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Zhang J, Shan R, Li X, Zeng Z, Sun D. [Enzymatic properties and degradation characterization of a bis(2-hydroxyethyl) terephthalate hydrolase from Saccharothrix sp.]. Sheng Wu Gong Cheng Xue Bao 2023; 39:2027-2039. [PMID: 37212229 DOI: 10.13345/j.cjb.220991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The discovery of new enzymes for poly(ethylene terephthalate) (PET) degradation has been a hot topic of research globally. Bis-(2-hydroxyethyl) terephthalate (BHET) is an intermediate compound in the degradation of PET and competes with PET for the substrate binding site of the PET-degrading enzyme, thereby inhibiting further degradation of PET. Discovery of new BHET degradation enzymes may contribute to improving the degradation efficiency of PET. In this paper, we discovered a hydrolase gene sle (ID: CP064192.1, 5085270-5086049) from Saccharothrix luteola, which can hydrolyze BHET into mono-(2-hydroxyethyl) terephthalate (MHET) and terephthalic acid (TPA). BHET hydrolase (Sle) was heterologously expressed in Escherichia coli using a recombinant plasmid, and the highest protein expression was achieved at a final concentration of 0.4 mmol/L of isopropyl-β-d-thiogalactoside (IPTG), an induction duration of 12 h and an induction temperature of 20 ℃. The recombinant Sle was purified by nickel affinity chromatography, anion exchange chromatography, and gel filtration chromatography, and its enzymatic properties were also characterized. The optimum temperature and pH of Sle were 35 ℃ and 8.0, and more than 80% of the enzyme activity could be maintained in the range of 25-35 ℃ and pH 7.0-9.0 and Co2+ could improve the enzyme activity. Sle belongs to the dienelactone hydrolase (DLH) superfamily and possesses the typical catalytic triad of the family, and the predicted catalytic sites are S129, D175, and H207. Finally, the enzyme was identified as a BHET degrading enzyme by high performance liquid chromatography (HPLC). This study provides a new enzyme resource for the efficient enzymatic degradation of PET plastics.
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Affiliation(s)
- Jie Zhang
- School of Biological Engineering, Qilu University of Technology (Shandong Academy of Sciences), Ji'nan 250000, Shandong, China
| | - Ruida Shan
- School of Biological Engineering, Qilu University of Technology (Shandong Academy of Sciences), Ji'nan 250000, Shandong, China
| | - Xia Li
- School of Biological Engineering, Qilu University of Technology (Shandong Academy of Sciences), Ji'nan 250000, Shandong, China
- State Key Laboratory of Bio-based Materials and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Ji'nan 250000, Shandong, China
| | - Zhixiong Zeng
- School of Biological Engineering, Qilu University of Technology (Shandong Academy of Sciences), Ji'nan 250000, Shandong, China
| | - Dengyue Sun
- School of Biological Engineering, Qilu University of Technology (Shandong Academy of Sciences), Ji'nan 250000, Shandong, China
- State Key Laboratory of Bio-based Materials and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Ji'nan 250000, Shandong, China
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2
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Sun J, Han X, Song G, Gong Q, Yu W. Cloning, Expression, and Characterization of a New Glycosaminoglycan Lyase from Microbacterium sp. H14. Mar Drugs 2019; 17:md17120681. [PMID: 31810166 PMCID: PMC6950261 DOI: 10.3390/md17120681] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 12/19/2022] Open
Abstract
Glycosaminoglycan (GAG) lyase is an effective tool for the structural and functional studies of glycosaminoglycans and preparation of functional oligosaccharides. A new GAG lyase from Microbacterium sp. H14 was cloned, expressed, purified, and characterized, with a molecular weight of approximately 85.9 kDa. The deduced lyase HCLaseM belonged to the polysaccharide lyase (PL) family 8. Based on the phylogenetic tree, HCLaseM could not be classified into the existing three subfamilies of this family. HCLaseM showed almost the same enzyme activity towards hyaluronan (HA), chondroitin sulfate A (CS-A), CS-B, CS-C, and CS-D, which was different from reported GAG lyases. HCLaseM exhibited the highest activities to both HA and CS-A at its optimal temperature (35 °C) and pH (pH 7.0). HCLaseM was stable in the range of pH 5.0–8.0 and temperature below 30 °C. The enzyme activity was independent of divalent metal ions and was not obviously affected by most metal ions. HCLaseM is an endo-type enzyme yielding unsaturated disaccharides as the end products. The facilitated diffusion effect of HCLaseM is dose-dependent in animal experiments. These properties make it a candidate for further basic research and application.
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Affiliation(s)
- Junhao Sun
- School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (J.S.); (G.S.)
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao 266237, China
- Provincial Key Laboratory of Glycoscience and Glycotechnology, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Xu Han
- School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (J.S.); (G.S.)
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao 266237, China
- Provincial Key Laboratory of Glycoscience and Glycotechnology, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Guanrui Song
- School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (J.S.); (G.S.)
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao 266237, China
- Provincial Key Laboratory of Glycoscience and Glycotechnology, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Qianhong Gong
- School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (J.S.); (G.S.)
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao 266237, China
- Provincial Key Laboratory of Glycoscience and Glycotechnology, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
- Correspondence: (Q.G.); (W.Y.); Tel.: +86-532-8203-2067 (Q.G.); +86-532-8203-1680 (W.Y.)
| | - Wengong Yu
- School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China; (J.S.); (G.S.)
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao 266237, China
- Provincial Key Laboratory of Glycoscience and Glycotechnology, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
- Correspondence: (Q.G.); (W.Y.); Tel.: +86-532-8203-2067 (Q.G.); +86-532-8203-1680 (W.Y.)
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3
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Islam S, Apitius L, Jakob F, Schwaneberg U. Targeting microplastic particles in the void of diluted suspensions. Environ Int 2019; 123:428-435. [PMID: 30622067 DOI: 10.1016/j.envint.2018.12.029] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 12/10/2018] [Accepted: 12/13/2018] [Indexed: 05/22/2023]
Abstract
Accumulation of microplastic in the environment and food chain will be a grand challenge for our society. Polyurethanes are widely used synthetic polymers in medical (e.g. catheters) and industrial products (especially as foams). Polyurethane is not abundant in nature and only a few microbial strains (fungi and bacteria) and enzymes (polyurethaneases and cutinases) have been reported to efficiently degrade polyurethane. Notably, in nature a long period of time (from 50 to >100 years depending on the literature) is required for degradation of plastics. Material binding peptides (e.g. anchor peptides) bind strongly to polymers such as polypropylene, polyethylene terephthalate, and polyurethane and can target specifically polymers. In this study we report the fusion of the anchor peptide Tachystatin A2 to the bacterial cutinase Tcur1278 which accelerated the degradation of polyester-polyurethane nanoparticles by a factor of 6.6 in comparison to wild-type Tcur1278. Additionally, degradation half-lives of polyester-polyurethane nanoparticles were reduced from 41.8 h to 6.2 h (6.7-fold) in a diluted polyester-polyurethane suspension (0.04% w/v).
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Affiliation(s)
- Shohana Islam
- DWI - Leibniz-Institut für Interaktive Materialien e.V., Forckenbeckstraße 50, 52056 Aachen, Germany; Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Lina Apitius
- DWI - Leibniz-Institut für Interaktive Materialien e.V., Forckenbeckstraße 50, 52056 Aachen, Germany; Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Felix Jakob
- DWI - Leibniz-Institut für Interaktive Materialien e.V., Forckenbeckstraße 50, 52056 Aachen, Germany; Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
| | - Ulrich Schwaneberg
- DWI - Leibniz-Institut für Interaktive Materialien e.V., Forckenbeckstraße 50, 52056 Aachen, Germany; Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074 Aachen, Germany.
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4
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Wan N, Tian J, Wang H, Tian M, He Q, Ma R, Cui B, Han W, Chen Y. Identification and characterization of a highly S-enantioselective halohydrin dehalogenase from Tsukamurella sp. 1534 for kinetic resolution of halohydrins. Bioorg Chem 2018; 81:529-535. [PMID: 30245234 DOI: 10.1016/j.bioorg.2018.09.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 08/28/2018] [Accepted: 09/07/2018] [Indexed: 02/05/2023]
Abstract
Halohydrin dehalogenases are remarkable enzymes which possess promiscuous catalytic activity and serve as potential biocatalysts for the synthesis of chiral halohydrins, epoxides and β-substituted alcohols. The enzyme HheC exhibits a highly R enantioselectivity in the processes of dehalogenation of vicinal halohydrins and ring-opening of epoxides, which attracts more attentions in organic synthesis. Recently dozens of novel potential halohydrin dehalogenases have been identified by gene mining, however, most of the characterized enzymes showed low stereoselectivity. In this study, a novel halohydrin dehalogenase of HheA10 from Tsukamurella sp. 1534 has been heterologously expressed, purified and characterized. Substrate spectrum and kinetic resolution studies indicated the HheA10 was a highly S enantioselective enzyme toward several halohydrins, which produced the corresponding epoxides with the ee (enantiomeric excess) and E values up to >99% and >200 respectively. Our results revealed the HheA10 was a promising biocatalyst for the synthesis of enantiopure aromatic halohydrins and epoxides via enzymatic kinetic resolution of racemic halohydrins. What's more important, the HheA10 as the first individual halohydrin dehalogenase with the highly S enantioselectivity provides a complementary enantioselectivity to the HheC.
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Affiliation(s)
- Nanwei Wan
- Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China.
| | - Jiawei Tian
- Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China
| | - Huihui Wang
- Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China
| | - Meiting Tian
- Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China
| | - Qing He
- Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China
| | - Ran Ma
- Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China
| | - Baodong Cui
- Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China
| | - Wenyong Han
- Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China
| | - Yongzheng Chen
- Generic Drug Research Center of Guizhou Province, Green Pharmaceuticals Engineering Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China.
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Ligaba-Osena A, Hankoua B, DiMarco K, Pace R, Crocker M, McAtee J, Nagachar N, Tien M, Richard TL. Reducing biomass recalcitrance by heterologous expression of a bacterial peroxidase in tobacco (Nicotiana benthamiana). Sci Rep 2017; 7:17104. [PMID: 29213132 PMCID: PMC5719049 DOI: 10.1038/s41598-017-16909-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 10/25/2017] [Indexed: 11/13/2022] Open
Abstract
Commercial scale production of biofuels from lignocellulosic feed stocks has been hampered by the resistance of plant cell walls to enzymatic conversion, primarily owing to lignin. This study investigated whether DypB, the lignin-degrading peroxidase from Rodococcus jostii, depolymerizes lignin and reduces recalcitrance in transgenic tobacco (Nicotiana benthamiana). The protein was targeted to the cytosol or the ER using ER-targeting and retention signal peptides. For each construct, five independent transgenic lines were characterized phenotypically and genotypically. Our findings reveal that expression of DypB in the cytosol and ER does not affect plant development. ER-targeting increased protein accumulation, and extracts from transgenic leaves showed higher activity on classic peroxidase substrates than the control. Intriguingly, in situ DypB activation and subsequent saccharification released nearly 200% more fermentable sugars from transgenic lines than controls, which were not explained by variation in initial structural and non-structural carbohydrates and lignin content. Pyrolysis-GC-MS analysis showed more reduction in the level of lignin associated pyrolysates in the transgenic lines than the control primarily when the enzyme is activated prior to pyrolysis, consistent with increased lignin degradation and improved saccharification. The findings reveal for the first time that accumulation and in situ activation of a peroxidase improves biomass digestibility.
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Affiliation(s)
- Ayalew Ligaba-Osena
- College of Agriculture and Related Sciences, Delaware State University, 1200 N DuPont Highway, Dover, DE, 19901, USA
| | - Bertrand Hankoua
- College of Agriculture and Related Sciences, Delaware State University, 1200 N DuPont Highway, Dover, DE, 19901, USA.
| | - Kay DiMarco
- Agricultural and Biological Engineering, Pennsylvania State University, 111 Research Unit A, University Park, Pennsylvania, PA, 16802, USA
| | - Robert Pace
- Center for Applied Energy Research, University of Kentucky, 2540 Research Park Drive, Lexington, KY, 40511, USA
| | - Mark Crocker
- Center for Applied Energy Research, University of Kentucky, 2540 Research Park Drive, Lexington, KY, 40511, USA
| | - Jesse McAtee
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA
| | - Nivedita Nagachar
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, 305 South Frear Laboratory, University Park, Pennsylvania, PA, 16802, USA
| | - Ming Tien
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, 305 South Frear Laboratory, University Park, Pennsylvania, PA, 16802, USA
| | - Tom L Richard
- Agricultural and Biological Engineering, Pennsylvania State University, 111 Research Unit A, University Park, Pennsylvania, PA, 16802, USA
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Abstract
Expression of a cyclodipeptide synthase gene from Nocardiopsis prasina (CDPS-Np) in Escherichia coli resulted in the formation of cyclo-(l-Tyr-l-Tyr) (1) as the minor and cyclo-(l-Tyr-l-Phe) (2) as the major products. Site-directed mutagenesis revealed a strong influence on product accumulation of the amino acid residues in pocket P1. An 8-fold increase in product formation for 1 and 10-fold for 2 were detected in the double mutant T82V_Y196F compared with the wild type.
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Affiliation(s)
- Kirsten Brockmeyer
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg , Robert-Koch-Straße 4, 35037 Marburg, Germany
| | - Shu-Ming Li
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg , Robert-Koch-Straße 4, 35037 Marburg, Germany
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7
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Thapa SP, Pattathil S, Hahn MG, Jacques MA, Gilbertson RL, Coaker G. Genomic Analysis of Clavibacter michiganensis Reveals Insight Into Virulence Strategies and Genetic Diversity of a Gram-Positive Bacterial Pathogen. Mol Plant Microbe Interact 2017; 30:786-802. [PMID: 28677494 DOI: 10.1094/mpmi-06-17-0146-r] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Clavibacter michiganensis subsp. michiganensis is a gram-positive bacterial pathogen that proliferates in the xylem vessels of tomato, causing bacterial canker disease. In this study, we sequenced and assembled genomes of 11 C. michiganensis subsp. michiganensis strains isolated from infected tomato fields in California as well as five Clavibacter strains that colonize tomato endophytically but are not pathogenic in this host. The analysis of the C. michiganensis subsp. michiganensis genomes supported the monophyletic nature of this pathogen but revealed genetic diversity among strains, consistent with multiple introduction events. Two tomato endophytes that clustered phylogenetically with C. michiganensis strains capable of infecting wheat and pepper and were also able to cause disease in these plants. Plasmid profiles of the California strains were variable and supported the essential role of the pCM1-like plasmid and the CelA cellulase in virulence, whereas the absence of the pCM2-like plasmid in some pathogenic C. michiganensis subsp. michiganensis strains revealed it is not essential. A large number of secreted C. michiganensis subsp. michiganensis proteins were carbohydrate-active enzymes (CAZymes). Glycome profiling revealed that C. michiganensis subsp. michiganensis but not endophytic Clavibacter strains is able to extensively alter tomato cell-wall composition. Two secreted CAZymes found in all C. michiganensis subsp. michiganensis strains, CelA and PelA1, enhanced pathogenicity on tomato. Collectively, these results provide a deeper understanding of C. michiganensis subsp. michiganensis diversity and virulence strategies.
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Affiliation(s)
- Shree P Thapa
- 1 Department of Plant Pathology, University of California, Davis, California, U.S.A
| | - Sivakumar Pattathil
- 2 Complex Carbohydrate Research Center, The University of Georgia, Athens, Georgia, U.S.A.; and
| | - Michael G Hahn
- 2 Complex Carbohydrate Research Center, The University of Georgia, Athens, Georgia, U.S.A.; and
| | | | - Robert L Gilbertson
- 1 Department of Plant Pathology, University of California, Davis, California, U.S.A
| | - Gitta Coaker
- 1 Department of Plant Pathology, University of California, Davis, California, U.S.A
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Setter-Lamed E, Moraïs S, Stern J, Lamed R, Bayer EA. Modular Organization of the Thermobifida fusca Exoglucanase Cel6B Impacts Cellulose Hydrolysis and Designer Cellulosome Efficiency. Biotechnol J 2017; 12. [PMID: 28901714 DOI: 10.1002/biot.201700205] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 09/06/2017] [Indexed: 11/09/2022]
Abstract
Cellulose deconstruction can be achieved by three distinct enzymatic paradigms: free enzymes, multifunctional enzymes, and self-assembled, multi-enzyme complexes (cellulosomes). To study their comparative efficiency, the simple and efficient cellulolytic system of the aerobic bacterium, Thermobifida fusca, is developed as an enzymatic model. In previous studies, most of its cellulases are successfully converted to the cellulosomal mode and exhibited high cellulolytic activities, except for Cel6B, a key exoglucanase of the T. fusca enzymatic system. Here, the impact of the modular organization of Cel6B on enzymatic activity is investigated. The position of the cellulose-binding module (CBM), its family and linker segment are shown to affect activity. Surprisingly, exchange of the native family-2 CBM to family-3 generates an increase in Cel6B activity on cellulosic substrates. Conversion of Cel6B to the cellulosomal mode by fusing a cohesin to the catalytic module enables formation of divalent enzyme complexes with dockerin-bearing enzymes. The resultant pseudo-cellulosomes, containing Cel6B combined with endoglucanase Cel5A, exhibits enhanced enzymatic activity, compared to mixtures of wild-type enzymes or bifunctional enzymes, unlike similar pseudo-cellulosomes containing endoglucanase Cel6A or proccessive endoglucanase Cel9A. Insight into the different enzymatic paradigms benefits ongoing development of efficient cellulolytic systems for conversion of plant-derived biomass into valuable sugars. NOVELTY STATEMENT The protein engineering of the modular arrangement of a key exoglucanase from a highly cellulolytic bacterium, Thermobifida fusca, served to explore and compare three major enzymatic paradigms for cellulose degradation. This approach revealed highly active chimaeric forms of the exoglucanase that act in synergy together with a potent endoglucanase in bifunctional enzymes or divalent pseudo-cellulosome-like complexes. Such engineered enzymes could be further integrated into larger enzymatic complexes, thereby providing a significant step forward towards conversion of the entire T. fusca free cellulolytic system into the cellulosomal modex and the enhanced conversion of cellulosic biomass into soluble sugars.
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Affiliation(s)
- Eva Setter-Lamed
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sarah Moraïs
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Johanna Stern
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Raphael Lamed
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
| | - Edward A Bayer
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
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9
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Abstract
N-Hydroxylating monooxygenases (NMOs) are involved in siderophore biosynthesis. Siderophores are high affinity iron chelators composed of catechol and hydroxamate functional groups that are synthesized and secreted by microorganisms and plants. Recently, a new siderophore named albachelin was isolated from a culture of Amycolatopsis alba growing under iron-limiting conditions. This work focuses on the expression, purification, and characterization of the NMO, abachelin monooxygenase (AMO) from A. alba. This enzyme was purified and characterized in its holo (FAD-bound) and apo (FAD-free) forms. The apo-AMO could be reconstituted by addition of free FAD. The two forms of AMO hydroxylate ornithine, while lysine increases oxidase activity but is not hydroxylated and display low affinity for NADPH.
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Affiliation(s)
- Kendra Bufkin
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA.
| | - Pablo Sobrado
- Department of Biochemistry, Virginia Tech, Blacksburg, VA 24061, USA.
- Center for Drug Discovery, Virginia Tech, Blacksburg, VA 24061, USA.
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10
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Han J, Chen J, Shao L, Zhang J, Dong X, Liu P, Chen D. Production of the Ramoplanin Activity Analogue by Double Gene Inactivation. PLoS One 2016; 11:e0154121. [PMID: 27149627 PMCID: PMC4858212 DOI: 10.1371/journal.pone.0154121] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 04/09/2016] [Indexed: 11/19/2022] Open
Abstract
Glycopeptides such as vancomycin and telavancin are essential for treating infections caused by Gram-positive bacteria. But the dwindling availability of new antibiotics and the emergence of resistant bacteria are making effective antibiotic treatment increasingly difficult. Ramoplanin, an inhibitor of bacterial cell wall biosynthesis, is a highly effective antibiotic against a wide range of Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus, vancomycin-intermediate resistant Clostridium difficile and vancomycin-resistant Enterococcus sp. Here, two tailoring enzyme genes in the biosynthesis of ramoplanin were deleted by double in-frame gene knockouts to produce new ramoplanin derivatives. The deschlororamoplanin A2 aglycone was purified and its structure was identified with LC-MS/MS. Deschlororamoplanin A2 aglycone and ramoplanin aglycone showed similar activity to ramoplanin A2. The results showed that α-1,2-dimannosyl disaccharide at Hpg11 and chlorination at Chp17 in the ramoplanin structure are not essential for its antimicrobial activity. This work provides new precursor compounds for the semisynthetic modification of ramoplanin.
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Affiliation(s)
- Jungang Han
- State Key Laboratory of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, 1320 West Beijing Rd., Shanghai 200040, China
| | - Junsheng Chen
- State Key Laboratory of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, 1320 West Beijing Rd., Shanghai 200040, China
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dongchuan Rd., Minhang District, Shanghai 200240, China
| | - Lei Shao
- State Key Laboratory of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, 1320 West Beijing Rd., Shanghai 200040, China
- * E-mail: (DC); (LS)
| | - Junliang Zhang
- State Key Laboratory of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, 1320 West Beijing Rd., Shanghai 200040, China
| | - Xiaojing Dong
- State Key Laboratory of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, 1320 West Beijing Rd., Shanghai 200040, China
| | - Pengyu Liu
- State Key Laboratory of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, 1320 West Beijing Rd., Shanghai 200040, China
| | - Daijie Chen
- State Key Laboratory of New Drug and Pharmaceutical Process, Shanghai Institute of Pharmaceutical Industry, 1320 West Beijing Rd., Shanghai 200040, China
- * E-mail: (DC); (LS)
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Hongmin S, Liyan Y, Yuqin Z. [Recent advance in Geodermatophilaceae--A review]. Wei Sheng Wu Xue Bao 2015; 55:1521-1529. [PMID: 27101693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The family Geodermatophilaceae is a newly established actinobacterial taxon. Normand ever proposed the family Geodermatophilaceae in 1996, which was recognized as an invalid taxon at that time. In 2006, based on the common characteristics of the genera Geodermatophilus, Blastococcus and Modestobacter, Normand summarized the typical characteristics of Geodermatophilaceae, then the family Geodermatophilaceae was finally accommodated as a validly described taxon in the phylum Actinobacteria. Up to date, the family Geodermatophilaceae consisted of 3 genera, i. e., Geodermatophilus, Blastococcus and Modestobacter, including 25 validly described species. The members of the family Geodermatophilaceae were considered as biologic pioneers in extreme environments, exhibiting many potential advantages in the study of mechanism of stress resistance, desertification control and environmental remediation. The objective of this review is to summarize the research advances in the family Geodermatophilaceae, including the establishment and taxonomic characteristics of the family, as well as their application prospect and the roles in the field of ecology.
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Pagé AP, Yergeau É, Greer CW. Salix purpurea Stimulates the Expression of Specific Bacterial Xenobiotic Degradation Genes in a Soil Contaminated with Hydrocarbons. PLoS One 2015; 10:e0132062. [PMID: 26161539 PMCID: PMC4498887 DOI: 10.1371/journal.pone.0132062] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 06/09/2015] [Indexed: 12/30/2022] Open
Abstract
The objectives of this study were to uncover Salix purpurea-microbe xenobiotic degradation systems that could be harnessed in rhizoremediation, and to identify microorganisms that are likely involved in these partnerships. To do so, we tested S. purpurea's ability to stimulate the expression of 10 marker microbial oxygenase genes in a soil contaminated with hydrocarbons. In what appeared to be a detoxification rhizosphere effect, transcripts encoding for alkane 1-monooxygenases, cytochrome P450 monooxygenases, laccase/polyphenol oxidases, and biphenyl 2,3-dioxygenase small subunits were significantly more abundant in the vicinity of the plant's roots than in bulk soil. This gene expression induction is consistent with willows' known rhizoremediation capabilities, and suggests the existence of S. purpurea-microbe systems that target many organic contaminants of interest (i.e. C4-C16 alkanes, fluoranthene, anthracene, benzo(a)pyrene, biphenyl, polychlorinated biphenyls). An enhanced expression of the 4 genes was also observed within the bacterial orders Actinomycetales, Rhodospirillales, Burkholderiales, Alteromonadales, Solirubrobacterales, Caulobacterales, and Rhizobiales, which suggest that members of these taxa are active participants in the exposed partnerships. Although the expression of the other 6 marker genes did not appear to be stimulated by the plant at the community level, signs of additional systems that rest on their expression by members of the orders Solirubrobacterales, Sphingomonadales, Actinomycetales, and Sphingobacteriales were observed. Our study presents the first transcriptomics-based identification of microbes whose xenobiotic degradation activity in soil appears stimulated by a plant. It paints a portrait that contrasts with the current views on these consortia's composition, and opens the door for the development of laboratory test models geared towards the identification of root exudate characteristics that limit the efficiency of current willow-based rhizoremediation applications.
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Affiliation(s)
- Antoine P. Pagé
- Department of Natural Resource Sciences, McGill University, Montréal, Québec, Canada
- * E-mail:
| | - Étienne Yergeau
- Energy, Mining and Environment, National Research Council Canada, Montréal, Québec, Canada
| | - Charles W. Greer
- Department of Natural Resource Sciences, McGill University, Montréal, Québec, Canada
- Energy, Mining and Environment, National Research Council Canada, Montréal, Québec, Canada
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Yamada Y, Arima S, Nagamitsu T, Johmoto K, Uekusa H, Eguchi T, Shin’ya K, Cane DE, Ikeda H. Novel terpenes generated by heterologous expression of bacterial terpene synthase genes in an engineered Streptomyces host. J Antibiot (Tokyo) 2015; 68:385-94. [PMID: 25605043 PMCID: PMC4727541 DOI: 10.1038/ja.2014.171] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 11/20/2014] [Accepted: 12/12/2014] [Indexed: 11/09/2022]
Abstract
Mining of bacterial genome data has revealed numerous presumptive terpene synthases. Heterologous expression of several putative terpene synthase genes in an engineered Streptomyces host has revealed 13 newly discovered terpenes whose GC-MS and NMR data did not match with any known compounds in spectroscopic databases. Each of the genes encoding the corresponding terpene synthases were silent in their parent microorganisms. Heterologous expression and detailed NMR spectroscopic analysis allowed assignment of the structures of 13 new cyclic terpenes. Among these newly identified compounds, two were found to be linear triquinane sesquiterpenes that have never previously been isolated from bacteria or any other source. The remaining 11 new compounds were shown to be diterpene hydrocarbons and alcohol, including hydropyrene (1), hydropyrenol (2), tsukubadiene (11) and odyverdienes A (12) and B (13) each displaying a novel diterpene skeleton that had not previously been reported.
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Affiliation(s)
- Yuuki Yamada
- Kitasato Institute for Life Sciences, Kitasato University, Kitasato, Sagamihara, Kanagawa 252-0373, Japan
| | - Shiho Arima
- School of Pharmacy, Kitasato University, Shirokane, Minato-ku, Tokyo 108-8641 Japan
| | - Tohru Nagamitsu
- School of Pharmacy, Kitasato University, Shirokane, Minato-ku, Tokyo 108-8641 Japan
| | - Kohei Johmoto
- Department of Chemistry and Materials Science, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Hidehiro Uekusa
- Department of Chemistry and Materials Science, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Tadashi Eguchi
- Department of Chemistry and Materials Science, Tokyo Institute of Technology, O-okayama, Meguro-ku, Tokyo 152-8551, Japan
| | - Kazuo Shin’ya
- National Institute of Advanced Industrial Science and Technology, Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - David E. Cane
- Department of Chemistry, Box H, Brown University, Providence, RI 02912-9108, USA
| | - Haruo Ikeda
- Kitasato Institute for Life Sciences, Kitasato University, Kitasato, Sagamihara, Kanagawa 252-0373, Japan
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Kim HJ, Kim MK, Lee MJ, Won HJ, Choi SS, Kim ES. Post-PKS tailoring steps of a disaccharide-containing polyene NPP in Pseudonocardia autotrophica. PLoS One 2015; 10:e0123270. [PMID: 25849545 PMCID: PMC4388683 DOI: 10.1371/journal.pone.0123270] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 02/17/2015] [Indexed: 12/21/2022] Open
Abstract
A novel polyene compound NPP identified in a rare actinomycetes, Pseudonocardia autotrophica KCTC9441, was shown to contain an aglycone identical to nystatin but to harbor a unique di-sugar moiety, mycosaminyl-(α1-4)-N-acetyl-glucosamine, which led to higher solubility and reduced hemolytic activity. Although the nppDI was proved to be responsible for the transfer of first polyene sugar, mycosamine in NPP biosynthesis, the gene responsible for the second sugar extending glycosyltransferase (GT) as well as NPP post-PKS tailoring mechanism remained unknown. Here, we identified a NPP-specific second sugar extending GT gene named nppY, located at the edge of the NPP biosynthetic gene cluster. Targeted nppY gene deletion and its complementation proved that nppY is indeed responsible for the transfer of second sugar, N-acetyl-glucosamine in NPP biosynthesis. Site-directed mutagenesis on nppY also revealed several amino acid residues critical for NppY GT function. Moreover, a combination of deletions and complementations of two GT genes (nppDI and nppY) and one P450 hydroxylase gene (nppL) involved in the NPP post-PKS biosynthesis revealed that NPP aglycone is sequentially modified by the two different GTs encoded by nppDI and nppY, respectively, followed by the nppL-driven regio-specific hydroxylation at the NPP C10 position. These results set the stage for the biotechnological application of sugar diversification for the biosynthesis of novel polyene compounds in actinomycetes.
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Affiliation(s)
- Hye-Jin Kim
- Department of Biological Engineering, Inha University, Incheon, Korea
| | - Min-Kyung Kim
- Department of Biological Engineering, Inha University, Incheon, Korea
| | - Mi-Jin Lee
- Department of Biological Engineering, Inha University, Incheon, Korea
| | - Hyung-Jin Won
- Department of Biological Engineering, Inha University, Incheon, Korea
| | - Si-Sun Choi
- Department of Biological Engineering, Inha University, Incheon, Korea
| | - Eung-Soo Kim
- Department of Biological Engineering, Inha University, Incheon, Korea
- * E-mail:
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Ban JG, Woo MW, Lee BR, Lee MJ, Choi SS, Kim ES. A novel regio‑specific cyclosporin hydroxylase gene revealed through the genome mining of Pseudonocardia autotrophica. J Ind Microbiol Biotechnol 2014; 41:879-86. [PMID: 24659179 DOI: 10.1007/s10295-014-1432-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 02/26/2014] [Indexed: 11/24/2022]
Abstract
The regio-specific hydroxylation at the 4th N-methyl leucine of the immunosuppressive agent cyclosporin A (CsA) was previously proposed to be mediated by a unique cytochrome P450 hydroxylase (CYP), CYP-sb21 from the rare actinomycetes Sebekia benihana. Interestingly, a different rare actinomycetes species, Pseudonocardia autotrophica, was found to possess a different regio-selectivity, the preferential hydroxylation at the 9th N-methyl leucine of CsA. Through an in silico analysis of the whole genome of P. autotrophica, we describe here the classification of 31 total CYPs in P. autotrophica. Three putative CsA CYP genes, showing the highest sequence homologies with CYPsb21, were successfully inactivated using PCR-targeted gene disruption. Only one knock-out mutant, ΔCYP-pa1, failed to convert CsA to its hydroxylated forms. The hydroxylation activity of CsA by CYP-pa1 was confirmed by CYP-pa1 gene complementation as well as heterologous expression in the CsA non-hydroxylating Streptomyces coelicolor. Moreover, the cyclosporine regio-selectivity of CYP-pa1 expressed in the ΔCYP-sb21 S. benihana mutant strain was also confirmed unchanged through cross complementation. These results show that preferential regio-specific hydroxylation at the 9th N-methyl leucine of CsA is carried out by a specific P450 hydroxylase gene in P. autotrophica, CYP-pa1, setting the stage for the biotechnological application of CsA regioselective hydroxylation.
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Kenny AJ, Wolt JD. Activity and ecological implications of maize-expressed transgenic endo-1,4-β-D-glucanase in agricultural soils. Environ Toxicol Chem 2014; 33:1996-2003. [PMID: 24863456 DOI: 10.1002/etc.2645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Revised: 05/14/2014] [Accepted: 05/23/2014] [Indexed: 06/03/2023]
Abstract
Plant expression of thermostable endoglucanase (E1) has been proposed for improved conversion of lignocellulose to ethanol for fuel production. Residues of E1-expressing maize may affect ecological services (e.g., C mineralization and biogeochemical cycling) on soils where they occur. Therefore, the activity of residual E1 was investigated using soils amended with bacterial and plant-solubilized E1 compared with soil endogenous activity and residual activity from a mesostable cellulase (Aspergillus and Trichoderma spp.). An optimized analytical method involving a carboxymethyl cellulose substrate and dinitrosalicylic acid detection effectively assayed endoglucanase activity in amended and unamended soils and was used for determining E1 activity in 3 representative soils. The effect of E1 on soil carbon mineralization was determined by comparing CO(2) evolution from soils amended with transgenic E1-expressing and wild-type maize tissue. Extraction and recovery of the mesostable comparator, bacterial E1, and plant-soluble E1 showed nearly complete loss of exogenous endoglucanase activity within a 24-h period. Carbon mineralization indicated no significant difference between soils amended with either the transgenic E1 or wild-type maize tissue. These results indicate that maize residues expressing up to 30 µg E1/g tissue negligibly affect soil endoglucanase activity and CO(2) respiration for representative soils where transgenic E1 maize may be grown.
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Affiliation(s)
- Adam J Kenny
- Department of Agronomy, Iowa State University, Ames, Iowa, United States
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Du J, Cui CH, Park SC, Kim JK, Yu HS, Jin FX, Sun C, Kim SC, Im WT. Identification and characterization of a ginsenoside-transforming β-glucosidase from Pseudonocardia sp. Gsoil 1536 and its application for enhanced production of minor ginsenoside Rg2(S). PLoS One 2014; 9:e96914. [PMID: 24911166 PMCID: PMC4049585 DOI: 10.1371/journal.pone.0096914] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 04/14/2014] [Indexed: 11/25/2022] Open
Abstract
The ginsenoside Rg2(S), which is one of the pharmaceutical components of ginseng, is known to have neuroprotective, anti-inflammation, and anti-diabetic effects. However, the usage of ginsenoside Rg2(S) is restricted owing to the small amounts found in white and red ginseng. To enhance the production of ginsenoside Rg2(S) as a 100 gram unit with high specificity, yield, and purity, an enzymatic bioconversion method was developed to adopt the recombinant glycoside hydrolase (BglPC28), which is a ginsenoside-transforming recombinant β-glucosidase from Pseudonocardia sp. strain Gsoil 1536. The gene, termed bglPC28, encoding β-glucosidase (BglPC28) belonging to the glycoside hydrolase family 3 was cloned. bglPC28 consists of 2,232 bp (743 amino acid residues) with a predicted molecular mass of 78,975 Da. This enzyme was overexpressed in Escherichia coli BL21(DE3) using a GST-fused pGEX 4T-1 vector system. The optimum conditions of the recombinant BglPC28 were pH 7.0 and 37°C. BglPC28 can effectively transform the ginsenoside Re to Rg2(S); the Km values of PNPG and Re were 6.36±1.10 and 1.42±0.13 mM, respectively, and the Vmax values were 40.0±2.55 and 5.62±0.21 µmol min−1 mg−1 of protein, respectively. A scaled-up biotransformation reaction was performed in a 10 L jar fermenter at pH 7.0 and 30°C for 12 hours with a concentration of 20 mg/ml of ginsenoside Re from American ginseng roots. Finally, 113 g of Rg2(S) was produced from 150 g of Re with 84.0±1.1% chromatographic purity. These results suggest that this enzymatic method could be usefully exploited in the preparation of ginsenoside Rg2(S) in the cosmetics, functional food, and pharmaceutical industries.
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Affiliation(s)
- Juan Du
- KAIST Institute for Biocentury, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon, Republic of Korea
- College of Biotechnology, Dalian Polytechnic University, Ganjingzi-qu, Dalian, P. R. China
| | - Chang-Hao Cui
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon, Republic of Korea
| | - Sung Chul Park
- Intelligent Synthetic Biology Center, Yuseong-gu, Daejeon, Republic of Korea
| | - Jin-Kwang Kim
- KAIST Institute for Biocentury, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon, Republic of Korea
| | - Hong-Shan Yu
- College of Biotechnology, Dalian Polytechnic University, Ganjingzi-qu, Dalian, P. R. China
| | - Feng-Xie Jin
- College of Biotechnology, Dalian Polytechnic University, Ganjingzi-qu, Dalian, P. R. China
| | - Changkai Sun
- Institute for Brain Disorders, Dalian Medical University, Dalian, P.R. China
| | - Sun-Chang Kim
- KAIST Institute for Biocentury, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon, Republic of Korea
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon, Republic of Korea
- Intelligent Synthetic Biology Center, Yuseong-gu, Daejeon, Republic of Korea
| | - Wan-Taek Im
- Department of Biotechnology, Hankyoung National University, Chungang-no Anseong-si, Republic of Korea
- * E-mail:
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Walia A, Mehta P, Chauhan A, Kulshrestha S, Shirkot CK. Purification and characterization of cellulase-free low molecular weight endo β-1,4 xylanase from an alkalophilic Cellulosimicrobium cellulans CKMX1 isolated from mushroom compost. World J Microbiol Biotechnol 2014; 30:2597-608. [PMID: 24908422 DOI: 10.1007/s11274-014-1683-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Accepted: 06/02/2014] [Indexed: 11/26/2022]
Abstract
Alkalophilic Cellulosimicrobium cellulans CKMX1 isolated from mushroom compost is first report on actinomycetes that has the ability to produce thermostable cellulase-free xylanase, which is an important industrial enzyme used in the pulp and paper industry. Strain CKMX1 was characterized by metabolic fingerprinting, whole-cell fatty acids methyl ester analysis and 16Sr DNA and found to be C. cellulans CKMX1.The enzyme was purified by gel permeation and anion exchange chromatography and had a molecular mass of 29 kDa. Xylanase activity was optimum at pH 8.0 and 55 °C. The enzyme was somewhat thermostable, retaining 50 % of the original activity after incubation at 50 °C for 30 min. The xylanase had K m and V max values of 2.64 mg/ml and 2,000 µmol/min/mg protein in oat spelt xylan, respectively. All metal ions except HgCl2, CoCl2 as well as CdCl2 were well tolerated and did not adversely affect xylanase activity. The deduced internal amino acid sequence of C. cellulans CKMX1 xylanase by matrix assisted laser desorption ionization-time of flight mass spectrometry resembled the sequence of β-1,4-endoxylanase, which is a member of glycoside hydrolase family 11. Some of the novel characteristics that make this enzyme potentially effective in xylan biodegradation could be useful for pulp and paper biobleaching are discussed in this manuscript.
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Affiliation(s)
- Abhishek Walia
- Department of Basic Sciences (Microbiology Section), Dr. Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan, 173230, H.P., India,
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Nadar SV, Yoshinaga M, Kandavelu P, Sankaran B, Rosen BP. Crystallization and preliminary X-ray crystallographic studies of the ArsI C-As lyase from Thermomonospora curvata. Acta Crystallogr F Struct Biol Commun 2014; 70:761-4. [PMID: 24915088 PMCID: PMC4051532 DOI: 10.1107/s2053230x14008814] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 04/17/2014] [Indexed: 11/10/2022] Open
Abstract
Arsenic is a ubiquitous and carcinogenic environmental element that enters the biosphere primarily from geochemical sources, but also through anthropogenic activities. Microorganisms play an important role in the arsenic biogeochemical cycle by biotransformation of inorganic arsenic into organic arsenicals and vice versa. ArsI is a microbial nonheme ferrous-dependent dioxygenase that transforms toxic methylarsonous acid to the less toxic inorganic arsenite by C-As bond cleavage. An ArsI ortholog from the thermophilic bacterium Thermomonospora curvata was expressed, purified and crystallized. The crystals diffracted to 1.46 Å resolution and belonged to space group P4₃2₁2 or its enantiomer P4₁2₁2, with unit-cell parameters a=b=42.2, c=118.5 Å.
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Affiliation(s)
- S. Venkadesh Nadar
- Department of Cellular Biology and Pharmacology, Florida International University, Herbert Wertheim College of Medicine, Miami, FL 33199, USA
| | - Masafumi Yoshinaga
- Department of Cellular Biology and Pharmacology, Florida International University, Herbert Wertheim College of Medicine, Miami, FL 33199, USA
| | - Palani Kandavelu
- SER-CAT and the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Banumathi Sankaran
- Berkeley Center for Structural Biology, Lawrence Berkeley Laboratory, Berkeley, CA 94720, USA
| | - Barry P. Rosen
- Department of Cellular Biology and Pharmacology, Florida International University, Herbert Wertheim College of Medicine, Miami, FL 33199, USA
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Kingsbury NJ, McDonald KA. Quantitative evaluation of E1 endoglucanase recovery from tobacco leaves using the vacuum infiltration-centrifugation method. Biomed Res Int 2014; 2014:483596. [PMID: 24971334 PMCID: PMC4058203 DOI: 10.1155/2014/483596] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 04/04/2014] [Accepted: 04/29/2014] [Indexed: 01/23/2023]
Abstract
As a production platform for recombinant proteins, plant leaf tissue has many advantages, but commercialization of this technology has been hindered by high recovery and purification costs. Vacuum infiltration-centrifugation (VI-C) is a technique to obtain extracellularly-targeted products from the apoplast wash fluid (AWF). Because of its selective recovery of secreted proteins without homogenizing the whole tissue, VI-C can potentially reduce downstream production costs. Lab scale experiments were conducted to quantitatively evaluate the VI-C method and compared to homogenization techniques in terms of product purity, concentration, and other desirable characteristics. From agroinfiltrated Nicotiana benthamiana leaves, up to 81% of a truncated version of E1 endoglucanase from Acidothermus cellulolyticus was recovered with VI-C versus homogenate extraction, and average purity and concentration increases of 4.2-fold and 3.1-fold, respectively, were observed. Formulas were developed to predict recovery yields of secreted protein obtained by performing multiple rounds of VI-C on the same leaf tissue. From this, it was determined that three rounds of VI-C recovered 97% of the total active recombinant protein accessible to the VI-C procedure. The results suggest that AWF recovery is an efficient process that could reduce downstream processing steps and costs for plant-made recombinant proteins.
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Affiliation(s)
- Nathaniel J. Kingsbury
- Department of Chemical Engineering and Materials Science, University of California at Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Karen A. McDonald
- Department of Chemical Engineering and Materials Science, University of California at Davis, 1 Shields Avenue, Davis, CA 95616, USA
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Abstract
A bacterium, identified as Microbacterium liquefaciens MIM-CG-9535-I, was isolated from a soil sample taken from the industrial site of a gelatin manufacturer. A new type of protease, which restrictively decomposes gelatin at one or two positions, was purified from the bacterial culture. The molecular mass of the purified enzyme was 21 kDa by SDS-polyacrylamide gel electrophoresis. The purified enzyme specifically degraded the alpha-chain of gelatin with a molecular weight of 100 kDa into two peptides of 60 kDa and 40 kDa. Native collagen was not a substrate for the enzyme.
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Alahuhta M, Adney WS, Himmel ME, Lunin VV. Structure of Acidothermus cellulolyticus family 74 glycoside hydrolase at 1.82 Å resolution. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1335-8. [PMID: 24316824 PMCID: PMC3855714 DOI: 10.1107/s1744309113030005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 11/01/2013] [Indexed: 11/11/2022]
Abstract
Here, a 1.82 Å resolution X-ray structure of a glycoside hydrolase family 74 (GH74) enzyme from Acidothermus cellulolyticus is reported. The resulting structure was refined to an R factor of 0.150 and an Rfree of 0.196. Structural analysis shows that five related structures have been reported with a secondary-structure similarity of between 75 and 89%. The five similar structures were all either Clostridium thermocellum or Geotrichum sp. M128 GH74 xyloglucanases. Structural analysis indicates that the A. cellulolyticus GH74 enzyme is an endoxyloglucanase, as it lacks a characteristic loop that blocks one end of the active site in exoxyloglucanases. Superimposition with the C. thermocellum GH74 shows that Asp451 and Asp38 are the catalytic residues.
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Affiliation(s)
- Markus Alahuhta
- BioSciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - William S. Adney
- BioSciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Michael E. Himmel
- BioSciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Vladimir V. Lunin
- BioSciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
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Kim EJ, Fathoni A, Jeong GT, Jeong HD, Nam TJ, Kong IS, Kim JK. Microbacterium oxydans, a novel alginate- and laminarin-degrading bacterium for the reutilization of brown-seaweed waste. J Environ Manage 2013; 130:153-159. [PMID: 24076515 DOI: 10.1016/j.jenvman.2013.08.064] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Revised: 08/25/2013] [Accepted: 08/31/2013] [Indexed: 06/02/2023]
Abstract
There is a growing demand for the efficient treatment of seaweed waste. We identified six bacterial strains from the marine environment for the reutilization of brown-seaweed waste, and the most potentially useful strain, Microbacterium oxydans, was chosen and further investigated. Plate assays indicated that this bacterial isolate possessed both alginate lyase and laminarinase activities. The optimal inoculum size, pH, temperature and substrate concentration for the degradation of brown-seaweed polysaccharides by the isolate were as follows: 20% (v v(-1)), pH 6.0, 37 °C, and 5 g L(-1) for alginate and 20% (v v(-1)), pH 6.0, 30 °C, and 10 g L(-1) for laminarin, respectively. During 6 d in culture under the optimal conditions, the isolate produced 0.17 g L(-1) of reducing sugars from alginate with 11.0 U mL(-1) of maximal alginate lyase activity, and 5.11 and 2.88 g L(-1) of reducing sugars and glucose from laminarin, respectively. In particular, a fair amount of laminarin was degraded to glucose (28.8%) due to the isolate's exolytic laminarinase activity. As a result, the reutilization of brown-seaweed waste by this isolate appears to be possible for the production of reducing sugars as a valuable resource. This is the first study to directly demonstrate the ability of M. oxydans to degrade both alginate and laminarin.
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Affiliation(s)
- Eun Jung Kim
- Department of Biotechnology, Pukyong National University, Busan 608-737, Republic of Korea
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Jacquiod S, Franqueville L, Cécillon S, M. Vogel T, Simonet P. Soil bacterial community shifts after chitin enrichment: an integrative metagenomic approach. PLoS One 2013; 8:e79699. [PMID: 24278158 PMCID: PMC3835784 DOI: 10.1371/journal.pone.0079699] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 09/25/2013] [Indexed: 11/19/2022] Open
Abstract
Chitin is the second most produced biopolymer on Earth after cellulose. Chitin degrading enzymes are promising but untapped sources for developing novel industrial biocatalysts. Hidden amongst uncultivated micro-organisms, new bacterial enzymes can be discovered and exploited by metagenomic approaches through extensive cloning and screening. Enrichment is also a well-known strategy, as it allows selection of organisms adapted to feed on a specific compound. In this study, we investigated how the soil bacterial community responded to chitin enrichment in a microcosm experiment. An integrative metagenomic approach coupling phylochips and high throughput shotgun pyrosequencing was established in order to assess the taxonomical and functional changes in the soil bacterial community. Results indicate that chitin enrichment leads to an increase of Actinobacteria, γ-proteobacteria and β-proteobacteria suggesting specific selection of chitin degrading bacteria belonging to these classes. Part of enriched bacterial genera were not yet reported to be involved in chitin degradation, like the members from the Micrococcineae sub-order (Actinobacteria). An increase of the observed bacterial diversity was noticed, with detection of specific genera only in chitin treated conditions. The relative proportion of metagenomic sequences related to chitin degradation was significantly increased, even if it represents only a tiny fraction of the sequence diversity found in a soil metagenome.
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Affiliation(s)
- Samuel Jacquiod
- Environmental Microbial Genomics Group, Ecole Centrale de Lyon, Laboratoire Ampère UMR5005 CNRS, Ecully, France
- Microbial Molecular Ecology Group, Section of Microbiology, København Universitat, København, Denmark
| | - Laure Franqueville
- Environmental Microbial Genomics Group, Ecole Centrale de Lyon, Laboratoire Ampère UMR5005 CNRS, Ecully, France
| | - Sébastien Cécillon
- Environmental Microbial Genomics Group, Ecole Centrale de Lyon, Laboratoire Ampère UMR5005 CNRS, Ecully, France
| | - Timothy M. Vogel
- Environmental Microbial Genomics Group, Ecole Centrale de Lyon, Laboratoire Ampère UMR5005 CNRS, Ecully, France
| | - Pascal Simonet
- Environmental Microbial Genomics Group, Ecole Centrale de Lyon, Laboratoire Ampère UMR5005 CNRS, Ecully, France
- * E-mail:
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Huo X, Zhuge B, Fang H, Zong H, Song J, Zhuge J. [Cloning and application of a novel hydroxylase in lovastatin conversion]. Sheng Wu Gong Cheng Xue Bao 2013; 29:1590-1598. [PMID: 24701824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Wuxistatin, a novel and potent statin, is converted from lovastatin by Amycolatopsis sp. CGMCC1149. In the bioconversion, lovastatin is firstly hydroxylated by a hydroxylase. To obtain the critical hydroxylase, a novel hydroxylase gene was isolated from Amycolatopsis sp. CGMCC1149 by Degenerate PCR and Self-Formed Adaptor PCR and expressed in Escherichia coli. BLAST sequence analysis revealed that the gene belonged to cytochrome P450 gene superfamily and could encode a 403-amino-acid protein with a molecular weight of 44.8 kDa. The secondary structure prediction result showed that this protein contained many typical functional regions of P450, such as oxygen binding site, ion-pair region and heme binding region. Meanwhile, a catalytic function verification system was constructed by NADH, ferredoxin and ferredoxin reductase which could catalyze lovastatin hydroxylation into the target product. These would be helpful for further studies in large-scale production of wuxistatin.
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Habbeche A, Saoudi B, Jaouadi B, Haberra S, Kerouaz B, Boudelaa M, Badis A, Ladjama A. Purification and biochemical characterization of a detergent-stable keratinase from a newly thermophilic actinomycete Actinomadura keratinilytica strain Cpt29 isolated from poultry compost. J Biosci Bioeng 2013; 117:413-21. [PMID: 24140106 DOI: 10.1016/j.jbiosc.2013.09.006] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 09/10/2013] [Accepted: 09/11/2013] [Indexed: 11/20/2022]
Abstract
An extracellular thermostable keratinase (KERAK-29) was purified and biochemically characterized from a thermophilic actinomycete Actinomadura keratinilytica strain Cpt29 newly isolated from Algerian poultry compost. The isolate exhibited high keratinase production when grown in chicken feather meal media (24,000 U/ml). Based on matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF/MS) analysis, the purified enzyme is a monomer with a molecular mass of 29,233.10-Da. The data revealed that the 25 N-terminal residue sequence displayed by KERAK-29 was TQADPPSWGLNNIDRQTAFTKATSI, which showed high homology with those of Streptomyces proteases. This keratinase was completely inhibited by phenylmethanesulfonyl fluoride (PMSF) and diiodopropyl fluorophosphates (DFP), which suggests that it belongs to the serine protease family. Using keratin azure as a substrate, the optimum pH and temperature values for keratinase activity were pH 10 and 70°C, respectively. KERAK-29 was stable between 20 and 60°C and pH 3 and 10 for 5 and 120 h, respectively, and its thermoactivity and thermostability were enhanced in the presence of 5 mM Mn(2+). Its catalytic efficiency was higher than that of the KERAB keratinase from Streptomyces sp. strain AB1. KERAK-29 was also noted to show high keratinolytic activity and significant stability in the presence of detergents, which made it able to accomplish the entire feather-biodegradation process on its own. The ability of the A. keratinilytica strain Cpt29 to grow and produce substantial levels of keratinase using feather as a substrate could open new promising opportunities for the valorization of keratin-containing wastes and reduction of its impacts on the environment.
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Affiliation(s)
- Amina Habbeche
- Laboratory of Applied Biochemistry and Microbiology (LABM), Faculty of Science of Annaba (FSA), Badji Mokhtar-Annaba University, P.O. Box 12, 23000 Annaba, Algeria
| | - Boudjema Saoudi
- Laboratory of Applied Biochemistry and Microbiology (LABM), Faculty of Science of Annaba (FSA), Badji Mokhtar-Annaba University, P.O. Box 12, 23000 Annaba, Algeria
| | - Bassem Jaouadi
- Laboratory of Microorganisms and Biomolecules (LMB), Centre of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, Sfax 3018, Tunisia
| | - Soumaya Haberra
- Laboratory of Applied Biochemistry and Microbiology (LABM), Faculty of Science of Annaba (FSA), Badji Mokhtar-Annaba University, P.O. Box 12, 23000 Annaba, Algeria
| | - Bilal Kerouaz
- Laboratory of Applied Biochemistry and Microbiology (LABM), Faculty of Science of Annaba (FSA), Badji Mokhtar-Annaba University, P.O. Box 12, 23000 Annaba, Algeria
| | - Mokhtar Boudelaa
- Laboratory of Applied Biochemistry and Microbiology (LABM), Faculty of Science of Annaba (FSA), Badji Mokhtar-Annaba University, P.O. Box 12, 23000 Annaba, Algeria
| | - Abdelmalek Badis
- Laboratory of Natural Products Chemistry and Biomolecules (LNPCB), University of Saàd Dahlab (USD) of Blida, P.O. Box 270, 09000 Blida, Algeria
| | - Ali Ladjama
- Laboratory of Applied Biochemistry and Microbiology (LABM), Faculty of Science of Annaba (FSA), Badji Mokhtar-Annaba University, P.O. Box 12, 23000 Annaba, Algeria.
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Zhang D, Li W, Huang X, Qin W, Liu M. Removal of ammonium in surface water at low temperature by a newly isolated Microbacterium sp. strain SFA13. Bioresour Technol 2013; 137:147-152. [PMID: 23584414 DOI: 10.1016/j.biortech.2013.03.094] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 03/09/2013] [Accepted: 03/13/2013] [Indexed: 06/02/2023]
Abstract
The strain SFA13, isolated from Songhua River, demonstrates ability to convert ammonium to nitrogen under aerobic conditions at low temperature. On the basis of 16S rRNA gene sequence, the strain SFA13 was a species in genera Microbacterium. The isolate showed unusual ability of autotrophic nitrification with the ratio of 0.11 mg NH4(+)-N/L/h at 5°C. Ammonium was consumed by the strain SFA13 with the biodegradation of organic carbon and without nitrite or nitrate accumulation. NO3(-)-N or NO2(-)-N was reduced by the strain SFA13. The denitrification ratio was 0.24mgNO3(-)-N/L/h. Hydroxylamine oxidase, nitrite reductase and nitrate reductase were detectable. The putative nitrogen removal process by the strain SFA13 was as follows: NH4(+)→NH2OH→NO2(-)→NO3(-), then NO3(-)→NO2(-)→N2. Biological activated carbon attached with the strain SFA13 could effectively remove ammonium in surface water with the rate of 2.68±0.27-3.16±0.25 mg NH4(+)-N/L/h at C/N 2-10, temperature 10°C, and DO>5.2 mg/L.
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Affiliation(s)
- Duoying Zhang
- School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090, PR China
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Quan LH, Wang C, Jin Y, Wang TR, Kim YJ, Yang DC. Isolation and characterization of novel ginsenoside-hydrolyzing glycosidase from Microbacterium esteraromaticum that transforms ginsenoside Rb2 to rare ginsenoside 20(S)-Rg3. Antonie Van Leeuwenhoek 2013; 104:129-37. [PMID: 23670791 DOI: 10.1007/s10482-013-9933-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 05/03/2013] [Indexed: 11/27/2022]
Abstract
Ginsenoside Rb2 was transformed by recombinant glycosidase (Bgp2) into ginsenosides Rd and 20(S)-Rg3. The bgp2 gene consists of 2,430 bp that encode 809 amino acids, and this gene has homology to the glycosyl hydrolase family 2 protein domain. SDS-PAGE was used to determine that the molecular mass of purified Bgp2 was 87 kDa. Using 0.1 mg ml(-1) of enzyme in 20 mM sodium phosphate buffer at 40 °C and pH 7.0, 1.0 mg ml(-1) ginsenoside Rb2 was transformed into 0.47 mg ml(-1) ginsenoside 20(S)-Rg3 within 120 min, with a corresponding molar conversion yield of 65 %. Bgp2 hydrolyzed the ginsenoside Rb2 along the following pathway: Rb2 → Rd → 20(S)-Rg3. This is the first report of the biotransformation of ginsenoside Rb2 to ginsenoside 20(S)-Rg3 using the recombinant glycosidase.
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Affiliation(s)
- Lin-Hu Quan
- Department of Oriental Medicinal Material and Processing, College of Life Science, Kyung-Hee University, Seocheon-dong, Giheung-gu, Yongin-si, Gyeonggi-do, 446-701, Republic of Korea.
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29
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Dutta A, Flores M, Roy S, Schmitt JC, Hamilton GA, Hartnett HE, Shearer J, Jones AK. Sequential oxidations of thiolates and the cobalt metallocenter in a synthetic metallopeptide: implications for the biosynthesis of nitrile hydratase. Inorg Chem 2013; 52:5236-45. [PMID: 23587023 PMCID: PMC4046696 DOI: 10.1021/ic400171z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cobalt nitrile hydratases (Co-NHase) contain a catalytic cobalt(III) ion coordinated in an N2S3 first coordination sphere composed of two amidate nitrogens and three cysteine-derived sulfur donors: a thiolate (-SR), a sulfenate (-S(R)O(-)), and a sulfinate (-S(R)O2(-)). The sequence of biosynthetic reactions that leads to the post-translational oxidations of the metal and the sulfur ligands is unknown, but the process is believed to be initiated directly by oxygen. Herein we utilize cobalt bound in an N2S2 first coordination sphere by a seven amino acid peptide known as SODA (ACDLPCG) to model this oxidation process. Upon exposure to oxygen, Co-SODA is oxidized in two steps. In the first fast step (seconds), magnetic susceptibility measurements demonstrated that the metallocenter remains paramagnetic, that is, Co(2+), and sulfur K-edge X-ray absorption spectroscopy (XAS) is used to show that one of the thiolates is oxidized to sulfinate. In a second process on a longer time scale (hours), magnetic susceptibility measurements and Co K-edge XAS show that the metal is oxidized to Co(3+). Unlike other model complexes, additional slow oxidation of the second thiolate in Co-SODA is not observed, and a catalytically active complex is never formed. The likely reason is the absence of the axial thiolate ligand. In essence, the reactivity of Co-SODA can be described as between previously described models which either quickly convert to final product or are stable in air, and it offers a first glimpse into a possible oxidation pathway for nitrile hydratase biosynthesis.
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Affiliation(s)
- Arnab Dutta
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287
- Center for Bio-Inspired Solar Fuel Production, Arizona State University, Tempe, AZ 85287
| | - Marco Flores
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287
| | - Souvik Roy
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287
- Center for Bio-Inspired Solar Fuel Production, Arizona State University, Tempe, AZ 85287
| | | | | | - Hilairy E. Hartnett
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287
- School of Earth and Space Exploration; Arizona State University, Tempe, AZ 85287
| | - Jason Shearer
- Department of Chemistry, University of Nevada, Reno, Nevada 89557
| | - Anne K. Jones
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287
- Center for Bio-Inspired Solar Fuel Production, Arizona State University, Tempe, AZ 85287
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Abstract
Unusual deoxysugars found appended to natural products often provide or enhance the pharmacokinetic activities of the parent compound. The preferred carbohydrate donors for the biosynthesis of such glycosylated natural products are the dTDP-linked sugars. Many of the biologically relevant dTDP-deoxysugars are constructed around the 2,6-dideoxyhexoses or the 2,3(4),6-trideoxyhexoses. A key step in the biosynthesis of these sugars is the removal of the hexose C-2' hydroxyl group and the oxidation of the C-3' hydroxyl group to a carbonyl moiety. Enzymes that catalyze these reactions are referred to as 2,3-dehydratases and have been, for the most part, largely uncharacterized. Here we report the first structural analysis of a sugar 2,3-dehydratase. For this investigation, the enzyme, EvaA, was cloned from Amycolatopsis orientalis, and the structure was solved and refined to a nominal resolution of 1.7 Å. On the basis of the resulting model, it is clear that EvaA belongs to the large Nudix hydrolase superfamily and is most similar to GDP-mannose hydrolase. Each subunit of the EvaA dimer folds into two domains that clearly arose via gene duplication. Two dTDP-sugar binding pockets, A and B, are present in each EvaA subunit. On the basis of site-directed mutagenesis experiments and activity assays, it appears that pocket A functions as the active site and pocket B is simply a remnant left behind from the gene duplication event. As 2,3-dehydration is crucial for the biosynthesis of many unusual deoxysugars, this investigation provides key structural insight into this widely conserved reaction.
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Affiliation(s)
- Rachel L Kubiak
- Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
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Zervosen A, Zapun A, Frère JM. Inhibition of Streptococcus pneumoniae penicillin-binding protein 2x and Actinomadura R39 DD-peptidase activities by ceftaroline. Antimicrob Agents Chemother 2013; 57:661-3. [PMID: 23147739 PMCID: PMC3535952 DOI: 10.1128/aac.01593-12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 11/04/2012] [Indexed: 11/20/2022] Open
Abstract
Although the rate of acylation of a penicillin-resistant form of Streptococcus pneumoniae penicillin-binding protein 2x (PBP2x) by ceftaroline is 80-fold lower than that of its penicillin-sensitive counterpart, it remains sufficiently high (k(2)/K = 12,600 M(-1) s(-1)) to explain the sensitivity of the penicillin-resistant strain to this new cephalosporin. Surprisingly, the Actinomadura R39 DD-peptidase is not very sensitive to ceftaroline.
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Affiliation(s)
- Astrid Zervosen
- Centre de Recherches du Cyclotron, Université de Liège, Sart-Tilman, Liège, Belgium.
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Menon V, Rao M. Inhibition of xyloglucanase from an alkalothermophilic Thermomonospora sp. by a peptidic aspartic protease inhibitor from Penicillium sp. VM24. Bioresour Technol 2012; 123:390-399. [PMID: 22940347 DOI: 10.1016/j.biortech.2012.07.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 07/14/2012] [Accepted: 07/16/2012] [Indexed: 06/01/2023]
Abstract
A bifunctional inhibitor from Penicillium sp VM24 causing inactivation of xyloglucanase from Thermomonospora sp and an aspartic protease from Aspergillus saitoi was identified. Steady state kinetics studies of xyloglucanase and the inhibitor revealed an irreversible, non-competitive, two-step inhibition mechanism with IC(50) and K(i) values of 780 and 500nM respectively. The interaction of o-phthalaldehyde (OPTA)-labeled xyloglucanase with the inhibitor revealed that the inhibitor binds to the active site of the enzyme. Far- and near-UV spectrophotometric analysis suggests that the conformational changes induced in xyloglucanase by the inhibitor may be due to irreversible denaturation of enzyme. The bifunctional inhibitor may have potential as a biocontrol agent for the protection of plants against phytopathogenic fungi.
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Affiliation(s)
- Vishnu Menon
- Division of Biochemical Sciences, National Chemical Laboratory, Pune 411 008, India
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Isotani K, Kurokawa J, Itoh N. Production of (R)-3-quinuclidinol by E. coli biocatalysts possessing NADH-dependent 3-quinuclidinone reductase (QNR or bacC) from Microbacterium luteolum and Leifsonia alcohol dehydrogenase (LSADH). Int J Mol Sci 2012. [PMID: 23202966 PMCID: PMC3497340 DOI: 10.3390/ijms131013542] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
We found two NADH-dependent reductases (QNR and bacC) in Microbacterium luteolum JCM 9174 (M. luteolum JCM 9174) that can reduce 3-quinuclidinone to optically pure (R)-(−)-3-quinuclidinol. Alcohol dehydrogenase from Leifsonia sp. (LSADH) was combined with these reductases to regenerate NAD+ to NADH in situ in the presence of 2-propanol as a hydrogen donor. The reductase and LSADH genes were efficiently expressed in E. coli cells. A number of constructed E. coli biocatalysts (intact or immobilized) were applied to the resting cell reaction and optimized. Under the optimized conditions, (R)-(−)-3-quinuclidinol was synthesized from 3-quinuclidinone (15% w/v, 939 mM) giving a conversion yield of 100% for immobilized QNR. The optical purity of the (R)-(−)-3-quinuclidinol produced by the enzymatic reactions was >99.9%. Thus, E. coli biocatalysis should be useful for the practical production of the pharmaceutically important intermediate, (R)-(−)-3-quinuclidinol.
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Affiliation(s)
- Kentaro Isotani
- Department of Biotechnology, Faculty of Engineering, Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan.
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Hwang MS, Lindenmuth BE, McDonald KA, Falk BW. Bipartite and tripartite Cucumber mosaic virus-based vectors for producing the Acidothermus cellulolyticus endo-1,4-β-glucanase and other proteins in non-transgenic plants. BMC Biotechnol 2012; 12:66. [PMID: 22999234 PMCID: PMC3582468 DOI: 10.1186/1472-6750-12-66] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 09/11/2012] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Using plant viruses to produce desirable proteins in plants allows for using non-transgenic plant hosts and if necessary, the ability to make rapid changes in the virus construct for increased or modified protein product yields. The objective of this work was the development of advanced CMV-based protein production systems to produce Acidothermus cellulolyticus endo-1, 4-β-glucanase (E1) in non-transgenic plants. RESULTS We used two new Cucumber mosaic virus (CMV)-based vector systems for producing the green fluorescent protein (GFP) and more importantly, the Acidothermus cellulolyticus endo-1, 4-β-glucanase (E1) in non-transgenic Nicotiana benthamiana plants. These are the inducible CMVin (CMV-based inducible) and the autonomously replicating CMVar (CMV-based advanced replicating) systems. We modified a binary plasmid containing the complete CMV RNA 3 cDNA to facilitate insertion of desired sequences, and to give modifications of the subgenomic mRNA 4 leader sequence yielding several variants. Quantitative RT-PCR and immunoblot analysis showed good levels of CMV RNA and coat protein accumulation for some variants of both CMVin and CMVar. When genes for E1 or GFP were inserted in place of the CMV coat protein, both were produced in plants as shown by fluorescence (GFP) and immunoblot analysis. Enzymatic activity assays showed that active E1 was produced in plants with yields up to ~ 11 μg/g fresh weight (FW) for specific variant constructs. We also compared in vitro CMV genomic RNA reassortants, and CMV RNA 3 mutants which lacked the C' terminal 33 amino acids of the 3A movement protein in attempts to further increase E1 yield. Taken together specific variant constructs yielded up to ~21 μg/g FW of E1 in non-transgenic plants. CONCLUSIONS Intact, active E1 was rapidly produced in non-transgenic plants by using agroinfiltration with the CMV-based systems. This reduces the time and cost compared to that required to generate transgenic plants and still gives the comparable yields of active E1. Our modifications described here, including manipulating cloning sites for foreign gene introduction, enhance the ease of use. Also, N. benthamiana, which is particularly suitable for agroinfiltration, is a very good plant for transient protein production.
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Affiliation(s)
- Min Sook Hwang
- Department of Plant Pathology, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Benjamin E Lindenmuth
- Department of Chemical Engineering and Materials Science, University of California, One Shields Avenue, Davis, CA, 95616, USA
- Present address: Bayer HealthCare Pharmaceuticals, 800 Dwight Way, Berkeley, CA, 94710, USA
| | - Karen A McDonald
- Department of Chemical Engineering and Materials Science, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Bryce W Falk
- Department of Plant Pathology, University of California, One Shields Avenue, Davis, CA, 95616, USA
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35
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Shen Y, Huang H, Zhu L, Luo M, Chen D. Type II thioesterase gene (ECO-orf27) from Amycolatopsis orientalis influences production of the polyketide antibiotic, ECO-0501 (LW01). Biotechnol Lett 2012; 34:2087-91. [PMID: 22850790 DOI: 10.1007/s10529-012-1010-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 07/05/2012] [Indexed: 11/26/2022]
Abstract
ECO-orf27 associated with the cluster of ECO-0501 (LW01) from Amycolatopsis orientalis is deduced to encode a type II thioesterase. Disruption of ECO-orf27 reduced LW01 production by 95 %. Complementation of the disrupted mutant with intact ECO-orf27 restored the production of LW01 suggesting that ECO-orf27 is crucial for LW01 biosynthesis. ECO-TE I, the gene encoding type I thioesterase from LW01 polyketide synthases, cannot complement ECO-orf27 deficient mutant distinguishing ECO-orf27 from type I thioesterase gene. Type II thioesterase gene pikAV from Streptomyces venezuelae could complement ECO-orf27 in A. orientalis indicating that the two genes are equivalent in their function. Overexpression of ECO-orf27 resulted in a 20 % increase in LW01 production providing an alternative approach for yield improvement.
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Affiliation(s)
- Yang Shen
- School of Biotechnology, East China University of Science and Technology, Meilong Rd. 130#, Shanghai, People's Republic of China
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36
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Zhang P, Lu X, Li Q, Lin X, Liu H, Ma X. [Cloning and characterization of a thermostable urate oxidase from Microbacterium sp. strain ZZJ4-1]. Sheng Wu Gong Cheng Xue Bao 2012; 28:813-822. [PMID: 23167193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
In order to characterize a thermostable urate oxidase (Uox) from Microbacterium sp. strain ZZJ4-1, we cloned its gene (uox). The open reading frame of uox contained 894 base pairs and encoded a protein with 297 amino acids. Alignment of gene sequences indicated there was no obvious identity with the most reported uox and that 72% identity was found with uox from Arthrobacter globiformis. We inserted the gene into the plasmid pET-15b to construct an expression vector pET-15b-uox and got it induced expression in Escherichia coli BL21 (DE3). After the purification of the recombinant Uox by the HisBind column, we studied some properties of it. It was composed of subunits with a molecular mass of about 35 kDa. The optimal temperature and pH was 30 degrees C and pH 7.5. It was stable below 65 degrees C and from pH 8.5 to 11.0. The Km value was 0.22 mmol/L with the uric acid as the substrate. Ag+, Zn2+, CU2+ and SDS could totally inhibit its activity while Tween 20, Tween 80 and Triton X-100 had a slight promotion effect. The thermal stability of this enzyme was the most excellent among the reported recombinant Uox. Based on this property, it would be very useful in the application.
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Affiliation(s)
- Pengcheng Zhang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
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37
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Quan LH, Min JW, Jin Y, Wang C, Kim YJ, Yang DC. Enzymatic biotransformation of ginsenoside Rb1 to compound K by recombinant β-glucosidase from Microbacterium esteraromaticum. J Agric Food Chem 2012; 60:3776-3781. [PMID: 22428991 DOI: 10.1021/jf300186a] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We cloned and characterized a β-glucosidase (bgp3) gene from Microbacterium esteraromaticum isolated from ginseng field. The bgp3 gene consists of 2,271 bp encoding 756 amino acids which have homology to the glycosyl hydrolase family 3 protein domain. The molecular mass of purified Bgp3 was 80 kDa, as determined by SDS-PAGE. The enzyme (Bgp3) catalyzed the conversion of ginsenoside Rb1 to the more pharmacologically active minor ginsenoside Rd and compound K. The Bgp3 hydrolyzed the outer glucose moiety attached to the C-20 position of ginsenoside Rb1, followed by hydrolysis of the inner glucose moiety attached to the C-3 position. Using 0.1 mg mL(-1) enzyme in 20 mM sodium phosphate buffer at 40 °C and pH 7.0, 1.0 mg mL(-1) ginsenoside Rb1 was transformed into 0.46 mg mL(-1) compound K within 60 min with a corresponding molar conversion yield of 77%. Bgp3 hydrolyzed the ginsenoside Rb1 along the following pathway: Rb1 → Rd → compound K.
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Affiliation(s)
- Lin-Hu Quan
- Department of Oriental Medicinal Material & Processing, College of Life Science, Kyung Hee University, Yongin, Korea.
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Lee MJ, Kong D, Han K, Sherman DH, Bai L, Deng Z, Lin S, Kim ES. Structural analysis and biosynthetic engineering of a solubility-improved and less-hemolytic nystatin-like polyene in Pseudonocardia autotrophica. Appl Microbiol Biotechnol 2012; 95:157-68. [PMID: 22382166 DOI: 10.1007/s00253-012-3955-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Revised: 02/07/2012] [Accepted: 02/08/2012] [Indexed: 11/27/2022]
Abstract
Polyene antibiotics such as nystatin are a large family of very valuable antifungal polyketide compounds typically produced by soil actinomycetes. Previously, using a polyene cytochrome P450 hydroxylase-specific genome screening strategy, Pseudonocardia autotrophica KCTC9441 was determined to contain an approximately 125.7-kb region of contiguous DNA with a total of 23 open reading frames, which are involved in the biosynthesis and regulation of a structurally unique polyene natural product named NPP. Here, we report the complete structure of NPP, which contains an aglycone identical to nystatin and harbors a unique di-sugar moiety, mycosaminyl-(α1-4)-N-acetyl-glucosamine. A mutant generated by inactivation of a sole glycosyltransferase gene (nppDI) within the npp gene cluster can be complemented in trans either by nppDI-encoded protein or by its nystatin counterpart, NysDI, suggesting that the two sugars might be attached by two different glycosyltransferases. Compared with nystatin (which bears a single sugar moiety), the di-sugar containing NPP exhibits approximately 300-fold higher water solubility and 10-fold reduced hemolytic activity, while retaining about 50% antifungal activity against Candida albicans. These characteristics reveal NPP as a promising candidate for further development into a pharmacokinetically improved, less-cytotoxic polyene antifungal antibiotic.
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Affiliation(s)
- Mi-Jin Lee
- Department of Biological Engineering, Inha University, Incheon 402-751, South Korea
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Lammerts van Bueren A, Otani S, Friis EP, Wilson KS, Davies GJ. Three-dimensional structure of a thermophilic family GH11 xylanase from Thermobifida fusca. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:141-4. [PMID: 22297985 PMCID: PMC3274389 DOI: 10.1107/s1744309111049608] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Accepted: 11/21/2011] [Indexed: 11/10/2022]
Abstract
Thermostable enzymes employ various structural features dictated at the amino-acid sequence level that allow them to maintain their integrity at higher temperatures. Many hypotheses as to the nature of thermal stability have been proposed, including optimized core hydrophobicity and an increase in charged surface residues to enhance polar solvent interactions for solubility. Here, the three-dimensional structure of the family GH11 xylanase from the moderate thermophile Thermobifida fusca in its trapped covalent glycosyl-enzyme intermediate complex is presented. Interactions with the bound ligand show fewer direct hydrogen bonds from ligand to protein than observed in previous complexes from other species and imply that binding of the xylan substrate involves several water-mediated hydrogen bonds.
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Affiliation(s)
| | - Suzie Otani
- Novozymes A/S, Krogshoejvej 36, 2880 Bagsvaerd, Denmark
| | | | - Keith S. Wilson
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England
| | - Gideon J. Davies
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England
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Quan LH, Min JW, Yang DU, Kim YJ, Yang DC. Enzymatic biotransformation of ginsenoside Rb1 to 20(S)-Rg3 by recombinant β-glucosidase from Microbacterium esteraromaticum. Appl Microbiol Biotechnol 2012; 94:377-84. [PMID: 22249721 DOI: 10.1007/s00253-011-3861-7] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 12/18/2011] [Accepted: 12/21/2011] [Indexed: 11/25/2022]
Abstract
Microbacterium esteraromaticum was isolated from ginseng field. The β-glucosidase gene (bgp1) from M. esteraromaticum was cloned and expressed in Escherichia coli BL21 (DE3). The bgp1 gene consists of 2,496 bp encoding 831 amino acids which have homology to the glycosyl hydrolase family 3 protein domain. The recombinant β-glucosidase enzyme (Bgp1) was purified and characterized. The molecular mass of purified Bgp1 was 87.5 kDa, as determined by SDS-PAGE. Using 0.1 mg ml(-1) enzyme in 20 mM sodium phosphate buffer at 37°C and pH 7.0, 1.0 mg ml(-1) ginsenoside Rb1 was transformed into 0.444 mg ml(-1) ginsenoside Rg3 within 6 h. The Bgp1 sequentially hydrolyzed the outer and inner glucose attached to the C-20 position of ginsenosides Rb1. Bgp1 hydrolyzed the ginsenoside Rb1 along the following pathway: Rb1 → Rd → 20(S)-Rg3. This is the first report of the biotransformation of ginsenoside Rb1 to ginsenoside 20(S)-Rg3 using the recombinant β-glucosidase.
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Affiliation(s)
- Lin-Hu Quan
- Department of Oriental Medicinal Material and Processing, Korean Ginseng Center, Kyung Hee University, Yongin, South Korea
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Winter RT, Heuts DPHM, Rijpkema EMA, van Bloois E, Wijma HJ, Fraaije MW. Hot or not? Discovery and characterization of a thermostable alditol oxidase from Acidothermus cellulolyticus 11B. Appl Microbiol Biotechnol 2012; 95:389-403. [PMID: 22231860 PMCID: PMC3371188 DOI: 10.1007/s00253-011-3750-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Revised: 11/01/2011] [Accepted: 11/17/2011] [Indexed: 11/26/2022]
Abstract
We describe the discovery, isolation and characterization of a highly thermostable alditol oxidase from Acidothermus cellulolyticus 11B. This protein was identified by searching the genomes of known thermophiles for enzymes homologous to Streptomyces coelicolor A3(2) alditol oxidase (AldO). A gene (sharing 48% protein sequence identity to AldO) was identified, cloned and expressed in Escherichia coli. Following 6xHis tag purification, characterization revealed the protein to be a covalent flavoprotein of 47 kDa with a remarkably similar reactivity and substrate specificity to that of AldO. A steady-state kinetic analysis with a number of different polyol substrates revealed lower catalytic rates but slightly altered substrate specificity when compared to AldO. Thermostability measurements revealed that the novel AldO is a highly thermostable enzyme with an unfolding temperature of 84 °C and an activity half-life at 75 °C of 112 min, prompting the name HotAldO. Inspired by earlier studies, we attempted a straightforward, exploratory approach to improve the thermostability of AldO by replacing residues with high B-factors with corresponding residues from HotAldO. None of these mutations resulted in a more thermostable oxidase; a fact that was corroborated by in silico analysis.
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Affiliation(s)
- Remko T. Winter
- Laboratory of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Dominic P. H. M. Heuts
- Manchester Interdisciplinary Biocentre and Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester, M1 7DN UK
| | - Egon M. A. Rijpkema
- Laboratory of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Edwin van Bloois
- Laboratory of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Hein J. Wijma
- Laboratory of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Marco W. Fraaije
- Laboratory of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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Brunecky R, Baker JO, Wei H, Taylor LE, Himmel ME, Decker SR. Analysis of transgenic glycoside hydrolases expressed in plants: T. reesei CBH I and A. cellulolyticus EI. Methods Mol Biol 2012; 908:197-211. [PMID: 22843401 DOI: 10.1007/978-1-61779-956-3_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Plant cell walls are composed of three basic structural biomolecules: cellulose, hemicellulose, and lignin with cellulose being the most abundant biopolymer on earth. Cellulose is composed of cellodextrins, which are linear polymers of glucose, and considered to be microcrystalline in structure. The conversion of cellulose to free glucose is one of the primary steps in the fermentative conversion of biomass to fuels and chemicals. However, the crystalline nature of this complex, noncovalent structure is highly resistant to enzymatic hydrolysis. Thus, the substantial cost currently associated with biomass saccharification primarily represents the cost of biomass degrading enzymes. Despite the fact that the microbial cellulose hydrolytic "machinery" for the recycling of carbon from plant biomass already exists in nature, the natural enzymatic degradation of plant material is typically a slow and complex process. Thus, if commercial biofuels production is to become a reality, it must be more cost-effective. One method proposed for achieving this objective is to express all or some of the requisite cellulolytic enzymes in planta, thus reducing both enzyme and thermochemical pretreatment costs.
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Affiliation(s)
- Roman Brunecky
- National Renewable Energy Laboratory, Biosciences Center, Golden, CO, USA.
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Abstract
There are two types of processive cellulases, exocellulases and processive endoglucanases. There are also two classes of exocellulases, ones that attack the reducing ends of cellulose chains and ones that attack the nonreducing ends. There are a number of ways of assaying processivity but none of them are ideal. It appears that exocellulases, all of which have their active sites in a tunnel, couple movement along a cellulose chain with cleavage of cellobiose from the end of the cellulose molecule. There are two sets of structures that suggest how an exocellulase might move along a cellulose chain. For family 48 exocellulases there are two different ways that a chain can be bound in the active site while for family 6 exocellulases there are several different ligand-bound structures. Site-directed mutagenesis of Thermobifida fusca exocellulases Cel48A and Cel6B and the processive endoglucanase Cel9A have identified some mutations that increase processivity and some that decrease processivity. In addition a mutation in Cel6B was identified that appears to allow the mutant enzyme to move along a cellulose chain in the absence of cleavage.
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Affiliation(s)
- David B Wilson
- Department of Molecular Biology & Genetics, Cornell University, Ithaca, NY, USA.
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Zhang F, Chen JJ, Ren WZ, Nie GX, Ming H, Tang SK, Li WJ. Cloning, expression and characterization of an alkaline thermostable GH9 endoglucanase from Thermobifida halotolerans YIM 90462 T. Bioresour Technol 2011; 102:10143-10146. [PMID: 21907577 DOI: 10.1016/j.biortech.2011.08.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2011] [Revised: 08/01/2011] [Accepted: 08/03/2011] [Indexed: 05/31/2023]
Abstract
The endoglucanase gene, thcel9A, from Thermobifida halotolerans YIM 90462(T) was cloned and expressed in Escherichia coli BL 21(DE). The 2895-bp full-length gene encodes a 964-residue polypeptide (Thcel9A) containing a catalytic domain belonging to glycosyl hydrolases (GH) family 9. Phylogenetic analysis indicated that Thcel9A is closely related to Cel9A of Thermobifidafusca YX. Thcel9A was purified from the culture supernatant by Ni(2+)-affinity chromatography and the purified enzyme exhibited optimal activity at 55°C and pH 8.0. Substrate specificity assays showed that it not only had CMCase activity, but also hydrolase activity on microcrystalline cellulose and filter paper. These properties suggested that Thcel9A is a classical GH9 group A endoglucanase.
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Affiliation(s)
- Feng Zhang
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education and Laboratory for Conservation and Utilization of Bio-Resources, Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, PR China
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Xing K, Bian GK, Qin S, Klenk HP, Yuan B, Zhang YJ, Li WJ, Jiang JH. Kibdelosporangium phytohabitans sp. nov., a novel endophytic actinomycete isolated from oil-seed plant Jatropha curcas L. containing 1-aminocyclopropane-1-carboxylic acid deaminase. Antonie Van Leeuwenhoek 2011; 101:433-41. [PMID: 21989686 DOI: 10.1007/s10482-011-9652-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2011] [Accepted: 09/30/2011] [Indexed: 11/25/2022]
Abstract
A novel actinomycete, designated strain KLBMP 1111(T), was isolated from the root of the oil-seed plant Jatropha curcas L. collected from Sichuan Province, south-west China. Strain KLBMP 1111(T) formed a distinct branch in the 16S rRNA gene phylogenetic tree together with the type strains in the genus Kibdelosporangium, with the highest similarity to Kibdelosporangium aridum subsp. aridum DSM 43828(T) (98.8%), K. aridum subsp. largum DSM 44150(T) (98.1%) and Kibdelosporangium philippinense DSM 44226(T) (98.1%). The organism produced sporangium-like structures, the typical morphological characteristic of the genus Kibdelosporangium. The chemotaxonomic properties of this strain were also consistent with those of the genus Kibdelosporangium: the peptidoglycan contained meso-diaminopimelic acid; the predominant menaquinone was MK-9(H(4)); phospholipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylinositol and an unknown phospholipid; iso-C(16:0), C(16:0), anteiso-C(15:0) and iso-C(15:0) as the predominant cellular fatty acids and the G+C content was 67.2 mol%. DNA-DNA hybridization values between strain KLBMP 1111(T) and the three Kibdelosporangium species were less than 50%. This strain had the ability to produce a siderophore, utilized 1-aminocyclopropane-1-carboxylic acid (ACC) as sole source of nitrogen and possessed ACC deaminase enzyme. Based on genotypic and phenotypic data, strain KLBMP 1111(T) represents a novel species in the genus Kibdelosporangium. We propose the name Kibdelosporangium phytohabitans sp. nov. for this species. The type strain is the strain KLBMP 1111(T) (=KCTC 19775(T) = CCTCC AA 2010001(T)).
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Affiliation(s)
- Ke Xing
- School of Life Science, The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Xuzhou Normal University, Xuzhou, Jiangsu, 221116, People's Republic of China
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Nie Y, Liang J, Fang H, Tang YQ, Wu XL. Two novel alkane hydroxylase-rubredoxin fusion genes isolated from a Dietzia bacterium and the functions of fused rubredoxin domains in long-chain n-alkane degradation. Appl Environ Microbiol 2011; 77:7279-88. [PMID: 21873474 PMCID: PMC3194844 DOI: 10.1128/aem.00203-11] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 08/19/2011] [Indexed: 11/20/2022] Open
Abstract
Two alkane hydroxylase-rubredoxin fusion gene homologs (alkW1 and alkW2) were cloned from a Dietzia strain, designated DQ12-45-1b, which can grow on crude oil and n-alkanes ranging in length from 6 to 40 carbon atoms as sole carbon sources. Both AlkW1 and AlkW2 have an integral-membrane alkane monooxygenase (AlkB) conserved domain and a rubredoxin (Rd) conserved domain which are fused together. Phylogenetic analysis showed that these two AlkB-fused Rd domains formed a novel third cluster with all the Rds from the alkane hydroxylase-rubredoxin fusion gene clusters in Gram-positive bacteria and that this third cluster was distant from the known AlkG1- and AlkG2-type Rds. Expression of the alkW1 gene in DQ12-45-1b was induced when cells were grown on C(8) to C(32) n-alkanes as sole carbon sources, but expression of the alkW2 gene was not detected. Functional heterologous expression in an alkB deletion mutant of Pseudomonas fluorescens KOB2Δ1 suggested the alkW1 could restore the growth of KOB2Δ1 on C(14) and C(16) n-alkanes and induce faster growth on C(18) to C(32) n-alkanes than alkW1ΔRd, the Rd domain deletion mutant gene of alkW1, which also caused faster growth than KOB2Δ1 itself. In addition, the artificial fusion of AlkB from the Gram-negative P. fluorescens CHA0 and the Rds from both Gram-negative P. fluorescens CHA0 and Gram-positive Dietzia sp. DQ12-45-1b significantly increased the degradation of C(32) alkane compared to that seen with AlkB itself. In conclusion, the alkW1 gene cloned from Dietzia species encoded an alkane hydroxylase which increased growth on and degradation of n-alkanes up to C(32) in length, with its fused rubredoxin domain being necessary to maintain the functions. In addition, the fusion of alkane hydroxylase and rubredoxin genes from both Gram-positive and -negative bacteria can increase the degradation of long-chain n-alkanes (such as C(32)) in the Gram-negative bacterium.
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Affiliation(s)
- Yong Nie
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, People's Republic of China
| | - Jieliang Liang
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, People's Republic of China
| | - Hui Fang
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, People's Republic of China
| | - Yue-Qin Tang
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, People's Republic of China
| | - Xiao-Lei Wu
- Department of Energy and Resources Engineering, College of Engineering, Peking University, Beijing 100871, People's Republic of China
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Kim DY, Ham SJ, Lee HJ, Cho HY, Kim JH, Kim YJ, Shin DH, Rhee YH, Son KH, Park HY. Cloning and characterization of a modular GH5 β-1,4-mannanase with high specific activity from the fibrolytic bacterium Cellulosimicrobium sp. strain HY-13. Bioresour Technol 2011; 102:9185-9192. [PMID: 21767948 DOI: 10.1016/j.biortech.2011.06.073] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Revised: 06/18/2011] [Accepted: 06/20/2011] [Indexed: 05/31/2023]
Abstract
The gene (1272-bp) encoding a β-1,4-mannanase from a gut bacterium of Eisenia fetida, Cellulosimicrobium sp. strain HY-13 was cloned and expressed in Escherichia coli. The recombinant β-1,4-mannanase (rManH) was approximately 44.0 kDa and has a catalytic GH5 domain that is 65% identical to that of the Micromonospora sp. β-1,4-mannosidase. The enzyme exhibited the highest catalytic activity toward mannans at 50 °C and pH 6.0. rManH displayed a high specific activity of 14,711 and 8498 IU mg⁻¹ towards ivory nut mannan and locust bean gum, respectively; however it could not degrade the structurally unrelated polysaccharides, mannobiose, or p-nitrophenyl sugar derivatives. rManH was strongly bound to ivory nut mannan, Avicel, chitosan, and chitin but did not attach to curdlan, insoluble oat spelt xylan, lignin, or poly(3-hydroxybutyrate). The superior biocatalytic properties of rManH suggest that the enzyme can be exploited as an effective additive in the animal feed industry.
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Affiliation(s)
- Do Young Kim
- Industrial Bio-materials Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 305-806, Republic of Korea
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48
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Zhang J, Tuomainen P, Siika-Aho M, Viikari L. Comparison of the synergistic action of two thermostable xylanases from GH families 10 and 11 with thermostable cellulases in lignocellulose hydrolysis. Bioresour Technol 2011; 102:9090-5. [PMID: 21767947 DOI: 10.1016/j.biortech.2011.06.085] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 06/24/2011] [Accepted: 06/25/2011] [Indexed: 05/10/2023]
Abstract
Recombinant xylanase preparations from Nonomuraea flexuosa (Nf Xyn, GH11) and Thermoascus aurantiacus (Ta Xyn, GH10) were evaluated for their abilities to hydrolyze hydrothermally pretreated wheat straw. The GH family 10 enzyme Ta Xyn was clearly more efficient in solubilizing xylan from pretreated wheat straw. Improvement of the hydrolysis of hydrothermally pretreated wheat straw by addition of the thermostable xylanase preparations to thermostable cellulases was evaluated. Clear synergistic enhancement of hydrolysis of cellulose was observed when cellulases were supplemented even with a low amount of pure xylanases. Xylobiose was the main hydrolysis product from xylan. It was found that the hydrolysis of cellulose increased nearly linearly with xylan removal during the enzymatic hydrolysis. The results also showed that the xylanase preparation from T. aurantiacus, belonging to GH family 10 always showed better hydrolytic capacity of solubilizing xylan and acting synergistically with thermostable cellulases in the hydrolysis of hydrothermally pretreated wheat straw.
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Affiliation(s)
- Junhua Zhang
- College of Forestry, Northwest A&F University, 3 Taicheng Road, Yangling 712100, China.
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Dávila Costa JS, Albarracín VH, Abate CM. Responses of environmental Amycolatopsis strains to copper stress. Ecotoxicol Environ Saf 2011; 74:2020-2028. [PMID: 21764453 DOI: 10.1016/j.ecoenv.2011.06.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2011] [Revised: 06/15/2011] [Accepted: 06/17/2011] [Indexed: 05/31/2023]
Abstract
Copper is a redox-active metal, which acts as a catalyst in the formation of Reactive Oxygen Species (ROS) encouraging oxidative stress. Protection against oxidants is intrinsic to every living cell; however, in stress conditions, cells are forced to increase and expand their antioxidative network. In this work, the novel copper-resistant strain Amycolatopsis tucumanensis and the copper-sensitive Amycolatopsis eurytherma were grown under copper increasing concentrations in order to elucidate the dissimilar effects of the metal on the strains viability, mainly on morphology and antioxidant capacity. Although biosorbed copper encouraged ROS production in a dose-dependent manner in both strains, the increase in ROS production from the basal level to the stress conditions in A. tucumanensis is lesser than in the copper-sensitive strain; likewise, in presence of copper A. eurytherma suffered inexorable morphological alteration while A. tucumanensis was not affected. The levels of antioxidant enzymes and metallothioneins (MT) were all greater in A. tucumanensis than in A. eurytherma; in addition MT levels as well as superoxide dismutase and thioredoxin reductase activities in A. tucumanensis, were higher as higher the concentration of copper in the culture medium. This work has given evidence that an efficient antioxidant defense system might aid microorganisms to survive in copper-stress conditions; besides it constitutes the first report of oxidative stress study in the genus Amycolatopsis and contributes to enlarge the knowledge on the copper-resistance mechanisms of A. tucumanensis.
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Affiliation(s)
- José Sebastián Dávila Costa
- Pilot Plant of Industrial and Microbiological Processes, CONICET. Av. Belgrano y Pasaje Caseros, 4000 Tucumán, Argentina.
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50
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Procópio L, Alvarez VM, Jurelevicius DA, Hansen L, Sørensen SJ, Cardoso JS, Pádula M, Leitão ÁC, Seldin L, van Elsas JD. Insight from the draft genome of Dietzia cinnamea P4 reveals mechanisms of survival in complex tropical soil habitats and biotechnology potential. Antonie Van Leeuwenhoek 2011; 101:289-302. [PMID: 21901521 PMCID: PMC3261415 DOI: 10.1007/s10482-011-9633-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 08/20/2011] [Indexed: 01/17/2023]
Abstract
The draft genome of Dietzia cinnamea strain P4 was determined using pyrosequencing. In total, 428 supercontigs were obtained and analyzed. We here describe and interpret the main features of the draft genome. The genome contained a total of 3,555,295 bp, arranged in a single replicon with an average G+C percentage of 70.9%. It revealed the presence of complete pathways for basically all central metabolic routes. Also present were complete sets of genes for the glyoxalate and reductive carboxylate cycles. Autotrophic growth was suggested to occur by the presence of genes for aerobic CO oxidation, formate/formaldehyde oxidation, the reverse tricarboxylic acid cycle and the 3-hydropropionate cycle for CO2 fixation. Secondary metabolism was evidenced by the presence of genes for the biosynthesis of terpene compounds, frenolicin, nanaomycin and avilamycin A antibiotics. Furthermore, a probable role in azinomycin B synthesis, an important product with antitumor activity, was indicated. The complete alk operon for the degradation of n-alkanes was found to be present, as were clusters of genes for biphenyl ring dihydroxylation. This study brings new insights in the genetics and physiology of D. cinnamea P4, which is useful in biotechnology and bioremediation.
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Affiliation(s)
- Luciano Procópio
- Microbial Ecology Laboratory, Department of Microbial Ecology, CEES, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
- Laboratório de Genética Microbiana, Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Centro de Ciências da Saúde (CCS), Ilha do Fundão, Rio de Janeiro, RJ 21941-901 Brazil
| | - Vanessa M. Alvarez
- Laboratório de Genética Microbiana, Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Centro de Ciências da Saúde (CCS), Ilha do Fundão, Rio de Janeiro, RJ 21941-901 Brazil
| | - Diogo A. Jurelevicius
- Laboratório de Genética Microbiana, Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Centro de Ciências da Saúde (CCS), Ilha do Fundão, Rio de Janeiro, RJ 21941-901 Brazil
| | - Lars Hansen
- Department of Microbiology, Institute of Biology, University of Copenhagen, Sølvgade 83H, 1307 Copenhagen, Denmark
| | - Søren J. Sørensen
- Department of Microbiology, Institute of Biology, University of Copenhagen, Sølvgade 83H, 1307 Copenhagen, Denmark
| | - Janine S. Cardoso
- Laboratório de Diagnóstico Molecular e Hematologia, Faculdade de Farmácia, UFRJ, CCS, Ilha do Fundão, Rio de Janeiro, RJ 21941-540 Brazil
| | - Marcelo Pádula
- Laboratório de Diagnóstico Molecular e Hematologia, Faculdade de Farmácia, UFRJ, CCS, Ilha do Fundão, Rio de Janeiro, RJ 21941-540 Brazil
| | - Álvaro C. Leitão
- Laboratório de Radiobiologia Molecular, Instituto de Biofísica Carlos Chagas Filho, UFRJ, CCS, Ilha do Fundão, Rio de Janeiro, RJ 21941-540 Brazil
| | - Lucy Seldin
- Laboratório de Genética Microbiana, Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Centro de Ciências da Saúde (CCS), Ilha do Fundão, Rio de Janeiro, RJ 21941-901 Brazil
| | - Jan Dirk van Elsas
- Microbial Ecology Laboratory, Department of Microbial Ecology, CEES, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands
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