 10.3390/md20060341] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/11/2022] [Accepted: 05/20/2022] [Indexed: 12/29/2022] Open
Abstract
Marine natural products (MNPs) are an important source of biologically active metabolites, particularly for therapeutic agent development after terrestrial plants and nonmarine microorganisms. Sequencing technologies have revealed that the number of biosynthetic gene clusters (BGCs) in marine microorganisms and the marine environment is much higher than expected. Unfortunately, the majority of them are silent or only weakly expressed under traditional laboratory culture conditions. Furthermore, the large proportion of marine microorganisms are either uncultivable or cannot be genetically manipulated. Efficient heterologous expression systems can activate cryptic BGCs and increase target compound yield, allowing researchers to explore more unknown MNPs. When developing heterologous expression of MNPs, it is critical to consider heterologous host selection as well as genetic manipulations for BGCs. In this review, we summarize current progress on the heterologous expression of MNPs as a reference for future research.
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Affiliation(s)
- Yushan Xu
- Ocean College, Zhejiang University, Zhoushan 316021, China; (Y.X.); (X.D.); (X.Y.); (Q.J.); (K.Z.); (J.X.)
| | - Xinhua Du
- Ocean College, Zhejiang University, Zhoushan 316021, China; (Y.X.); (X.D.); (X.Y.); (Q.J.); (K.Z.); (J.X.)
| | - Xionghui Yu
- Ocean College, Zhejiang University, Zhoushan 316021, China; (Y.X.); (X.D.); (X.Y.); (Q.J.); (K.Z.); (J.X.)
| | - Qian Jiang
- Ocean College, Zhejiang University, Zhoushan 316021, China; (Y.X.); (X.D.); (X.Y.); (Q.J.); (K.Z.); (J.X.)
| | - Kaiwen Zheng
- Ocean College, Zhejiang University, Zhoushan 316021, China; (Y.X.); (X.D.); (X.Y.); (Q.J.); (K.Z.); (J.X.)
| | - Jinzhong Xu
- Ocean College, Zhejiang University, Zhoushan 316021, China; (Y.X.); (X.D.); (X.Y.); (Q.J.); (K.Z.); (J.X.)
| | - Pinmei Wang
- Ocean College, Zhejiang University, Zhoushan 316021, China; (Y.X.); (X.D.); (X.Y.); (Q.J.); (K.Z.); (J.X.)
- State Key Laboratory of Motor Vehicle Biofuel Technology, Zhejiang University, Zhoushan 316021, China
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Escuder-Rodríguez JJ, DeCastro ME, Saavedra-Bouza A, González-Siso MI, Becerra M. Bioprospecting for Thermozymes and Characterization of a Novel Lipolytic Thermozyme Belonging to the SGNH/GDSL Family of Hydrolases. Int J Mol Sci 2022; 23:5733. [PMID: 35628544 PMCID: PMC9145741 DOI: 10.3390/ijms23105733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/16/2022] [Accepted: 05/18/2022] [Indexed: 01/27/2023] Open
Abstract
Functional screenings were conducted on two metagenomic libraries from hot springs in order to find novel thermozymes with potential biotechnological applications. These included enzymes acting on plant cell walls such as endoglucanases and exoglucanases, β-glucosidases, xylanases, and β-xylosidases, and broad application enzymes such as proteases and lipolytic hydrolases. Of all the enzymes found by this bioprospection, we selected a novel lipolytic enzyme for further characterization. The protein was found to belong to the SGNH/GDSL family of hydrolases. It was purified and its biochemical parameters determined. We found that the enzyme was most active at 60 °C and pH 9 using pNP-laurate as substrate and was highly thermostable. It also showed preference for short-chained substrates and activation with temperature and with certain detergents such as Tween 80. Proteins of this family of hydrolases are relevant for their broad substrate specificity, that coupled with this protein's high temperature optima, broad pH range, and thermostability further highlights its biotechnological potential.
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Affiliation(s)
| | | | | | - María-Isabel González-Siso
- EXPRELA Group, Advanced Scientific Research Center (CICA), Department of Biology, Faculty of Sciences, Universidade da Coruña, 15071 A Coruña, Spain; (J.-J.E.-R.); (M.-E.D.); (A.S.-B.)
| | - Manuel Becerra
- EXPRELA Group, Advanced Scientific Research Center (CICA), Department of Biology, Faculty of Sciences, Universidade da Coruña, 15071 A Coruña, Spain; (J.-J.E.-R.); (M.-E.D.); (A.S.-B.)
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Müller H, Terholsen H, Godehard SP, Badenhorst CPS, Bornscheuer UT. Recent Insights and Future Perspectives on Promiscuous Hydrolases/Acyltransferases. ACS Catal 2021. [DOI: 10.1021/acscatal.1c04543] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Henrik Müller
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
- Competence Center for Biocatalysis, Institute of Chemistry and Biotechnology, Zurich University of Applied Sciences, 8820, Wädenswil, Switzerland
| | - Henrik Terholsen
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
| | - Simon P. Godehard
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
| | - Christoffel P. S. Badenhorst
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
| | - Uwe T. Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
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Park JE, Jeong GS, Lee HW, Kim H. Molecular Characterization of Novel Family IV and VIII Esterases from a Compost Metagenomic Library. Microorganisms 2021; 9:microorganisms9081614. [PMID: 34442693 PMCID: PMC8399190 DOI: 10.3390/microorganisms9081614] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 11/16/2022] Open
Abstract
Two novel esterase genes, est8L and est13L, were isolated and identified from a compost metagenomic library. The encoded Est8L and Est13L had molecular masses of 33,181 and 44,913 Da consisting of 314 and 411 amino acids, respectively, without signal peptides. Est8L showed the highest identity (32.9%) to a hyper-thermophilic carboxylesterase AFEST from Archaeoglobus fulgidus compared to other esterases reported and was classified to be a novel member of family IV esterases with conserved regions such as HGGG, DY, GXSXG, DPL, and GXIH. Est13L showed the highest identity (98.5%) to the family VIII esterase Est7K from the metagenome library. Est8L and Est13L had the highest activities for p-nitrophenyl butyrate (C4) and p-nitrophenyl caproate (C6), respectively, and Est13L showed a broad substrate specificity for p-nitrophenyl substrates. Est8L and Est13L effectively hydrolyzed glyceryl tributyrate. The optimum temperatures for activities of Est8L and Est13L were identical (40 °C), and the optimum pH values were 9.0 and 10.0, respectively. Est13L showed higher thermostability than Est8L. Sephacryl S-200 HR chromatography showed that the native form of Est8L was a dimer. Interestingly, Est13L was found to be a tetramer, contrary to other family VIII esterases reported. Est8L was inhibited by 30% isopropanol, methanol, and acetonitrile; however, Est13L was activated to 182.9% and 356.1%, respectively, by 30% isopropanol and methanol. Est8L showed enantioselectivity for the S-form, but Est13L showed no enantioselectivity. These results show that intracellular Est8L and/or Est13L are oligomeric in terms of native forms and can be used for pharmaceutical and industrial applications with organic solvents under alkaline conditions.
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Affiliation(s)
| | | | | | - Hoon Kim
- Correspondence: ; Tel.: +82-617503751
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11
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Ethanol as additive enhance the performance of immobilized lipase LipA from Pseudomonas aeruginosa on polypropylene support. ACTA ACUST UNITED AC 2021; 31:e00659. [PMID: 34367924 PMCID: PMC8326728 DOI: 10.1016/j.btre.2021.e00659] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/14/2021] [Indexed: 11/20/2022]
Abstract
Immobilization is practical to upgrade enzymes, increasing their performance and expanding their applications. The recombinant, solvent tolerant lipase LipA PSA01 from Pseudomonas aeruginosa was immobilized on polypropylene Accurel® MP1004 to improve its performance. We investigated the effect of ethanol as an additive during the immobilization process at three concentrations (20%, 25%, and 30%) on the operational behavior of the enzyme. The immobilization efficiency was higher than 92%, and the immobilized enzymes showed hyperactivation and thermal resistance depending on the concentration of ethanol. For example, at 70 °C, the free enzyme lost the activity, while the prepared one with ethanol 25% conserved a residual activity of up to 73.3% (∆ T15 50 = 27.1 °C). LipA immobilized had an optimal pH value lower than that of the free enzyme, and the organic solvent tolerance of the immobilized enzymes depended on the ethanol used. Hence, the immobilized enzyme with ethanol 25% showed hyperactivation to more solvents than the soluble enzyme. Remarkable stability towards methanol (up to 8 folds) was evidenced in all the immobilized preparations. The immobilized enzyme changed their chemo preference, and it hydrolyzed oils preferentially with short-chain than those with long-chain. LipA had a notable shelf-life after one year, keeping its activity up to 87%. Ethanol facilitated the access of the enzyme to the hydrophobic support and increased its activity and stability according to the amount of ethanol added.
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12
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Qiu J, Han R, Wang C. Microbial halophilic lipases: A review. J Basic Microbiol 2021; 61:594-602. [PMID: 34096085 DOI: 10.1002/jobm.202100107] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/23/2021] [Indexed: 11/08/2022]
Abstract
Microbial lipases are commercially significant due to their versatile catalytic function of hydrolysis triacylglycerol. Among these, lipases from extremophiles are optimal for industrial application. Halophilic microorganisms living in a high salinity environment, such as the ocean, salt lakes, salt wells, and so on, produce halophilic lipases. In recent decades, many remarkable achievements have been made related to the properties and application of halophilic lipases. This review offers information collected over the last decades on halophilic lipase sources as well as advances in production, factors influencing activity, stability under various conditions, structural characteristics, progress in industrial applications such as food flavor modification, biodiesel production, and waste treatment, to provide theoretical and methodological references for the research in this direction.
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Affiliation(s)
- Junjie Qiu
- College of Bioengineering, Sichuan University of Science and Engineering, Zigong, China
| | - Rui Han
- College of Bioengineering, Sichuan University of Science and Engineering, Zigong, China
| | - Chuan Wang
- College of Bioengineering, Sichuan University of Science and Engineering, Zigong, China
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13
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Zhu C, Chen Y, Isupov MN, Littlechild JA, Sun L, Liu X, Wang Q, Gong H, Dong P, Zhang N, Wu Y. Structural Insights into a Novel Esterase from the East Pacific Rise and Its Improved Thermostability by a Semirational Design. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:1079-1090. [PMID: 33445864 DOI: 10.1021/acs.jafc.0c06338] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Lipolytic enzymes are essential biocatalysts in food processing as well as pharmaceutical and pesticide industries, catalyzing the cleavage of ester bonds in a variety of acyl chain substrates. Here, we report the crystal structure of an esterase from the deep-sea hydrothermal vent of the East Pacific Rise (EprEst). The X-ray structure of EprEst in complex with the ligand, acetate, has been determined at 2.03 Å resolution. The structure reveals a unique spatial arrangement and orientation of the helix cap domain and α/β hydrolase domain, which form a substrate pocket with preference for short-chain acyl groups. Molecular docking analysis further demonstrated that the active site pocket could accommodate p-nitrophenyl (pNP) carboxyl ligands of varying lengths (≤6 C atoms), with pNP-butyrate ester predicted to have the highest binding affinity. Additionally, the semirational design was conducted to improve the thermostability of EprEst by enzyme engineering based on the established structure and multiple sequence alignment. A mutation, K114P, introduced in the hinge region of the esterase, which displayed increased thermostability and enzyme activity. Collectively, the structural and functional data obtained herein could be used as basis for further protein engineering to ultimately expand the scope of industrial applications of marine-derived lipolytic enzymes.
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Affiliation(s)
- Chunhua Zhu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
| | - Yayu Chen
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou 350117, China
| | - Michail N Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom
| | - Jennifer A Littlechild
- Henry Wellcome Building for Biocatalysis, Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, United Kingdom
| | - Lifang Sun
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou 350117, China
| | - Xiaodong Liu
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
- College of Life Science, Fujian Normal University, Fuzhou 350117, China
| | - Qianchao Wang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Gong
- Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China
| | - Panpan Dong
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou 350117, China
| | - Na Zhang
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou 350117, China
| | - Yunkun Wu
- Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou 350117, China
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Müller H, Godehard SP, Palm GJ, Berndt L, Badenhorst CPS, Becker A, Lammers M, Bornscheuer UT. Entdeckung und Design promiskuitiver Acyltransferase‐Aktivität in Carboxylesterasen der Familie VIII. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Henrik Müller
- Abt. Biotechnologie und Enzymkatalyse Institut für Biochemie Universität Greifswald 17487 Greifswald Deutschland
| | - Simon P. Godehard
- Abt. Biotechnologie und Enzymkatalyse Institut für Biochemie Universität Greifswald 17487 Greifswald Deutschland
| | - Gottfried J. Palm
- Abt. Synthetische und strukturelle Biochemie Institut für Biochemie Universität Greifswald 17487 Greifswald Deutschland
| | - Leona Berndt
- Abt. Synthetische und strukturelle Biochemie Institut für Biochemie Universität Greifswald 17487 Greifswald Deutschland
| | - Christoffel P. S. Badenhorst
- Abt. Biotechnologie und Enzymkatalyse Institut für Biochemie Universität Greifswald 17487 Greifswald Deutschland
| | - Ann‐Kristin Becker
- Institut für Bioinformatik Universitätsmedizin Greifswald 17487 Greifswald Deutschland
| | - Michael Lammers
- Abt. Synthetische und strukturelle Biochemie Institut für Biochemie Universität Greifswald 17487 Greifswald Deutschland
| | - Uwe T. Bornscheuer
- Abt. Biotechnologie und Enzymkatalyse Institut für Biochemie Universität Greifswald 17487 Greifswald Deutschland
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15
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Müller H, Godehard SP, Palm GJ, Berndt L, Badenhorst CPS, Becker A, Lammers M, Bornscheuer UT. Discovery and Design of Family VIII Carboxylesterases as Highly Efficient Acyltransferases. Angew Chem Int Ed Engl 2021; 60:2013-2017. [PMID: 33140887 PMCID: PMC7894173 DOI: 10.1002/anie.202014169] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Indexed: 12/21/2022]
Abstract
Promiscuous acyltransferase activity is the ability of certain hydrolases to preferentially catalyze acyl transfer over hydrolysis, even in bulk water. However, poor enantioselectivity, low transfer efficiency, significant product hydrolysis, and limited substrate scope represent considerable drawbacks for their application. By activity-based screening of several hydrolases, we identified the family VIII carboxylesterase, EstCE1, as an unprecedentedly efficient acyltransferase. EstCE1 catalyzes the irreversible amidation and carbamoylation of amines in water, which enabled the synthesis of the drug moclobemide from methyl 4-chlorobenzoate and 4-(2-aminoethyl)morpholine (ca. 20 % conversion). We solved the crystal structure of EstCE1 and detailed structure-function analysis revealed a three-amino acid motif important for promiscuous acyltransferase activity. Introducing this motif into an esterase without acetyltransferase activity transformed a "hydrolase" into an "acyltransferase".
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Affiliation(s)
- Henrik Müller
- Department of Biotechnology & Enzyme CatalysisInstitute of BiochemistryUniversity of Greifswald17487GreifswaldGermany
| | - Simon P. Godehard
- Department of Biotechnology & Enzyme CatalysisInstitute of BiochemistryUniversity of Greifswald17487GreifswaldGermany
| | - Gottfried J. Palm
- Department of Synthetic and Structural BiochemistryInstitute of Biochemistry, University of Greifswald17487GreifswaldGermany
| | - Leona Berndt
- Department of Synthetic and Structural BiochemistryInstitute of Biochemistry, University of Greifswald17487GreifswaldGermany
| | - Christoffel P. S. Badenhorst
- Department of Biotechnology & Enzyme CatalysisInstitute of BiochemistryUniversity of Greifswald17487GreifswaldGermany
| | - Ann‐Kristin Becker
- Institute of BioinformaticsUniversity Medicine Greifswald17487GreifswaldGermany
| | - Michael Lammers
- Department of Synthetic and Structural BiochemistryInstitute of Biochemistry, University of Greifswald17487GreifswaldGermany
| | - Uwe T. Bornscheuer
- Department of Biotechnology & Enzyme CatalysisInstitute of BiochemistryUniversity of Greifswald17487GreifswaldGermany
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16
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A Novel Carboxylesterase Derived from a Compost Metagenome Exhibiting High Stability and Activity towards High Salinity. Genes (Basel) 2021; 12:genes12010122. [PMID: 33478024 PMCID: PMC7835964 DOI: 10.3390/genes12010122] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/09/2021] [Accepted: 01/13/2021] [Indexed: 01/08/2023] Open
Abstract
Halotolerant lipolytic enzymes have gained growing interest, due to potential applications under harsh conditions, such as hypersalinity and presence of organic solvents. In this study, a lipolytic gene, est56, encoding 287 amino acids was identified by functional screening of a compost metagenome. Subsequently, the gene was heterologously expressed, and the recombinant protein (Est56) was purified and characterized. Est56 is a mesophilic (Topt 50 °C) and moderate alkaliphilic (pHopt 8) enzyme, showing high thermostability at 30 and 40 °C. Strikingly, Est56 is halotolerant as it exhibited high activity and stability in the presence of up to 4 M NaCl or KCl. Est56 also displayed enhanced stability against high temperatures (50 and 60 °C) and urea (2, 4, and 6 M) in the presence of NaCl. In addition, the recently reported halotolerant lipolytic enzymes were summarized. Phylogenetic analysis grouped these enzymes into 13 lipolytic protein families. The majority (45%) including Est56 belonged to family IV. To explore the haloadaptation of halotolerant enzymes, the amino acid composition between halotolerant and halophilic enzymes was statistically compared. The most distinctive feature of halophilic from non-halophilic enzymes are the higher content of acidic residues (Asp and Glu), and a lower content of lysine, aliphatic hydrophobic (Leu, Met and Ile) and polar (Asn) residues. The amino acid composition and 3-D structure analysis suggested that the high content of acidic residues (Asp and Glu, 12.2%) and low content of lysine residues (0.7%), as well as the excess of surface-exposed acidic residues might be responsible for the haloadaptation of Est56.
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17
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Anteneh YS, Yang Q, Brown MH, Franco CMM. Antimicrobial Activities of Marine Sponge-Associated Bacteria. Microorganisms 2021; 9:171. [PMID: 33466936 PMCID: PMC7830929 DOI: 10.3390/microorganisms9010171] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 01/11/2021] [Indexed: 11/17/2022] Open
Abstract
The misuse and overuse of antibiotics have led to the emergence of multidrug-resistant microorganisms, which decreases the chance of treating those infected with existing antibiotics. This resistance calls for the search of new antimicrobials from prolific producers of novel natural products including marine sponges. Many of the novel active compounds reported from sponges have originated from their microbial symbionts. Therefore, this study aims to screen for bioactive metabolites from bacteria isolated from sponges. Twelve sponge samples were collected from South Australian marine environments and grown on seven isolation media under four incubation conditions; a total of 1234 bacterial isolates were obtained. Of these, 169 bacteria were tested in media optimized for production of antimicrobial metabolites and screened against eleven human pathogens. Seventy bacteria were found to be active against at least one test bacterial or fungal pathogen, while 37% of the tested bacteria showed activity against Staphylococcus aureus including methicillin-resistant strains and antifungal activity was produced by 21% the isolates. A potential novel active compound was purified possessing inhibitory activity against S. aureus. Using 16S rRNA, the strain was identified as Streptomyces sp. Our study highlights that the marine sponges of South Australia are a rich source of abundant and diverse bacteria producing metabolites with antimicrobial activities against human pathogenic bacteria and fungi.
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Affiliation(s)
- Yitayal S. Anteneh
- College of Medicine and Public Health, Flinders University, Bedford Park, SA 5042, Australia;
- Department of Medical Microbiology, College of Medicine, Addis Ababa University, Addis Ababa 9086, Ethiopia
| | - Qi Yang
- Center for Marine Drugs, State Key Laboratory of Oncogene and Related Genes, Department of Pharmacy, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China;
- Centre for Marine Bioproducts Development, College of Medicine and Public Health, Flinders University, Bedford Park, SA 5042, Australia
| | - Melissa H. Brown
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia;
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18
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Alnadari F, Xue Y, Almakas A, Mohedein A, Samie A, Abdel-Shafi M, Abdin M. Large batch production of Galactooligosaccharides using β-glucosidase immobilized on chitosan-functionalized magnetic nanoparticle. J Food Biochem 2020; 45:e13589. [PMID: 33368567 DOI: 10.1111/jfbc.13589] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/27/2020] [Accepted: 11/30/2020] [Indexed: 12/20/2022]
Abstract
β-glucosidase (BglA) immobilization from Thermotoga maritima on magnetic nanoparticles (MNPs) functionalized with chitosan (Cs) were efficiently investigated to improve lactose conversion and galactooligosaccharides (GOS) production. We used a batch method in order to improve the conversion of lactose to GOS. The efficiency and yield of immobilization were 79% and immobilized BglA was effectively recycled via a magnetic separation procedure through a batch-wise GOS with no activity lessening. Furthermore, analyses were done through screening kinetics of enzyme activity, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), Fourier transform infrared spectroscopy (FT-IR), and transmission electron microscopy (TEM). Proposed methodology of immobilization shows a potential application as it is stable which was proved through many methods including pH, temperature, heat treatment, storage, and kinetics of the enzyme. GOS and residual enzyme activity showed to be 28.76 and 40.44%, respectively. However, free enzyme synthesis of GOS yield was just 24% after 12 hr. This study proposed applying magnet in the immobilization process of BglA on Cs-MNPs to produce GOS as new method for immobilizing enzyme in a biostable and cost-efficient way. PRACTICAL APPLICATIONS: This paper focus on immobilization of BglA from T. maritima onto MNPs functionalized with CS to investigate their further possibility improving lactose conversion and GOS production. Interestingly, a successful immobilization of Tm-BglA on the substrates were achieved in Cs-MNPs. The obtained results from enzyme activity, SDS-PAGE, FT-IR, and TEM showed that the high binding capacity of BglA to Cs-MNPs was successfully obtained. Furthermore, the binding efficiency calculation indicated that the immobilized BglA-Cs-MNPs conserved 40.44% of its native activity at the end of its 6th repeated use. In addition, magnetic separation technique was successfully employed for reuse of the immobilized BglA for repetitive batch-wise GOS without significant loss of activity.
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Affiliation(s)
- Fawze Alnadari
- Department of Food Science and Engineering, School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, P.R. China.,Department of Food Science and Engineering, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, P.R. China.,Department of Food Science and Technology, Faculty of Agriculture, Sana'a University, Sana'a, Yemen
| | - Yemin Xue
- Department of Food Science and Engineering, School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, P.R. China
| | - Aisha Almakas
- Department of Crops and Pastures, Faculty of Agriculture, Sana'a University, Sana'a, Yemen
| | - Amani Mohedein
- Department of Food Science and Technology, Faculty of Agriculture, Sana'a University, Sana'a, Yemen
| | - Abdel Samie
- Department of Food and Dairy Sciences and Technology, Faculty of Environmental Agricultural Sciences, Arish University, Arish City, Egypt
| | - Mohamed Abdel-Shafi
- Department of Food and Dairy Sciences and Technology, Faculty of Environmental Agricultural Sciences, Arish University, Arish City, Egypt
| | - Mohamed Abdin
- Department of Food Science and Engineering, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, P.R. China.,Agriculture Research Center, Food Technology Research Institute, Giza, Egypt
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19
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Martínez-Pérez RB, Rodríguez JA, Leyva Soto LA, Gortáres-Moroyoqui P, Diaz-Tenorio LM. Cannonball jellyfish digestion: an insight into the lipolytic enzymes of the digestive system. PeerJ 2020; 8:e9794. [PMID: 33194347 PMCID: PMC7485504 DOI: 10.7717/peerj.9794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 08/01/2020] [Indexed: 11/20/2022] Open
Abstract
The digestive system and metabolism of the cannonball jellyfish Stomolophus sp. 2 are not well-known. The digestion study was critical to explain its ecology and bloom success. Different enzymes are involved in food digestion, which hydrolyze carbohydrates, proteins, and lipids. This study detected lipolytic activity in enzymatic extracts from gastric pouches of Stomolophus sp. 2 collected in the summer of 2013 at Bahía de Kino, Sonora, México (28°47′47″N 111°57′25″W). Lipase/esterase activity showed optimal pH at 11.0 and 50–60 °C with a half-life (t1/2) of 33 min at 55 °C, whereas halotolerance of this activity was recorded from 0-4 M NaCl. Metal ions Ca2+ and Mn2+ did not affect the activity, but Mg2+ decreased it 14.2% ± 3.15, while chelating agents as ethylenediaminetetraacetic acid reduced the activity 8.55% ± 2.13. Inhibition of lipase/esterase activity with tetrahydrolipstatin and paraoxon-ethyl decreased the activity 18.2% ± 2.3, and 62.80% ± 0.74, respectively, whereas phenylmethanesulfonyl fluoride (a protease inhibitor) did not affect it. The enzyme displayed a higher specificity for short-chain triglycerides, but triolein, coconut oil, olive oil, and fish oil were hydrolyzed. For the first time, phospholipase activity from the gastric pouch of Stomolophus sp. 2 was detected using L-α-phosphatidylethanolamine from chicken egg yolk as a substrate. These results suggest that Stomolophus sp. 2 hydrolyze several kinds of lipids, and lipolytic enzymes are active at alkaline pH under different saline conditions, which may be essential to digest different preys.
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Affiliation(s)
- Raul B. Martínez-Pérez
- Departamento de Biotecnología y Ciencias Alimentarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, Mexico
- Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C., Zapopan, Jalisco, Mexico
| | - Jorge A. Rodríguez
- Biotecnología Industrial, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C., Zapopan, Jalisco, Mexico
| | - Luis Alonso Leyva Soto
- Departamento de Biotecnología y Ciencias Alimentarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, Mexico
- Dirección de Cátedras, Consejo Nacional de Ciencia y Tecnología, Ciudad de México, Mexico
| | - Pablo Gortáres-Moroyoqui
- Departamento de Biotecnología y Ciencias Alimentarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, Mexico
| | - Lourdes M. Diaz-Tenorio
- Departamento de Biotecnología y Ciencias Alimentarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, Mexico
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20
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Chandra P, Enespa, Singh R, Arora PK. Microbial lipases and their industrial applications: a comprehensive review. Microb Cell Fact 2020; 19:169. [PMID: 32847584 PMCID: PMC7449042 DOI: 10.1186/s12934-020-01428-8] [Citation(s) in RCA: 265] [Impact Index Per Article: 66.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/17/2020] [Indexed: 12/12/2022] Open
Abstract
Lipases are very versatile enzymes, and produced the attention of the several industrial processes. Lipase can be achieved from several sources, animal, vegetable, and microbiological. The uses of microbial lipase market is estimated to be USD 425.0 Million in 2018 and it is projected to reach USD 590.2 Million by 2023, growing at a CAGR of 6.8% from 2018. Microbial lipases (EC 3.1.1.3) catalyze the hydrolysis of long chain triglycerides. The microbial origins of lipase enzymes are logically dynamic and proficient also have an extensive range of industrial uses with the manufacturing of altered molecules. The unique lipase (triacylglycerol acyl hydrolase) enzymes catalyzed the hydrolysis, esterification and alcoholysis reactions. Immobilization has made the use of microbial lipases accomplish its best performance and hence suitable for several reactions and need to enhance aroma to the immobilization processes. Immobilized enzymes depend on the immobilization technique and the carrier type. The choice of the carrier concerns usually the biocompatibility, chemical and thermal stability, and insolubility under reaction conditions, capability of easy rejuvenation and reusability, as well as cost proficiency. Bacillus spp., Achromobacter spp., Alcaligenes spp., Arthrobacter spp., Pseudomonos spp., of bacteria and Penicillium spp., Fusarium spp., Aspergillus spp., of fungi are screened large scale for lipase production. Lipases as multipurpose biological catalyst has given a favorable vision in meeting the needs for several industries such as biodiesel, foods and drinks, leather, textile, detergents, pharmaceuticals and medicals. This review represents a discussion on microbial sources of lipases, immobilization methods increased productivity at market profitability and reduce logistical liability on the environment and user.
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Affiliation(s)
- Prem Chandra
- Food Microbiology & Toxicology, Department of Microbiology, School for Biomedical and Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University (A Central) University, Lucknow, Uttar Pradesh 226025 India
| | - Enespa
- Department of Plant Pathology, School for Agriculture, SMPDC, University of Lucknow, Lucknow, 226007 U.P. India
| | - Ranjan Singh
- Department of Environmental Science, School for Environmental Science, Babasaheb Bhimrao Ambedkar University (A Central) University, Lucknow, U.P. India
| | - Pankaj Kumar Arora
- Department of Microbiology, School for Biomedical and Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University (A Central) University, Lucknow, U.P. India
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21
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de Oliveira BFR, Carr CM, Dobson ADW, Laport MS. Harnessing the sponge microbiome for industrial biocatalysts. Appl Microbiol Biotechnol 2020; 104:8131-8154. [PMID: 32827049 DOI: 10.1007/s00253-020-10817-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/29/2020] [Accepted: 08/05/2020] [Indexed: 12/31/2022]
Abstract
Within the marine sphere, host-associated microbiomes are receiving growing attention as prolific sources of novel biocatalysts. Given the known biocatalytic potential of poriferan microbial inhabitants, this review focuses on enzymes from the sponge microbiome, with special attention on their relevant properties and the wide range of their potential biotechnological applications within various industries. Cultivable bacterial and filamentous fungal isolates account for the majority of the enzymatic sources. Hydrolases, mainly glycoside hydrolases and carboxylesterases, are the predominant reported group of enzymes, with varying degrees of tolerance to alkaline pH and growing salt concentrations being common. Prospective areas for the application of these microbial enzymes include biorefinery, detergent, food and effluent treatment industries. Finally, alternative strategies to identify novel biocatalysts from the sponge microbiome are addressed, with an emphasis on modern -omics-based approaches that are currently available in the enzyme research arena. By providing this current overview of the field, we hope to not only increase the appetite of researchers to instigate forthcoming studies but also to stress how basic and applied research can pave the way for new biocatalysts from these symbiotic microbial communities in a productive fashion. KEY POINTS: • The sponge microbiome is a burgeoning source of industrial biocatalysts. • Sponge microbial enzymes have useful habitat-related traits for several industries. • Strategies are provided for the future discovery of microbial enzymes from sponges.
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Affiliation(s)
- Bruno Francesco Rodrigues de Oliveira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil. .,School of Microbiology, University College Cork, Cork, Ireland.
| | - Clodagh M Carr
- School of Microbiology, University College Cork, Cork, Ireland
| | - Alan D W Dobson
- School of Microbiology, University College Cork, Cork, Ireland.,Environmental Research Institute, University College Cork, Cork, Ireland
| | - Marinella Silva Laport
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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22
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Pulido IY, Prieto E, Pieffet GP, Méndez L, Jiménez-Junca CA. Functional Heterologous Expression of Mature Lipase LipA from Pseudomonas aeruginosa PSA01 in Escherichia coli SHuffle and BL21 (DE3): Effect of the Expression Host on Thermal Stability and Solvent Tolerance of the Enzyme Produced. Int J Mol Sci 2020; 21:E3925. [PMID: 32486240 PMCID: PMC7312249 DOI: 10.3390/ijms21113925] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/23/2020] [Accepted: 05/26/2020] [Indexed: 02/06/2023] Open
Abstract
This study aimed to express heterologously the lipase LipA from Pseudomonas aeruginosa PSA01 obtained from palm fruit residues. In previous approaches, LipA was expressed in Escherichia coli fused with its signal peptide and without its disulfide bond, displaying low activity. We cloned the mature LipA with its truncated chaperone Lif in a dual plasmid and overexpressed the enzyme in two E. coli strains: the traditional BL21 (DE3) and the SHuffle® strain, engineered to produce stable cytoplasmic disulfide bonds. We evaluated the effect of the disulfide bond on LipA stability using molecular dynamics. We expressed LipA successfully under isopropyl β-d-1-thio-galactopyranoside (IPTG) and slow autoinducing conditions. The SHuffle LipA showed higher residual activity at 45 °C and a greater hyperactivation after incubation with ethanol than the enzyme produced by E. coli BL21 (DE3). Conversely, the latter was slightly more stable in methanol 50% and 60% (t½: 49.5 min and 9 min) than the SHuffle LipA (t½: 31.5 min and 7.4 min). The molecular dynamics simulations showed that removing the disulfide bond caused some regions of LipA to become less flexible and some others to become more flexible, significantly affecting the closing lid and partially exposing the active site at all times.
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Affiliation(s)
- Ingrid Yamile Pulido
- Biosciences Doctoral Program, Universidad de La Sabana, km 7 Autopista Norte, Chía 250001, Colombia;
| | - Erlide Prieto
- Agro-industrial Processes Research Group, Engineering Faculty, Universidad de La Sabana, km 7 Autopista Norte, Chía, Cundinamarca 250001, Colombia; (E.P.); (L.M.)
| | - Gilles Paul Pieffet
- Science Faculty, Universidad Antonio Nariño, Calle 58 A # 37–94 Bogotá D.C.111511, Colombia;
| | - Lina Méndez
- Agro-industrial Processes Research Group, Engineering Faculty, Universidad de La Sabana, km 7 Autopista Norte, Chía, Cundinamarca 250001, Colombia; (E.P.); (L.M.)
| | - Carlos A. Jiménez-Junca
- Bioprospecting Research Group, Engineering Faculty, Universidad de La Sabana, km 7 Autopista Norte, Chía, Cundinamarca 250001, Colombia
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23
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Sahoo RK, Das A, Sahoo K, Sahu A, Subudhi E. Characterization of novel metagenomic–derived lipase from Indian hot spring. Int Microbiol 2019; 23:233-240. [DOI: 10.1007/s10123-019-00095-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 06/06/2019] [Accepted: 07/29/2019] [Indexed: 12/14/2022]
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24
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Mathivanan A, Ravikumar S, Selvakumar G. Bioprospecting of sponge and its symbionts: New tool for mosquitocidal & insecticidal metabolites. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2019.101158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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25
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Lu M, Dukunde A, Daniel R. Biochemical profiles of two thermostable and organic solvent-tolerant esterases derived from a compost metagenome. Appl Microbiol Biotechnol 2019; 103:3421-3437. [PMID: 30809711 DOI: 10.1007/s00253-019-09695-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 02/11/2019] [Accepted: 02/12/2019] [Indexed: 12/15/2022]
Abstract
Owing to the functional versatility and potential applications in industry, interest in lipolytic enzymes tolerant to organic solvents is increasing. In this study, functional screening of a compost soil metagenome resulted in identification of two lipolytic genes, est1 and est2, encoding 270 and 389 amino acids, respectively. The two genes were heterologously expressed and characterized. Est1 and Est2 are thermostable enzymes with optimal enzyme activities at 80 and 70 °C, respectively. A second-order rotatable design, which allows establishing the relationship between multiple variables with the obtained responses, was used to explore the combined effects of temperature and pH on esterase stability. The response curve indicated that Est1, and particularly Est2, retained high stability within a broad range of temperature and pH values. Furthermore, the effects of organic solvents on Est1 and Est2 activities and stabilities were assessed. Notably, Est2 activity was significantly enhanced (two- to tenfold) in the presence of ethanol, methanol, isopropanol, and 1-propanol over a concentration range between 6 and 30% (v/v). For the short-term stability (2 h of incubation), Est2 exhibited high tolerance against 60% (v/v) of ethanol, methanol, isopropanol, DMSO, and acetone, while Est1 activity resisted these solvents only at lower concentrations (below 30%, v/v). Est2 also displayed high stability towards some water-immiscible organic solvents, such as ethyl acetate, diethyl ether, and toluene. With respect to long-term stability, Est2 retained most of its activity after 26 days of incubation in the presence of 30% (v/v) ethanol, methanol, isopropanol, DMSO, or acetone. All of these features indicate that Est1 and Est2 possess application potential.
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Affiliation(s)
- Mingji Lu
- Department of Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Grisebachstraße 8, 37077, Göttingen, Germany
| | - Amélie Dukunde
- Department of Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Grisebachstraße 8, 37077, Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology, Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Grisebachstraße 8, 37077, Göttingen, Germany.
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26
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A Thermostable Monoacylglycerol Lipase from Marine Geobacillus sp. 12AMOR1: Biochemical Characterization and Mutagenesis Study. Int J Mol Sci 2019; 20:ijms20030780. [PMID: 30759774 PMCID: PMC6386982 DOI: 10.3390/ijms20030780] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 01/25/2019] [Accepted: 02/09/2019] [Indexed: 12/13/2022] Open
Abstract
Lipases with unique substrate specificity are highly desired in biotechnological applications. In this study, a putative marine Geobacillus sp. monoacylglycerol lipase (GMGL) encoded gene was identified by a genomic mining strategy. The gene was expressed in Escherichia coli as a His-tag fusion protein and purified by affinity chromatography with a yield of 264 mg per liter fermentation broth. The recombinant GMGL shows the highest hydrolysis activity at 60 °C and pH 8.0, and the half-life was 60 min at 70 °C. The GMGL is active on monoacylglycerol (MAG) substrate but not diacylglycerol (DAG) or triacylglycerol (TAG), and produces MAG as the single product in the esterification reaction. Modeling structure analysis showed that the catalytic triad is formed by Ser97, Asp196 and His226, and the flexible cap region is constituted by residues from Ala120 to Thr160. A mutagenesis study on Leu142, Ile145 and Ile170 located in the substrate binding tunnel revealed that these residues were related with its substrate specificity. The kcat/Km value toward the pNP-C6 substrate in mutants Leu142Ala, Ile145Ala and Ile170Phe increased to 2.3-, 1.4- and 2.2-fold as compared to that of the wild type, respectively.
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Ngara TR, Zhang H. Recent Advances in Function-based Metagenomic Screening. GENOMICS PROTEOMICS & BIOINFORMATICS 2018; 16:405-415. [PMID: 30597257 PMCID: PMC6411959 DOI: 10.1016/j.gpb.2018.01.002] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/05/2018] [Accepted: 01/09/2018] [Indexed: 12/01/2022]
Abstract
Metagenomes from uncultured microorganisms are rich resources for novel enzyme genes. The methods used to screen the metagenomic libraries fall into two categories, which are based on sequence or function of the enzymes. The sequence-based approaches rely on the known sequences of the target gene families. In contrast, the function-based approaches do not involve the incorporation of metagenomic sequencing data and, therefore, may lead to the discovery of novel gene sequences with desired functions. In this review, we discuss the function-based screening strategies that have been used in the identification of enzymes from metagenomes. Because of its simplicity, agar plate screening is most commonly used in the identification of novel enzymes with diverse functions. Other screening methods with higher sensitivity are also employed, such as microtiter plate screening. Furthermore, several ultra-high-throughput methods were developed to deal with large metagenomic libraries. Among these are the FACS-based screening, droplet-based screening, and the in vivo reporter-based screening methods. The application of these novel screening strategies has increased the chance for the discovery of novel enzyme genes.
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Affiliation(s)
- Tanyaradzwa Rodgers Ngara
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, MOE Key Laboratory of Molecular Biophysics, Wuhan 430074, China
| | - Houjin Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, MOE Key Laboratory of Molecular Biophysics, Wuhan 430074, China.
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28
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Kiran GS, Sekar S, Ramasamy P, Thinesh T, Hassan S, Lipton AN, Ninawe AS, Selvin J. Marine sponge microbial association: Towards disclosing unique symbiotic interactions. MARINE ENVIRONMENTAL RESEARCH 2018; 140:169-179. [PMID: 29935729 DOI: 10.1016/j.marenvres.2018.04.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 03/01/2018] [Accepted: 04/25/2018] [Indexed: 06/08/2023]
Abstract
Sponges are sessile benthic filter-feeding animals, which harbor numerous microorganisms. The enormous diversity and abundance of sponge associated bacteria envisages sponges as hot spots of microbial diversity and dynamics. Many theories were proposed on the ecological implications and mechanism of sponge-microbial association, among these, the biosynthesis of sponge derived bioactive molecules by the symbiotic bacteria is now well-indicated. This phenomenon however, is not exhibited by all marine sponges. Based on the available reports, it has been well established that the sponge associated microbial assemblages keep on changing continuously in response to environmental pressure and/or acquisition of microbes from surrounding seawater or associated macroorganisms. In this review, we have discussed nutritional association of sponges with its symbionts, interaction of sponges with other eukaryotic organisms, dynamics of sponge microbiome and sponge-specific microbial symbionts, sponge-coral association etc.
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Affiliation(s)
- G Seghal Kiran
- Department of Food Science and Technology, Pondicherry University, Puducherry, 605014, India
| | - Sivasankari Sekar
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - Pasiyappazham Ramasamy
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | | | - Saqib Hassan
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - Anuj Nishanth Lipton
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India
| | - A S Ninawe
- Department of Biotechnology, Ministry of Science and Technology, New Delhi, India
| | - Joseph Selvin
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry, 605014, India.
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29
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Castilla IA, Woods DF, Reen FJ, O'Gara F. Harnessing Marine Biocatalytic Reservoirs for Green Chemistry Applications through Metagenomic Technologies. Mar Drugs 2018; 16:E227. [PMID: 29973493 PMCID: PMC6071119 DOI: 10.3390/md16070227] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 06/13/2018] [Accepted: 06/22/2018] [Indexed: 01/24/2023] Open
Abstract
In a demanding commercial world, large-scale chemical processes have been widely utilised to satisfy consumer related needs. Chemical industries are key to promoting economic growth and meeting the requirements of a sustainable industrialised society. The market need for diverse commodities produced by the chemical industry is rapidly expanding globally. Accompanying this demand is an increased threat to the environment and to human health, due to waste produced by increased industrial production. This increased demand has underscored the necessity to increase reaction efficiencies, in order to reduce costs and increase profits. The discovery of novel biocatalysts is a key method aimed at combating these difficulties. Metagenomic technology, as a tool for uncovering novel biocatalysts, has great potential and applicability and has already delivered many successful achievements. In this review we discuss, recent developments and achievements in the field of biocatalysis. We highlight how green chemistry principles through the application of biocatalysis, can be successfully promoted and implemented in various industrial sectors. In addition, we demonstrate how two novel lipases/esterases were mined from the marine environment by metagenomic analysis. Collectively these improvements can result in increased efficiency, decreased energy consumption, reduced waste and cost savings for the chemical industry.
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Affiliation(s)
- Ignacio Abreu Castilla
- BIOMERIT Research Centre, School of Microbiology, University College Cork, T12 K8AF Cork, Ireland.
| | - David F Woods
- BIOMERIT Research Centre, School of Microbiology, University College Cork, T12 K8AF Cork, Ireland.
| | - F Jerry Reen
- School of Microbiology, University College Cork, T12 K8AF Cork, Ireland.
| | - Fergal O'Gara
- BIOMERIT Research Centre, School of Microbiology, University College Cork, T12 K8AF Cork, Ireland.
- Telethon Kids Institute, Perth, WA 6008, Australia.
- Human Microbiome Programme, School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia.
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Seghal Kiran G, Ramasamy P, Sekar S, Ramu M, Hassan S, Ninawe A, Selvin J. Synthetic biology approaches: Towards sustainable exploitation of marine bioactive molecules. Int J Biol Macromol 2018; 112:1278-1288. [DOI: 10.1016/j.ijbiomac.2018.01.149] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 01/18/2018] [Accepted: 01/21/2018] [Indexed: 12/18/2022]
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31
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Kiran GS, Priyadharsini S, Sajayan A, Ravindran A, Selvin J. An antibiotic agent pyrrolo[1,2-a]pyrazine-1,4-dione,hexahydro isolated from a marine bacteria Bacillus tequilensis MSI45 effectively controls multi-drug resistant Staphylococcus aureus. RSC Adv 2018; 8:17837-17846. [PMID: 35542054 PMCID: PMC9080480 DOI: 10.1039/c8ra00820e] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/21/2018] [Indexed: 11/22/2022] Open
Abstract
Sponge associated bacteria are a rich source of bioactive secondary metabolites. This study aims to isolate bacteria producing antimicrobial agents from a marine sponge, Callyspongia diffusa. A total of fifty-six bacteria were isolated and screened for antibacterial activity against multidrug resistant S. aureus. Based on the 16S rRNA sequence and phylogenetic analysis the antimicrobial producer strain MSI45 was identified as a novel Bacillus tequilensis. The culture conditions of strain MSI45 were optimized to enhance the yield of the antimicrobial compound. The antimicrobial compound was purified using a silica gel column chromatography and high performance liquid chromatography. On the basis of spectroscopic analysis such as FT-IR, NMR and GC-MS, the bioactive metabolite was identified as pyrrolo[1,2-a]pyrazine-1,4-dione,hexahydro. The extracted compound MSI45 showed a potent inhibitory effect on multidrug resistant S. aureus with an MIC of 15 ± 0.172 mg L−1 and MBC of 20 ± 0.072 mg L−1. The compound was non-hemolytic and showed high antioxidant activity. The antioxidant activity may increase the efficacy and safety of the molecule in drug development. Hence, this compound produced by Bacillus tequilensis MSI45 could have potent antimicrobial and antioxidant activity against S. aureus infection. A new antibiotic agent from sponge associated marine bacteria.![]()
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Affiliation(s)
| | | | - Arya Sajayan
- Department of Food Science and Technology
- Pondicherry University
- India
| | - Amrudha Ravindran
- Department of Food Science and Technology
- Pondicherry University
- India
| | - Joseph Selvin
- Department of Microbiology
- Pondicherry University
- India
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32
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Impact of signal peptide and transmembrane segments on expression and biochemical properties of a lipase from Bacillus sphaericus 205y. J Biotechnol 2017; 264:51-62. [PMID: 29107669 DOI: 10.1016/j.jbiotec.2017.10.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 10/18/2017] [Accepted: 10/23/2017] [Indexed: 11/22/2022]
Abstract
A total of 97 amino acids, considered as the signal peptide and transmembrane segments were removed from 205y lipase gene using polymerase chain reaction technique that abolished the low activity of this enzyme. The mature enzyme was expressed in Escherichia coli using pBAD expression vector, which gave up to a 13-fold increase in lipase activity. The mature 205y lipase (without signal peptide and transmembrane; -SP/TM) was purified to homogeneity using the isoelectric focusing technique with 53% recovery. Removing of the signal peptide and transmembrane segments had resulted in the shift of optimal pH, an increase in optimal temperature and tolerance towards more water-miscible organic solvents as compared to the characteristics of open reading frame (ORF) of 205y lipase. Also, in the presence of 1mM inhibitors, less decrease in the activity of mature 205y lipase was observed compared to the ORF of the enzyme. Protein structure modeling showed that 205y lipase consisted of an α/β hydrolase fold without lid domain. However, the transmembrane segment could effect on the enzyme activity by covering the active site or aggregation the protein.
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33
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Sánchez-Carbente MDR, Batista-García RA, Sánchez-Reyes A, Escudero-Garcia A, Morales-Herrera C, Cuervo-Soto LI, French-Pacheco L, Fernández-Silva A, Amero C, Castillo E, Folch-Mallol JL. The first description of a hormone-sensitive lipase from a basidiomycete: Structural insights and biochemical characterization revealed Bjerkandera adusta BaEstB as a novel esterase. Microbiologyopen 2017; 6. [PMID: 28251842 PMCID: PMC5552909 DOI: 10.1002/mbo3.463] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 01/25/2017] [Accepted: 02/02/2017] [Indexed: 11/06/2022] Open
Abstract
The heterologous expression and characterization of a Hormone-Sensitive Lipases (HSL) esterase (BaEstB) from the Basidiomycete fungus Bjerkandera adusta is reported for the first time. According to structural analysis, amino acid similarities and conservation of particular motifs, it was established that this enzyme belongs to the (HSL) family. The cDNA sequence consisted of 969 nucleotides, while the gene comprised 1133, including three introns of 57, 50, and 57 nucleotides. Through three-dimensional modeling and phylogenetic analysis, we conclude that BaEstB is an ortholog of the previously described RmEstB-HSL from the phylogenetically distant fungus Rhizomucor miehei. The purified BaEstB was characterized in terms of its specificity for the hydrolysis of different acyl substrates confirming its low lipolytic activity and a noticeable esterase activity. The biochemical characterization of BaEstB, the DLS analysis and the kinetic parameters determination revealed this enzyme as a true esterase, preferentially found in a dimeric state, displaying activity under alkaline conditions and relative low temperature (pH = 10, 20°C). Our data suggest that BaEstB is more active on substrates with short acyl chains and bulky aromatic moieties. Phylogenetic data allow us to suggest that a number of fungal hypothetical proteins could belong to the HSL family.
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Affiliation(s)
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Ayixón Sánchez-Reyes
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico.,Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Angela Escudero-Garcia
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Catalina Morales-Herrera
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Laura I Cuervo-Soto
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico.,Departamento de Biología, Facultad de Ciencias, Universidad Antonio Nariño, Bogota, Colombia
| | - Leidys French-Pacheco
- Centro de Investigaciones Químicas, Instituto de Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Arline Fernández-Silva
- Centro de Investigaciones Químicas, Instituto de Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Carlos Amero
- Centro de Investigaciones Químicas, Instituto de Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Edmundo Castillo
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Jorge Luis Folch-Mallol
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
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34
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A novel, versatile family IV carboxylesterase exhibits high stability and activity in a broad pH spectrum. Biotechnol Lett 2017; 39:577-587. [DOI: 10.1007/s10529-016-2282-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 12/21/2016] [Indexed: 10/20/2022]
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35
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Weiland-Bräuer N, Langfeldt D, Schmitz RA. Construction and Screening of Marine Metagenomic Large Insert Libraries. Methods Mol Biol 2017; 1539:23-42. [PMID: 27900682 DOI: 10.1007/978-1-4939-6691-2_3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The marine environment covers more than 70 % of the world's surface. Marine microbial communities are highly diverse and have evolved during extended evolutionary processes of physiological adaptations under the influence of a variety of ecological conditions and selection pressures. They harbor an enormous diversity of microbes with still unknown and probably new physiological characteristics. In the past, marine microbes, mostly bacteria of microbial consortia attached to marine tissues of multicellular organisms, have proven to be a rich source of highly potent bioactive compounds, which represent a considerable number of drug candidates. However, to date, the biodiversity of marine microbes and the versatility of their bioactive compounds and metabolites have not been fully explored. This chapter describes sampling in the marine environment, construction of metagenomic large insert libraries from marine habitats, and exemplarily one function based screen of metagenomic clones for identification of quorum quenching activities.
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Affiliation(s)
- Nancy Weiland-Bräuer
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, 24118, Kiel, Germany
| | - Daniela Langfeldt
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, 24118, Kiel, Germany
| | - Ruth A Schmitz
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, 24118, Kiel, Germany.
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36
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Sathiyanarayanan G, Saibaba G, Kiran GS, Yang YH, Selvin J. Marine sponge-associated bacteria as a potential source for polyhydroxyalkanoates. Crit Rev Microbiol 2016; 43:294-312. [DOI: 10.1080/1040841x.2016.1206060] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Ganesan Sathiyanarayanan
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, South Korea
| | - Ganesan Saibaba
- Centre for Pheromone Technology, Department of Animal Science, School of Life Sciences, Bharathidasan University, Tiruchirappalli, India
| | - George Seghal Kiran
- Department of Food Science and Technology, Pondicherry University, Kalapet, India
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, South Korea
- Microbial Carbohydrate Resource Bank, Konkuk University, Seoul, South Korea
| | - Joseph Selvin
- Department of Microbiology, Pondicherry University, Kalapet, India
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37
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Baweja M, Nain L, Kawarabayasi Y, Shukla P. Current Technological Improvements in Enzymes toward Their Biotechnological Applications. Front Microbiol 2016; 7:965. [PMID: 27379087 PMCID: PMC4909775 DOI: 10.3389/fmicb.2016.00965] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 06/03/2016] [Indexed: 01/07/2023] Open
Abstract
Enzymes from extremophiles are creating interest among researchers due to their unique properties and the enormous power of catalysis at extreme conditions. Since community demands are getting more intensified, therefore, researchers are applying various approaches viz. metagenomics to increase the database of extremophilic species. Furthermore, the innovations are being made in the naturally occurring enzymes utilizing various tools of recombinant DNA technology and protein engineering, which allows redesigning of the enzymes for its better fitment into the process. In this review, we discuss the biochemical constraints of psychrophiles during survival at the lower temperature. We summarize the current knowledge about the sources of such enzymes and their in vitro modification through mutagenesis to explore their biotechnological potential. Finally, we recap the microbial cell surface display to enhance the efficiency of the process in cost effective way.
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Affiliation(s)
- Mehak Baweja
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak India
| | - Lata Nain
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi India
| | - Yutaka Kawarabayasi
- National Institute of Advanced Industrial Science and Technology, Tsukuba Japan
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak India
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38
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Parages ML, Gutiérrez-Barranquero JA, Reen FJ, Dobson ADW, O'Gara F. Integrated (Meta) Genomic and Synthetic Biology Approaches to Develop New Biocatalysts. Mar Drugs 2016; 14:E62. [PMID: 27007381 PMCID: PMC4810074 DOI: 10.3390/md14030062] [Citation(s) in RCA: 18] [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] [Received: 02/18/2016] [Revised: 02/18/2016] [Accepted: 03/11/2016] [Indexed: 12/21/2022] Open
Abstract
In recent years, the marine environment has been the subject of increasing attention from biotechnological and pharmaceutical industries as a valuable and promising source of novel bioactive compounds. Marine biodiscovery programmes have begun to reveal the extent of novel compounds encoded within the enormous bacterial richness and diversity of the marine ecosystem. A combination of unique physicochemical properties and spatial niche-specific substrates, in wide-ranging and extreme habitats, underscores the potential of the marine environment to deliver on functionally novel biocatalytic activities. With the growing need for green alternatives to industrial processes, and the unique transformations which nature is capable of performing, marine biocatalysts have the potential to markedly improve current industrial pipelines. Furthermore, biocatalysts are known to possess chiral selectivity and specificity, a key focus of pharmaceutical drug design. In this review, we discuss how the explosion in genomics based sequence analysis, allied with parallel developments in synthetic and molecular biology, have the potential to fast-track the discovery and subsequent improvement of a new generation of marine biocatalysts.
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Affiliation(s)
- María L Parages
- BIOMERIT Research Centre, School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland.
| | - José A Gutiérrez-Barranquero
- BIOMERIT Research Centre, School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland.
| | - F Jerry Reen
- BIOMERIT Research Centre, School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland.
| | - Alan D W Dobson
- School of Microbiology, University College Cork, Cork, Ireland.
| | - Fergal O'Gara
- BIOMERIT Research Centre, School of Microbiology, University College Cork, National University of Ireland, Cork, Ireland.
- School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth WA 6845, Australia.
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39
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Maester TC, Pereira MR, Machado Sierra EG, Balan A, de Macedo Lemos EG. Characterization of EST3: a metagenome-derived esterase with suitable properties for biotechnological applications. Appl Microbiol Biotechnol 2016; 100:5815-27. [DOI: 10.1007/s00253-016-7385-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 01/31/2016] [Accepted: 02/02/2016] [Indexed: 10/22/2022]
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40
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O'Mahony MM, Henneberger R, Selvin J, Kennedy J, Doohan F, Marchesi JR, Dobson ADW. Inhibition of the growth of Bacillus subtilis DSM10 by a newly discovered antibacterial protein from the soil metagenome. Bioengineered 2016; 6:89-98. [PMID: 25692994 PMCID: PMC4601227 DOI: 10.1080/21655979.2015.1018493] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
A functional metagenomics based approach exploiting the microbiota of suppressive soils from an organic field site has succeeded in the identification of a clone with the ability to inhibit the growth of Bacillus subtilis DSM10. Sequencing of the fosmid identified a putative β-lactamase-like gene abgT. Transposon mutagenesis of the abgT gene resulted in a loss in ability to inhibit the growth of B. subtilis DSM10. Further analysis of the deduced amino acid sequence of AbgT revealed moderate homology to esterases, suggesting that the protein may possess hydrolytic activity. Weak lipolytic activity was detected; however the clone did not appear to produce any β-lactamase activity. Phylogenetic analysis revealed the protein is a member of the family VIII group of lipase/esterases and clusters with a number of proteins of metagenomic origin. The abgT gene was sub-cloned into a protein expression vector and when introduced into the abgT transposon mutant clones restored the ability of the clones to inhibit the growth of B. subtilis DSM10, clearly indicating that the abgT gene is involved in the antibacterial activity. While the precise role of this protein has yet to fully elucidated, it may be involved in the generation of free fatty acid with antibacterial properties. Thus functional metagenomic approaches continue to provide a significant resource for the discovery of novel functional proteins and it is clear that hydrolytic enzymes, such as AbgT, may be a potential source for the development of future antimicrobial therapies.
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Affiliation(s)
- Mark M O'Mahony
- a School of Microbiology and Marine Biotechnology Center; Environmental Research Institute; University College Cork ; Cork , Ireland
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Mori T, Iwamoto K, Wakaoji S, Araie H, Kohara Y, Okamura Y, Shiraiwa Y, Takeyama H. Characterization of a novel gene involved in cadmium accumulation screened from sponge-associated bacterial metagenome. Gene 2016; 576:618-25. [DOI: 10.1016/j.gene.2015.10.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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López-López O, Knapik K, Cerdán ME, González-Siso MI. Metagenomics of an Alkaline Hot Spring in Galicia (Spain): Microbial Diversity Analysis and Screening for Novel Lipolytic Enzymes. Front Microbiol 2015; 6:1291. [PMID: 26635759 PMCID: PMC4653306 DOI: 10.3389/fmicb.2015.01291] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 11/04/2015] [Indexed: 01/23/2023] Open
Abstract
A fosmid library was constructed with the metagenomic DNA from the water of the Lobios hot spring (76°C, pH = 8.2) located in Ourense (Spain). Metagenomic sequencing of the fosmid library allowed the assembly of 9722 contigs ranging in size from 500 to 56,677 bp and spanning ~18 Mbp. 23,207 ORFs (Open Reading Frames) were predicted from the assembly. Biodiversity was explored by taxonomic classification and it revealed that bacteria were predominant, while the archaea were less abundant. The six most abundant bacterial phyla were Deinococcus-Thermus, Proteobacteria, Firmicutes, Acidobacteria, Aquificae, and Chloroflexi. Within the archaeal superkingdom, the phylum Thaumarchaeota was predominant with the dominant species “Candidatus Caldiarchaeum subterraneum.” Functional classification revealed the genes associated to one-carbon metabolism as the most abundant. Both taxonomic and functional classifications showed a mixture of different microbial metabolic patterns: aerobic and anaerobic, chemoorganotrophic and chemolithotrophic, autotrophic and heterotrophic. Remarkably, the presence of genes encoding enzymes with potential biotechnological interest, such as xylanases, galactosidases, proteases, and lipases, was also revealed in the metagenomic library. Functional screening of this library was subsequently done looking for genes encoding lipolytic enzymes. Six genes conferring lipolytic activity were identified and one was cloned and characterized. This gene was named LOB4Est and it was expressed in a yeast mesophilic host. LOB4Est codes for a novel esterase of family VIII, with sequence similarity to β-lactamases, but with unusual wide substrate specificity. When the enzyme was purified from the mesophilic host it showed half-life of 1 h and 43 min at 50°C, and maximal activity at 40°C and pH 7.5 with p-nitrophenyl-laurate as substrate. Interestingly, the enzyme retained more than 80% of maximal activity in a broad range of pH from 6.5 to 8.
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Affiliation(s)
- Olalla López-López
- Grupo EXPRELA, Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Centro de Investigacións Científicas Avanzadas, Universidade da Coruña A Coruña, Spain
| | - Kamila Knapik
- Grupo EXPRELA, Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Centro de Investigacións Científicas Avanzadas, Universidade da Coruña A Coruña, Spain
| | - Maria-Esperanza Cerdán
- Grupo EXPRELA, Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Centro de Investigacións Científicas Avanzadas, Universidade da Coruña A Coruña, Spain
| | - María-Isabel González-Siso
- Grupo EXPRELA, Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Centro de Investigacións Científicas Avanzadas, Universidade da Coruña A Coruña, Spain
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Kathiravan MN, Gim GH, Ryu J, Kim PI, Lee CW, Kim SW. Enhanced method for microbial community DNA extraction and purification from agricultural yellow loess soil. J Microbiol 2015; 53:767-75. [DOI: 10.1007/s12275-015-5454-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 10/02/2015] [Accepted: 10/02/2015] [Indexed: 11/29/2022]
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Seghal Kiran G, Nishanth Lipton A, Kennedy J, Dobson ADW, Selvin J. A halotolerant thermostable lipase from the marine bacterium Oceanobacillus sp. PUMB02 with an ability to disrupt bacterial biofilms. Bioengineered 2015; 5:305-18. [PMID: 25482232 DOI: 10.4161/bioe.29898] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
A halotolerant thermostable lipase was purified and characterized from the marine bacterium Oceanobacillus sp. PUMB02. This lipase displayed a high degree of stability over a wide range of conditions including pH, salinity, and temperature. It was optimally active at 30 °C and pH 8.0 respectively and was stable at higher temperatures (50-70 °C) and alkaline pH. The molecular mass of the lipase was approximately 31 kDa based on SDS-PAGE and MALDI-ToF fingerprint analysis. Conditions for enhanced production of lipase by Oceanobacillus sp. PUMB02 were attained in response surface method-guided optimization with factors such as olive oil, sucrose, potassium chromate, and NaCl being evaluated, resulting in levels of 58.84 U/ml being achieved. The biofilm disruption potential of the PUMB02 lipase was evaluated and compared with a marine sponge metagenome derived halotolerant lipase Lpc53E1. Good biofilm disruption activity was observed with both lipases against potential food pathogens such as Bacillus cereus MTCC1272, Listeria sp. MTCC1143, Serratia sp. MTCC4822, Escherichia coli MTCC443, Pseudomonas fluorescens MTCC1748, and Vibrio parahemolyticus MTCC459. Phase contrast microscopy, scanning electron microscopy, and confocal laser scanning microscopy showed very effective disruption of pathogenic biofilms. This study reveals that marine derived hydrolytic enzymes such as lipases may have potential utility in inhibiting biofilm formation in a food processing environment and is the first report of the potential application of lipases from the genus Oceanobacillus in biofilm disruption strategies.
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Affiliation(s)
- George Seghal Kiran
- a Department of Food Science and Technology; Pondicherry University; Puducherry, India
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Jain D, Mishra S. Multifunctional solvent stable Bacillus lipase mediated biotransformations in the context of food and fuel. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2015.04.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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46
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López-López O, Cerdán ME, González Siso MI. New extremophilic lipases and esterases from metagenomics. Curr Protein Pept Sci 2015; 15:445-55. [PMID: 24588890 PMCID: PMC4093774 DOI: 10.2174/1389203715666140228153801] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 01/21/2014] [Accepted: 02/25/2014] [Indexed: 11/22/2022]
Abstract
Lipolytic enzymes catalyze the hydrolysis of ester bonds in the presence of water. In media with low water content or in organic solvents, they can catalyze synthetic reactions such as esterification and transesterification. Lipases and esterases, in particular those from extremophilic origin, are robust enzymes, functional under the harsh conditions of industrial processes owing to their inherent thermostability and resistance towards organic solvents, which combined with their high chemo-, regio- and enantioselectivity make them very attractive biocatalysts for a variety of industrial applications. Likewise, enzymes from extremophile sources can provide additional features such as activity at extreme temperatures, extreme pH values or high salinity levels, which could be interesting for certain purposes. New lipases and esterases have traditionally been discovered by the isolation of microbial strains producing lipolytic activity. The Genome Projects Era allowed genome mining, exploiting homology with known lipases and esterases, to be used in the search for new enzymes. The Metagenomic Era meant a step forward in this field with the study of the metagenome, the pool of genomes in an environmental microbial community. Current molecular biology techniques make it possible to construct total environmental DNA libraries, including the genomes of unculturable organisms, opening a new window to a vast field of unknown enzymes with new and unique properties. Here, we review the latest advances and findings from research into new extremophilic lipases and esterases, using metagenomic approaches, and their potential industrial and biotechnological applications.
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Affiliation(s)
| | | | - Maria I González Siso
- University of A Coruna, Faculty of Sciences, Department of Cellular and Molecular Biology, Biochemistry and Molecular Biology Area. Campus A Zapateira s/n, 15071, A Coruna, Spain.
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De Santi C, Ambrosino L, Tedesco P, Zhai L, Zhou C, Xue Y, Ma Y, de Pascale D. Identification and characterization of a novel salt-tolerant esterase from a Tibetan glacier metagenomic library. Biotechnol Prog 2015; 31:890-9. [PMID: 25920073 DOI: 10.1002/btpr.2096] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 03/23/2015] [Indexed: 12/12/2022]
Abstract
A salt-tolerant esterase, designated H9Est, was identified from a metagenomic library of the Karuola glacier. H9Est gene comprised 1071 bp and encoded a polypeptide of 357 amino acids with a molecular mass of 40 kDa. Sequence analysis revealed that H9Est belonged to the family IV of bacterial lypolitic enzyme. H9Est was overexpressed in Escherichia coli and the purified enzyme showed hydrolytic activity towards p-nitrophenyl esters with carbon chain from 2 to 8. The optimal esterase activity was at 40°C and pH 8.0 and the enzyme retained its activity towards some miscible organic solvents such as polyethylene glycol. A three-dimensional model of H9Est revealed that S200, D294, and H324 formed the H9Est catalytic triad. Circular Dichroism spectra and molecular dynamic simulation indicated that the esterase had a wide denaturation temperature range and flexible loops that would be beneficial for H9Est performance at low temperatures while retaining heat-resistant features.
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Affiliation(s)
- Concetta De Santi
- Inst. of Protein Biochemistry, National Research Council, Naples, I-80131, Italy
| | - Luca Ambrosino
- Inst. of Protein Biochemistry, National Research Council, Naples, I-80131, Italy
| | - Pietro Tedesco
- Inst. of Protein Biochemistry, National Research Council, Naples, I-80131, Italy
| | | | | | | | - Yanhe Ma
- State Key Laboratory of Microbial Resources and National Engineering Laboratory for Industrial Enzymes, Inst. of Microbiology, CAS, Beijing, 100101, China
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Bacterial Diversity Associated with Cinachyra cavernosa and Haliclona pigmentifera, Cohabiting Sponges in the Coral Reef Ecosystem of Gulf of Mannar, Southeast Coast of India. PLoS One 2015; 10:e0123222. [PMID: 25938436 PMCID: PMC4418615 DOI: 10.1371/journal.pone.0123222] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 03/02/2015] [Indexed: 11/22/2022] Open
Abstract
Sponges are abundant, diverse and functionally important organisms of coral reef ecosystems. Sponge-associated microorganisms have been receiving greater attention because of their significant contribution to sponge biomass, biogeochemical cycles and biotechnological potentials. However, our understanding of the sponge microbiome is limited to a few species of sponges from restricted geographical locations. Here, we report for the first time the bacterial diversity of two cohabiting sponges, viz. Cinachyra cavernosa and Haliclona pigmentifera, as well as that in the ambient water from the coral reef ecosystems of the Gulf of Mannar, located along the southeast coast of India. Two hundred and fifty two clones in the 16S rRNA gene library of these sponges were grouped into eight distinct phyla, of which four belonged to the core group that are associated only with sponges. Phylogenetic analysis of the core bacteria showed close affinity to other sponge-associated bacteria from different geographical locations. γ-Proteobacteria, Chloroflexi, Planctomycetes and Deferribacter were the core groups in C. cavernosa while β and δ-Proteobacteria performed this role in H. pigmentifera. We observed greater OTU diversity for C. cavernosa (Hǀ 2.07) compared to H. pigmentifera (Hǀ 1.97). UniFrac analysis confirmed the difference in bacterial diversity of the two sponge species and also between the sponges and the reef water (p<0.001). The results of our study restate the existence of a host driven force in shaping the sponge microbiome.
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Su J, Zhang F, Sun W, Karuppiah V, Zhang G, Li Z, Jiang Q. A new alkaline lipase obtained from the metagenome of marine sponge Ircinia sp. World J Microbiol Biotechnol 2015; 31:1093-102. [PMID: 25921581 DOI: 10.1007/s11274-015-1859-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 04/23/2015] [Indexed: 11/24/2022]
Abstract
Microorganisms associated with marine sponges are potential resources for marine enzymes. In this study, culture-independent metagenomic approach was used to isolate lipases from the complex microbiome of the sponge Ircinia sp. obtained from the South China Sea. A metagenomic library was constructed, containing 6568 clones, and functional screening on 1 % tributyrin agar resulted in the identification of a positive lipase clone (35F4). Following sequence analysis 35F4 clone was found to contain a putative lipase gene lipA. Sequence analysis of the predicted amino acid sequence of LipA revealed that it is a member of subfamily I.1 of lipases, with 63 % amino acid similarity to the lactonizing lipase from Aeromonas veronii (WP_021231793). Based on the predicted secondary structure, LipA was predicted to be an alkaline enzyme by sequence/structure analysis. Heterologous expression of lipA in E. coli BL21 (DE3) was performed and the characterization of the recombinant enzyme LipA showed that it is an alkaline enzyme with high tolerance to organic solvents. The isolated lipase LipA was active in the broad alkaline range, with the highest activity at pH 9.0, and had a high level of stability over a pH range of 7.0-12.0. The activity of LipA was increased in the presence of 5 mM Ca(2+) and some organic solvents, e.g. methanol, acetone and isopropanol. The optimum temperature for the activity of LipA is 40 °C and the molecular weight of LipA was determined to be ~30 kDa by SDS-PAGE. LipA is an alkaline lipase and shows good tolerance to some organic solvents, which make it of potential utility in the detergent industry and enzyme mediated organic synthesis. The result of this study has broadened the diversity of known lipolytic genes and demonstrated that marine sponges are an important source for new enzymes.
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Affiliation(s)
- Jing Su
- Marine Biotechnology Laboratory, State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, People's Republic China
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Alcaide M, Tchigvintsev A, Martínez-Martínez M, Popovic A, Reva ON, Lafraya Á, Bargiela R, Nechitaylo TY, Matesanz R, Cambon-Bonavita MA, Jebbar M, Yakimov MM, Savchenko A, Golyshina OV, Yakunin AF, Golyshin PN, Ferrer M. Identification and characterization of carboxyl esterases of gill chamber-associated microbiota in the deep-sea shrimp Rimicaris exoculata by using functional metagenomics. Appl Environ Microbiol 2015; 81:2125-36. [PMID: 25595762 PMCID: PMC4345394 DOI: 10.1128/aem.03387-14] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 01/05/2015] [Indexed: 01/03/2023] Open
Abstract
The shrimp Rimicaris exoculata dominates the fauna in deep-sea hydrothermal vent sites along the Mid-Atlantic Ridge (depth, 2,320 m). Here, we identified and biochemically characterized three carboxyl esterases from microbial communities inhabiting the R. exoculata gill that were isolated by naive screens of a gill chamber metagenomic library. These proteins exhibit low to moderate identity to known esterase sequences (≤52%) and to each other (11.9 to 63.7%) and appear to have originated from unknown species or from genera of Proteobacteria related to Thiothrix/Leucothrix (MGS-RG1/RG2) and to the Rhodobacteraceae group (MGS-RG3). A library of 131 esters and 31 additional esterase/lipase preparations was used to evaluate the activity profiles of these enzymes. All 3 of these enzymes had greater esterase than lipase activity and exhibited specific activities with ester substrates (≤356 U mg(-1)) in the range of similar enzymes. MGS-RG3 was inhibited by salts and pressure and had a low optimal temperature (30°C), and its substrate profile clustered within a group of low-activity and substrate-restricted marine enzymes. In contrast, MGS-RG1 and MGS-RG2 were most active at 45 to 50°C and were salt activated and barotolerant. They also exhibited wider substrate profiles that were close to those of highly active promiscuous enzymes from a marine hydrothermal vent (MGS-RG2) and from a cold brackish lake (MGS-RG1). The data presented are discussed in the context of promoting the examination of enzyme activities of taxa found in habitats that have been neglected for enzyme prospecting; the enzymes found in these taxa may reflect distinct habitat-specific adaptations and may constitute new sources of rare reaction specificities.
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Affiliation(s)
- María Alcaide
- Consejo Superior de Investigaciones Científicas (CSIC), Institute of Catalysis, Madrid, Spain
| | - Anatoli Tchigvintsev
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | | | - Ana Popovic
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Oleg N Reva
- Department of Biochemistry, University of Pretoria, Pretoria, South Africa
| | - Álvaro Lafraya
- Consejo Superior de Investigaciones Científicas (CSIC), Institute of Catalysis, Madrid, Spain
| | - Rafael Bargiela
- Consejo Superior de Investigaciones Científicas (CSIC), Institute of Catalysis, Madrid, Spain
| | - Taras Y Nechitaylo
- Insect Symbiosis Research Group, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Ruth Matesanz
- Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - Marie-Anne Cambon-Bonavita
- Ifremer, Centre de Brest, Laboratoire de Microbiologie des Environnements Extrêmes, REM/DEEP/LM2E, UMR 6197 (Ifremer-CNRS-UBO), ZI de la Pointe du Diable, Plouzané, France
| | - Mohamed Jebbar
- Université de Bretagne Occidentale, Laboratoire de Microbiologie des Environnements Extrêmes-UMR 6197 (CNRS-Ifremer-UBO), Plouzané, France
| | | | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Olga V Golyshina
- School of Biological Sciences, Bangor University, Gwynedd, United Kingdom
| | - Alexander F Yakunin
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Peter N Golyshin
- School of Biological Sciences, Bangor University, Gwynedd, United Kingdom
| | - Manuel Ferrer
- Consejo Superior de Investigaciones Científicas (CSIC), Institute of Catalysis, Madrid, Spain
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