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Dedeakayoğulları H, Valjakka J, Turunen O, Yilmazer B, Demir Ğ, Jänis J, Binay B. Application of reductive amination by heterologously expressed Thermomicrobium roseumL-alanine dehydrogenase to synthesize L-alanine derivatives. Enzyme Microb Technol 2023; 169:110265. [PMID: 37269617 DOI: 10.1016/j.enzmictec.2023.110265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/21/2023] [Accepted: 05/22/2023] [Indexed: 06/05/2023]
Abstract
Unnatural amino acids are unique building blocks in modern medicinal chemistry as they contain an amino and a carboxylic acid functional group, and a variable side chain. Synthesis of pure unnatural amino acids can be made through chemical modification of natural amino acids or by employing enzymes that can lead to novel molecules used in the manufacture of various pharmaceuticals. The NAD+ -dependent alanine dehydrogenase (AlaDH) enzyme catalyzes the conversion of pyruvate to L-alanine by transferring ammonium in a reversible reductive amination activity. Although AlaDH enzymes have been widely studied in terms of oxidative deamination activity, reductive amination activity studies have been limited to the use of pyruvate as a substrate. The reductive amination potential of heterologously expressed, highly pure Thermomicrobium roseum alanine dehydrogenase (TrAlaDH) was examined with regard to pyruvate, α-ketobutyrate, α-ketovalerate and α-ketocaproate. The biochemical properties were studied, which included the effects of 11 metal ions on enzymatic activity for both reactions. The enzyme accepted both derivatives of L-alanine (in oxidative deamination) and pyruvate (in reductive amination) as substrates. While the kinetic KM values associated with the pyruvate derivatives were similar to pyruvate values, the kinetic kcat values were significantly affected by the side chain increase. In contrast, KM values associated with the derivatives of L-alanine (L-α-aminobutyrate, L-norvaline, and L-norleucine) were approximately two orders of magnitude greater, which would indicate that they bind very poorly in a reactive way to the active site. The modeled enzyme structure revealed differences in the molecular orientation between L-alanine/pyruvate and L-norleucine/α-ketocaproate. The reductive activity observed would indicate that TrAlaDH has potential for the synthesis of pharmaceutically relevant amino acids.
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Affiliation(s)
- Huri Dedeakayoğulları
- Medical Biochemistry Department, Faculty of Medicine, Istinye University, 34010 Istanbul, Turkey
| | - Jarkko Valjakka
- Faculty of Medicine and Health Technology, Tampere University, FI-33100 Tampere, Finland
| | - Ossi Turunen
- School of Forest Sciences, University of Eastern Finland, FI-80101 Joensuu, Finland
| | - Berin Yilmazer
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, 41400 Kocaeli, Turkey
| | - Ğarip Demir
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, 41400 Kocaeli, Turkey
| | - Janne Jänis
- Department of Chemistry, University of Eastern Finland, FI-80101 Joensuu, Finland
| | - Barış Binay
- Department of Bioengineering, Gebze Technical University, Gebze, 41400 Kocaeli, Turkey; BAUZYME Biotechnology Co., Gebze Technical University Technopark, Gebze, 41400 Kocaeli, Turkey.
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Ketsakhon P, Thammasittirong A, Thammasittirong SNR. Adding value to rice straw waste for high-level xylanase production using a new isolate of Bacillus altitudinis RS3025. Folia Microbiol (Praha) 2023; 68:87-99. [PMID: 35945409 DOI: 10.1007/s12223-022-00998-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 07/27/2022] [Indexed: 11/04/2022]
Abstract
An investigation was carried out using rice straw as a low-cost substrate to study the optimization of xylanase production using a newly identified endospore-forming bacterium, Bacillus altitudinis RS3025. The highest xylanase activity was achieved using 2% rice straw (pretreated with 2% NaOH at 100 °C) at pH 7.0, 37 °C temperature, and with 72-h incubation time. Under the optimized conditions, xylanase activity reached 2518.51 U/mL, which was 11.56-fold higher than the activity under the initial conditions using untreated rice straw as substrate. Enzymatic hydrolysis of the rice straw using crude xylanase of B. altitudinis RS3025 demonstrated the hydrolyzation efficiency of the rice straw waste, especially alkaline rice straw. The highest level of released reducing sugars was 149.78 mg/g substrate. The study demonstrated the successful utilization of rice straw waste for high-level xylanase production using B. altitudinis RS3025 and reducing sugar production using low-cost crude enzyme, which has the advantages of reducing the processing cost and environmental concerns associated with rice straw waste management.
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Affiliation(s)
- Punpaporn Ketsakhon
- Department of Microbiology, Faculty of Liberal Arts and Science, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand
| | - Anon Thammasittirong
- Department of Microbiology, Faculty of Liberal Arts and Science, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand.,Microbial Biotechnology Unit, Faculty of Liberal Arts and Science, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand
| | - Sutticha Na-Ranong Thammasittirong
- Department of Microbiology, Faculty of Liberal Arts and Science, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand. .,Microbial Biotechnology Unit, Faculty of Liberal Arts and Science, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand.
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Chen L, Li W, Zhao Y, Zhang S, Meng L. Mechanism of sulfur-oxidizing inoculants and nitrate on regulating sulfur functional genes and bacterial community at the thermophilic compost stage. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 326:116733. [PMID: 36372033 DOI: 10.1016/j.jenvman.2022.116733] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 11/05/2022] [Accepted: 11/05/2022] [Indexed: 06/16/2023]
Abstract
The emission of H2S odors predominantly occurred at the thermophilic phase of composting, which could cause odorous gas pollution and reduce the fertilizer value of composting products. And sulfur-oxidizing bacteria (SOB) possess oxidative capacities for inorganic sulfur compounds with nitrate applied as electron acceptors. Therefore, this study aimed to assess the effectiveness of combined additives (SOB inoculants and nitrate) on the bacterial community diversity, sulfur-oxidizing gene abundances, and metabolic function prediction at the thermophilic stage of sewage sludge composting. The highest sulfate contents were increased by 1.02-1.34 folds, and the abundances of the sulfur-oxidizing genes (sqr, pdo, sox, and sor) were also enhanced by adding the combined additives. Network patterns revealed a strengthened interaction of inoculants and sulfur functional genes. Microbial functional pathways predicted higher metabolic levels of carbohydrate and amino acid metabolisms with the addition of combined additives, and the predicted relative abundances of sulfur metabolism and nitrogen metabolism were increased by 19.3 ± 2.5% and 24.7 ± 4.1%, respectively. Heatmap analysis showed that the SOB might have a competitive advantage over the indigenous denitrifying bacteria in using nitrate for biochemical reactions. Correlation analyses suggested that sulfur-oxidizing efficacy could be indirectly affected by the environmental parameters through changing the structure of bacterial community. These findings provide new insights toward an optimized inoculation strategy of using SOB and nitrate to enhance sulfur preservation and modulate the bacterial communities at the thermophilic phase of sewage sludge composting.
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Affiliation(s)
- Li Chen
- School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Weiguang Li
- School of Environment, Harbin Institute of Technology, Harbin, 150090, China; State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, Harbin, 150090, China.
| | - Yi Zhao
- School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Shumei Zhang
- Institute of Microbiology, Heilongjiang Academy of Sciences, Harbin, 150010, China
| | - Liqiang Meng
- Institute of Microbiology, Heilongjiang Academy of Sciences, Harbin, 150010, China
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Kellock M, Rahikainen J, Borisova AS, Voutilainen S, Koivula A, Kruus K, Marjamaa K. Inhibitory effect of lignin on the hydrolysis of xylan by thermophilic and thermolabile GH11 xylanases. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:49. [PMID: 35568899 PMCID: PMC9107766 DOI: 10.1186/s13068-022-02148-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 04/30/2022] [Indexed: 11/10/2022]
Abstract
Abstract
Background
Enzymatic hydrolysis of lignocellulosic biomass into platform sugars can be enhanced by the addition of accessory enzymes, such as xylanases. Lignin from steam pretreated biomasses is known to inhibit enzymes by non-productively binding enzymes and limiting access to cellulose. The effect of enzymatically isolated lignin on the hydrolysis of xylan by four glycoside hydrolase (GH) family 11 xylanases was studied. Two xylanases from the mesophilic Trichoderma reesei, TrXyn1, TrXyn2, and two forms of a thermostable metagenomic xylanase Xyl40 were compared.
Results
Lignin isolated from steam pretreated spruce decreased the hydrolysis yields of xylan for all the xylanases at 40 and 50 °C. At elevated hydrolysis temperature of 50 °C, the least thermostable xylanase TrXyn1 was most inhibited by lignin and the most thermostable xylanase, the catalytic domain (CD) of Xyl40, was least inhibited by lignin. Enzyme activity and binding to lignin were studied after incubation of the xylanases with lignin for up to 24 h at 40 °C. All the studied xylanases bound to lignin, but the thermostable xylanases retained 22–39% of activity on the lignin surface for 24 h, whereas the mesophilic T. reesei xylanases become inactive. Removing of N-glycans from the catalytic domain of Xyl40 increased lignin inhibition in hydrolysis of xylan when compared to the glycosylated form. By comparing the 3D structures of these xylanases, features contributing to the increased thermal stability of Xyl40 were identified.
Conclusions
High thermal stability of xylanases Xyl40 and Xyl40-CD enabled the enzymes to remain partially active on the lignin surface. N-glycosylation of the catalytic domain of Xyl40 increased the lignin tolerance of the enzyme. Thermostability of Xyl40 was most likely contributed by a disulphide bond and salt bridge in the N-terminal and α-helix regions.
Graphical Abstract
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Chen L, Jiang K, Zhou Y, Zhu L, Chen X. Improving the Thermostability of α-Glucosidase from Xanthomonas campestris through Proline Substitutions Guided by Semi-rational Design. BIOTECHNOL BIOPROC E 2022. [DOI: 10.1007/s12257-022-0129-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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6
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Li G, Zhou X, Li Z, Liu Y, Liu D, Miao Y, Wan Q, Zhang R. Significantly improving the thermostability of a hyperthermophilic GH10 family xylanase XynAF1 by semi-rational design. Appl Microbiol Biotechnol 2021; 105:4561-4576. [PMID: 34014347 DOI: 10.1007/s00253-021-11340-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 04/16/2021] [Accepted: 05/09/2021] [Indexed: 11/28/2022]
Abstract
Xylanases have a broad range of applications in industrial biotechnologies, which require the enzymes to resist the high-temperature environments. The majority of xylanases have maximum activity at moderate temperatures, which limited their potential applications in industries. In this study, a thermophilic GH10 family xylanase XynAF1 from the high-temperature composting strain Aspergillus fumigatus Z5 was characterized and engineered to further improve its thermostability. XynAF1 has the optimal reaction temperature of 90 °C. The crystal structure of XynAF1 was obtained by X-ray diffraction after heterologous expression, purification, and crystallization. The high-resolution X-ray crystallographic structure of the protein-product complex was obtained by soaking the apo-state crystal with xylotetraose. Structure analysis indicated that XynAF1 has a rigid skeleton, which helps to maintain the hyperthermophilic characteristic. The homologous structure analysis and the catalytic center mutant construction of XynAF1 indicated the conserved catalytic center contributed to the high optimum catalytic temperature. The amino acids in the surface of xylanase XynAF1 which might influence the enzyme thermostability were identified by the structure analysis. Combining the rational design with the saturation mutation at the high B-value regions, the integrative mutant XynAF1-AC with a 6-fold increase of thermostability was finally obtained. This study efficiently improved the thermostability of a GH10 family xylanase by semi-rational design, which provided a new biocatalyst for high-temperature biotechnological applications. KEY POINTS: • Obtained the crystal structure of GH10 family hyperthermophilic xylanase XynAF1. • Shed light on the understanding of the GH10 family xylanase thermophilic mechanism. • Constructed a 6-fold increased thermostability recombinant xylanase.
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Affiliation(s)
- Guangqi Li
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China.,Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Xuan Zhou
- National Agricultural Technology Extension and Service Center, Beijing, 100125, People's Republic of China
| | - Zhihong Li
- College of Science, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Yunpeng Liu
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China
| | - Dongyang Liu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Youzhi Miao
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Qun Wan
- College of Science, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China. .,The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
| | - Ruifu Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, People's Republic of China. .,Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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7
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Chi MC, Liao TY, Lin MG, Lin LL, Wang TF. Expression and physicochemical characterization of an N-terminal polyhistidine-tagged phosphotriesterase from the soil bacterium Brevundimonas diminuta. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101811] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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8
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Hebal H, Parviainen A, Anbarasan S, Li H, Makkonen L, Bankar S, King AW, Kilpeläinen I, Benallaoua S, Turunen O. Inhibition of hyperthermostable xylanases by superbase ionic liquids. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.03.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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9
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Li Q, Wu T, Duan Y, Pei J, Zhao L. Improving the Thermostability and pH Stability of Aspergillus niger Xylanase by Site-directed Mutagenesis. APPL BIOCHEM MICRO+ 2019. [DOI: 10.1134/s0003683819020108] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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On-site produced and commercially available alkali-active xylanases compared for xylan extraction from sugarcane bagasse. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2019. [DOI: 10.1016/j.bcab.2019.101081] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Li C, Li J, Wang R, Li X, Li J, Deng C, Wu M. Substituting Both the N-Terminal and “Cord” Regions of a Xylanase from Aspergillus oryzae to Improve Its Temperature Characteristics. Appl Biochem Biotechnol 2018; 185:1044-1059. [DOI: 10.1007/s12010-017-2681-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 12/19/2017] [Indexed: 10/18/2022]
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12
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Wang Y, Shu T, Fan P, Zhang H, Turunen O, Xiong H, Yu L. Characterization of a recombinant alkaline thermostable β-mannanase and its application in eco-friendly ramie degumming. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.06.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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13
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Bacterial community shift for monitoring the co-composting of oil palm empty fruit bunch and palm oil mill effluent anaerobic sludge. ACTA ACUST UNITED AC 2017; 44:869-877. [DOI: 10.1007/s10295-017-1916-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/31/2017] [Indexed: 11/26/2022]
Abstract
Abstract
A recently developed rapid co-composting of oil palm empty fruit bunch (OPEFB) and palm oil mill effluent (POME) anaerobic sludge is beginning to attract attention from the palm oil industry in managing the disposal of these wastes. However, a deeper understanding of microbial diversity is required for the sustainable practice of the co-compositing process. In this study, an in-depth assessment of bacterial community succession at different stages of the pilot scale co-composting of OPEFB-POME anaerobic sludge was performed using 454-pyrosequencing, which was then correlated with the changes of physicochemical properties including temperature, oxygen level and moisture content. Approximately 58,122 of 16S rRNA gene amplicons with more than 500 operational taxonomy units (OTUs) were obtained. Alpha diversity and principal component analysis (PCoA) indicated that bacterial diversity and distributions were most influenced by the physicochemical properties of the co-composting stages, which showed remarkable shifts of dominant species throughout the process. Species related to Devosia yakushimensis and Desemzia incerta are shown to emerge as dominant bacteria in the thermophilic stage, while Planococcus rifietoensis correlated best with the later stage of co-composting. This study proved the bacterial community shifts in the co-composting stages corresponded with the changes of the physicochemical properties, and may, therefore, be useful in monitoring the progress of co-composting and compost maturity.
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Chang X, Xu B, Bai Y, Luo H, Ma R, Shi P, Yao B. Role of N-linked glycosylation in the enzymatic properties of a thermophilic GH 10 xylanase from Aspergillus fumigatus expressed in Pichia pastoris. PLoS One 2017; 12:e0171111. [PMID: 28187141 PMCID: PMC5302446 DOI: 10.1371/journal.pone.0171111] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 01/15/2017] [Indexed: 11/18/2022] Open
Abstract
N-Glycosylation is a posttranslational modification commonly occurred in fungi and plays roles in a variety of enzyme functions. In this study, a xylanase (Af-XYNA) of glycoside hydrolase (GH) family 10 from Aspergillus fumigatus harboring three potential N-glycosylation sites (N87, N124 and N335) was heterologously produced in Pichia pastoris. The N-glycosylated Af-XYNA (WT) exhibited favorable temperature and pH optima (75°C and pH 5.0) and good thermostability (maintaining stable at 60°C). To reveal the role of N-glycosylation on Af-XYNA, the enzyme was deglycosylated by endo-β-N-acetylglucosaminidase H (DE) or modified by site-directed mutagenesis at N124 (N124T). The deglycosylated DE and mutant N124T showed narrower pH adaptation range, lower specific activity, and worse pH and thermal stability. Further thermodynamic analysis revealed that the enzyme with higher N-glycosylation degree was more thermostable. This study demonstrated that the effects of glycosylation at different degrees and sites were diverse, in which the glycan linked to N124 played a key role in pH and thermal stability of Af-XYNA.
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Affiliation(s)
- Xiaoyu Chang
- College of Biological Sciences and Engineering, Jiangxi Agricultural University, Nanchang, People’s Republic of China
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Bo Xu
- College of Biological Sciences and Engineering, Jiangxi Agricultural University, Nanchang, People’s Republic of China
- * E-mail: (BX); (PS)
| | - Yingguo Bai
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Huiying Luo
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Rui Ma
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Pengjun Shi
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
- * E-mail: (BX); (PS)
| | - Bin Yao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
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Nuylert A, Ishida Y, Asano Y. Effect of Glycosylation on the Biocatalytic Properties of Hydroxynitrile Lyase from the Passion Fruit, Passiflora edulis: A Comparison of Natural and Recombinant Enzymes. Chembiochem 2017; 18:257-265. [PMID: 27914120 DOI: 10.1002/cbic.201600447] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Indexed: 11/08/2022]
Abstract
A hydroxynitrile lyase from the passion fruit Passiflora edulis (PeHNL) was isolated from the leaves and showed high stability in biphasic co-organic solvent systems for cyanohydrin synthesis. Cyanohydrins are important building blocks for the production of fine chemicals and pharmaceuticals. Thus, to enhance production yields of PeHNL for industrial applications, we cloned and expressed recombinant PeHNL in Escherichia coli BL21(DE3) and Pichia pastoris GS115 cells without a signal peptide sequence. The aim of this study is to determine the effect of N-glycosylation on enzyme stability and catalytic properties in microbial expression systems. PeHNL from leaves (PeHNL-N) and that expressed in P. pastoris (PeHNL-P) were glycosylated, whereas that expressed in E. coli (PeHNL-E) was not. The enzymes PeHNL-N and PeHNL-P showed much better thermostability, pH stability, and organic solvent tolerance than the deglycosylated enzyme PeHNL-E and the deglycosylated mutant N105Q from P. pastoris (PeHNL-P-N105Q). The glycosylated PeHNL-P also efficiently performed transcyanation of (R)-mandelonitrile with a 98 % enantiomeric excess in a biphasic system with diisopropyl ether. These data demonstrate the efficacy of these methods for improving enzyme expression and stability for industrial application through N-glycosylation.
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Affiliation(s)
- Aem Nuylert
- Biotechnology Research Center, Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Yuko Ishida
- Biotechnology Research Center, Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan.,Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Yasuhisa Asano
- Biotechnology Research Center, Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan.,Asano Active Enzyme Molecule Project, ERATO, JST, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
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16
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Anbarasan S, Wahlström R, Hummel M, Ojamo H, Sixta H, Turunen O. High stability and low competitive inhibition of thermophilic Thermopolyspora flexuosa GH10 xylanase in biomass-dissolving ionic liquids. Appl Microbiol Biotechnol 2016; 101:1487-1498. [DOI: 10.1007/s00253-016-7922-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 09/17/2016] [Accepted: 10/04/2016] [Indexed: 12/24/2022]
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17
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Ergün BG, Çalık P. Lignocellulose degrading extremozymes produced by Pichia pastoris: current status and future prospects. Bioprocess Biosyst Eng 2016; 39:1-36. [PMID: 26497303 DOI: 10.1007/s00449-015-1476-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 09/21/2015] [Indexed: 02/06/2023]
Abstract
In this review article, extremophilic lignocellulosic enzymes with special interest on xylanases, β-mannanases, laccases and finally cellulases, namely, endoglucanases, exoglucanases and β-glucosidases produced by Pichia pastoris are reviewed for the first time. Recombinant lignocellulosic extremozymes are discussed from the perspectives of their potential application areas; characteristics of recombinant and native enzymes; the effects of P. pastoris expression system on recombinant extremozymes; and their expression levels and applied strategies to increase the enzyme expression yield. Further, effects of enzyme domains on activity and stability, protein engineering via molecular dynamics simulation and computational prediction, and site-directed mutagenesis and amino acid modifications done are also focused. Superior enzyme characteristics and improved stability due to the proper post-translational modifications and better protein folding performed by P. pastoris make this host favourable for extremozyme production. Especially, glycosylation contributes to the structure, function and stability of enzymes, as generally glycosylated enzymes produced by P. pastoris exhibit better thermostability than non-glycosylated enzymes. However, there has been limited study on enzyme engineering to improve catalytic efficiency and stability of lignocellulosic enzymes. Thus, in the future, studies should focus on protein engineering to improve stability and catalytic efficiency via computational modelling, mutations, domain replacements and fusion enzyme technology. Also metagenomic data need to be used more extensively to produce novel enzymes with extreme characteristics and stability.
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18
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Yu T, Anbarasan S, Wang Y, Telli K, Aslan AS, Su Z, Zhou Y, Zhang L, Iivonen P, Havukainen S, Mentunen T, Hummel M, Sixta H, Binay B, Turunen O, Xiong H. Hyperthermostable Thermotoga maritima xylanase XYN10B shows high activity at high temperatures in the presence of biomass-dissolving hydrophilic ionic liquids. Extremophiles 2016; 20:515-24. [PMID: 27240671 PMCID: PMC4921120 DOI: 10.1007/s00792-016-0841-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 05/15/2016] [Indexed: 01/16/2023]
Abstract
The gene of Thermotoga maritima GH10 xylanase (TmXYN10B) was synthesised to study the extreme limits of this hyperthermostable enzyme at high temperatures in the presence of biomass-dissolving hydrophilic ionic liquids (ILs). TmXYN10B expressed from Pichia pastoris showed maximal activity at 100 °C and retained 92 % of maximal activity at 105 °C in a 30-min assay. Although the temperature optimum of activity was lowered by 1-ethyl-3-methylimidazolium acetate ([EMIM]OAc), TmXYN10B retained partial activity in 15-35 % hydrophilic ILs, even at 75-90 °C. TmXYN10B retained over 80 % of its activity at 90 °C in 15 % [EMIM]OAc and 15-25 % 1-ethyl-3-methylimidazolium dimethylphosphate ([EMIM]DMP) during 22-h reactions. [EMIM]OAc may rigidify the enzyme and lower V max. However, only minor changes in kinetic parameter K m showed that competitive inhibition by [EMIM]OAc of TmXYN10B is minimal. In conclusion, when extended enzymatic reactions under extreme conditions are required, TmXYN10B shows extraordinary potential.
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Affiliation(s)
- Tianyi Yu
- South-Central University for Nationalities, College of Life Science, Wuhan, 430074, China
| | - Sasikala Anbarasan
- Department of Biotechnology and Chemical Technology, School of Chemical Technology, Aalto University, 00076, Aalto, Finland
| | - Yawei Wang
- South-Central University for Nationalities, College of Life Science, Wuhan, 430074, China
| | - Kübra Telli
- Department of Biotechnology and Chemical Technology, School of Chemical Technology, Aalto University, 00076, Aalto, Finland
| | - Aşkın Sevinç Aslan
- Department of Biotechnology and Chemical Technology, School of Chemical Technology, Aalto University, 00076, Aalto, Finland
| | - Zhengding Su
- Hubei University of Technology, Wuhan, 430068, China
| | - Yin Zhou
- Wuhan Sunhy Biology Co., Ltd, Wuhan, 430074, China
| | - Li Zhang
- South-Central University for Nationalities, College of Life Science, Wuhan, 430074, China
| | - Piia Iivonen
- Department of Biotechnology and Chemical Technology, School of Chemical Technology, Aalto University, 00076, Aalto, Finland
| | - Sami Havukainen
- Department of Biotechnology and Chemical Technology, School of Chemical Technology, Aalto University, 00076, Aalto, Finland
| | - Tero Mentunen
- Department of Biotechnology and Chemical Technology, School of Chemical Technology, Aalto University, 00076, Aalto, Finland
| | - Michael Hummel
- Department of Forest Products Technology, School of Chemical Technology, Aalto University, 00076, Aalto, Finland
| | - Herbert Sixta
- Department of Forest Products Technology, School of Chemical Technology, Aalto University, 00076, Aalto, Finland
| | - Baris Binay
- Department of Bioengineering, Gebze Technical University, 41400, Gebze Kocaeli, Turkey
| | - Ossi Turunen
- Department of Biotechnology and Chemical Technology, School of Chemical Technology, Aalto University, 00076, Aalto, Finland.
| | - Hairong Xiong
- South-Central University for Nationalities, College of Life Science, Wuhan, 430074, China.
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19
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Characterization of a new acidic NAD + -dependent formate dehydrogenase from thermophilic fungus Chaetomium thermophilum. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2015.09.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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20
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Zhang L, Ma H, Zhang H, Xun L, Chen G, Wang L. Thermomyces lanuginosus is the dominant fungus in maize straw composts. BIORESOURCE TECHNOLOGY 2015; 197:266-75. [PMID: 26342338 DOI: 10.1016/j.biortech.2015.08.089] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 08/22/2015] [Accepted: 08/24/2015] [Indexed: 05/22/2023]
Abstract
The microbial community composition and function of three self-heating maize straw composts were compared by integrated meta-omics. The results revealed that the fungal communities were primarily dominated by the phylum Ascomycota (>90%) regardless of different nitrogen sources, which were exclusively composed of the Thermomyces, a genus of hemicellulose degraders. The bacterial community composition was affected by the addition of nitrogen sources, as the abundance of the Actinobacteria increased, while the Proteobacteria and Bacteroidetes decreased. Various hemicellulases and cellulases were detected in the composts, and the major xylanase secreted by Thermomyces lanuginosus was always present, revealing that it was the dominant fungus in hemicellulose hydrolysis and that bacteria and fungi might synergistically degrade lignocellulose. Thus, microbial communities in composts may develop a simple and stable structure of a dominant fungal species and limited numbers of bacterial species under the selective pressure of high temperature and maize straw as starting materials.
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Affiliation(s)
- Lili Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Haixia Ma
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Huaiqiang Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Luying Xun
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Guanjun Chen
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China.
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21
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Amore A, Serpico A, Amoresano A, Vinciguerra R, Faraco V. Analysis of the role of O-glycosylation in GH51 α-L-arabinofuranosidase from Pleurotus ostreatus. Biotechnol Appl Biochem 2015; 62:727-37. [PMID: 25471797 PMCID: PMC5032992 DOI: 10.1002/bab.1325] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 11/25/2014] [Indexed: 11/11/2022]
Abstract
In this study, the recombinant α-L-arabinofuranosidase from the fungus Pleurotus ostreatus (rPoAbf) was subjected to site-directed mutagenesis with the aim of elucidating the role of glycosylation on the properties of the enzyme at the level of S160 residue. As a matter of fact, previous mass spectral analyses had led to the localization of a single O-glycosylation at this site. Recombinant expression and characterization of the rPoAbf mutant S160G was therefore performed. It was shown that the catalytic properties are slightly changed by the mutation, with a more evident modification of the Kcat and KM toward the synthetic substrate pN-glucopyranoside. More importantly, the mutation negatively affected the stability of the enzyme at various pHs and temperatures. Circular dichroism (CD) analyses showed a minimum at 210 nm for wild-type (wt) rPoAbf, typical of the beta-sheets structure, whereas this minimum is shifted for rPoAbf S160G, suggesting the presence of an unfolded structure. A similar behavior was revealed when wt rPoAbf was enzymatically deglycosylated. CD structural analyses of both the site-directed mutant and the enzymatically deglycosylated wild-type enzyme indicate a role of the glycosylation at the S160 residue in rPoAbf secondary structure stability.
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Affiliation(s)
- Antonella Amore
- Department of Chemical SciencesUniversity of Naples “Federico II,” Complesso Universitario Monte S. Angelovia CinthiaNaplesItaly
| | - Annabel Serpico
- Department of Chemical SciencesUniversity of Naples “Federico II,” Complesso Universitario Monte S. Angelovia CinthiaNaplesItaly
| | - Angela Amoresano
- Department of Chemical SciencesUniversity of Naples “Federico II,” Complesso Universitario Monte S. Angelovia CinthiaNaplesItaly
| | - Roberto Vinciguerra
- Department of Chemical SciencesUniversity of Naples “Federico II,” Complesso Universitario Monte S. Angelovia CinthiaNaplesItaly
| | - Vincenza Faraco
- Department of Chemical SciencesUniversity of Naples “Federico II,” Complesso Universitario Monte S. Angelovia CinthiaNaplesItaly
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22
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Gavrilov Y, Shental-Bechor D, Greenblatt HM, Levy Y. Glycosylation May Reduce Protein Thermodynamic Stability by Inducing a Conformational Distortion. J Phys Chem Lett 2015; 6:3572-3577. [PMID: 26722726 DOI: 10.1021/acs.jpclett.5b01588] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Glycosylation plays not only a functional role but can also modify the biophysical properties of the modified protein. Usually, natural glycosylation results in protein stabilization; however, in vitro and in silico studies showed that sometimes glycosylation results in thermodynamic destabilization. Here, we applied coarse-grained and all-atom molecular dynamics simulations to understand the mechanism underlying the loss of stability of the MM1 protein by glycosylation. We show that the origin of the destabilization is a conformational distortion of the protein caused by the interaction of the monosaccharide with the protein surface. Though glycosylation creates new short-range glycan-protein interactions that stabilize the conjugated protein, it breaks long-range protein-protein interactions. This has a destabilizing effect because the probability of long- and short-range interactions forming differs between the folded and unfolded states. The destabilization originates not from simple loss of interactions but due to a trade-off between the short- and long-range interactions.
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Affiliation(s)
- Yulian Gavrilov
- Department of Structural Biology, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Dalit Shental-Bechor
- Department of Structural Biology, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Harry M Greenblatt
- Department of Structural Biology, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Yaakov Levy
- Department of Structural Biology, Weizmann Institute of Science , Rehovot 76100, Israel
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23
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Anbarasan S, Timoharju T, Barthomeuf J, Pastinen O, Rouvinen J, Leisola M, Turunen O. Effect of active site mutation on pH activity and transglycosylation of Sulfolobus acidocaldarius β-glycosidase. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2015.05.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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24
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Li H, Voutilainen S, Ojamo H, Turunen O. Stability and activity of Dictyoglomus thermophilum GH11 xylanase and its disulphide mutant at high pressure and temperature. Enzyme Microb Technol 2015; 70:66-71. [DOI: 10.1016/j.enzmictec.2014.12.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 12/20/2014] [Indexed: 01/16/2023]
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25
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Effect of Temperature on Xylanase II from Trichoderma reesei QM 9414: A Calorimetric, Catalytic, and Conformational Study. Enzyme Res 2014; 2014:708676. [PMID: 25276420 PMCID: PMC4170777 DOI: 10.1155/2014/708676] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 07/23/2014] [Accepted: 07/24/2014] [Indexed: 11/17/2022] Open
Abstract
The secondary structure of xylanase II from Trichoderma reesei is lost in an apparent irreversible cooperative process as temperature is increased with a midpoint transition of 58.8 ± 0.1°C. The shift of the spectral centre of mass above 50°C is also apparently cooperative with midpoint transition of 56.3 ± 0.2°C, but the existence of two isofluorescent points in the fluorescence emission spectra suggests a non-two-state process. Further corroboration comes from differential scanning calorimetry experiments. At protein concentrations ≤0.56 mg·mL−1 the calorimetric transition is reversible and the data were fitted to a non-two-state model and deconvoluted into six transitions, whereas at concentrations greater than 0.56 mg·mL−1 the calorimetric transition is irreversible with an exothermic contribution to the thermogram. The apparent Tm increased linearly with the scan rate according to first order inactivation kinetics. The effect of additives on the calorimetric transition of xylanase is dependent on their nature. The addition of sorbitol transforms reversible transitions into irreversible transitions while stabilizing the protein as the apparent Tm increases linearly with sorbitol concentration. d-Glucono-1,5-lactone, a noncompetitive inhibitor in xylanase kinetics, and soluble xylan change irreversible processes into reversible processes at high protein concentration.
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26
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Zhang X, Zhong Y, Yang S, Zhang W, Xu M, Ma A, Zhuang G, Chen G, Liu W. Diversity and dynamics of the microbial community on decomposing wheat straw during mushroom compost production. BIORESOURCE TECHNOLOGY 2014; 170:183-195. [PMID: 25129234 DOI: 10.1016/j.biortech.2014.07.093] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 07/21/2014] [Accepted: 07/23/2014] [Indexed: 05/05/2023]
Abstract
The development of communities of three important composting players including actinobacteria, fungi and clostridia was explored during the composting of wheat straw for mushroom production. The results revealed the presence of highly diversified actinobacteria and fungal communities during the composting process. The diversity of the fungal community, however, sharply decreased in the mature compost. Furthermore, an apparent succession of both actinobacteria and fungi with intensive changes in the composition of communities was demonstrated during composting. Notably, cellulolytic actinomycetal and fungal genera represented by Thermopolyspora, Microbispora and Humicola were highly enriched in the mature compost. Analysis of the key cellulolytic genes revealed their prevalence at different composting stages including several novel glycoside hydrolase family 48 exocellulase lineages. The community of cellulolytic microbiota also changed substantially over time. The prevalence of the diversified cellulolytic microorganisms holds the great potential of mining novel lignocellulose decomposing enzymes from this specific ecosystem.
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Affiliation(s)
- Xi Zhang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, No. 27, Shanda South Road, Jinan 250100, Shandong, PR China
| | - Yaohua Zhong
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, No. 27, Shanda South Road, Jinan 250100, Shandong, PR China.
| | - Shida Yang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, No. 27, Shanda South Road, Jinan 250100, Shandong, PR China
| | - Weixin Zhang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, No. 27, Shanda South Road, Jinan 250100, Shandong, PR China
| | - Meiqing Xu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, No. 27, Shanda South Road, Jinan 250100, Shandong, PR China
| | - Anzhou Ma
- Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, No. 85, Shuangqing Road, Beijing, PR China
| | - Guoqiang Zhuang
- Research Center for Eco-Environment Sciences, Chinese Academy of Sciences, No. 85, Shuangqing Road, Beijing, PR China
| | - Guanjun Chen
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, No. 27, Shanda South Road, Jinan 250100, Shandong, PR China
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, No. 27, Shanda South Road, Jinan 250100, Shandong, PR China.
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27
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Thermal behaviour and tolerance to ionic liquid [emim]OAc in GH10 xylanase from Thermoascus aurantiacus SL16W. Extremophiles 2014; 18:1023-34. [DOI: 10.1007/s00792-014-0679-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 07/13/2014] [Indexed: 02/01/2023]
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28
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Tu T, Bai Y, Luo H, Ma R, Wang Y, Shi P, Yang P, Meng K, Yao B. A novel bifunctional pectinase from Penicillium oxalicum SX6 with separate pectin methylesterase and polygalacturonase catalytic domains. Appl Microbiol Biotechnol 2014; 98:5019-28. [DOI: 10.1007/s00253-014-5533-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 01/07/2014] [Accepted: 01/12/2014] [Indexed: 01/28/2023]
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29
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Thermostability improvement of a streptomyces xylanase by introducing proline and glutamic acid residues. Appl Environ Microbiol 2014; 80:2158-65. [PMID: 24463976 DOI: 10.1128/aem.03458-13] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Protein engineering is commonly used to improve the robustness of enzymes for activity and stability at high temperatures. In this study, we identified four residues expected to affect the thermostability of Streptomyces sp. strain S9 xylanase XynAS9 through multiple-sequence analysis (MSA) and molecular dynamic simulations (MDS). Site-directed mutagenesis was employed to construct five mutants by replacing these residues with proline or glutamic acid (V81P, G82E, V81P/G82E, D185P/S186E, and V81P/G82E/D185P/S186E), and the mutant and wild-type enzymes were expressed in Pichia pastoris. Compared to the wild-type XynAS9, all five mutant enzymes showed improved thermal properties. The activity and stability assays, including circular dichroism and differential scanning calorimetry, showed that the mutations at positions 81 and 82 increased the thermal performance more than the mutations at positions 185 and 186. The mutants with combined substitutions (V81P/G82E and V81P/G82E/D185P/S186E) showed the most pronounced shifts in temperature optima, about 17°C upward, and their half-lives for thermal inactivation at 70°C and melting temperatures were increased by >9 times and approximately 7.0°C, respectively. The mutation combination of V81P and G82E in adjacent positions more than doubled the effect of single mutations. Both mutation regions were at the end of long secondary-structure elements and probably rigidified the local structure. MDS indicated that a long loop region after positions 81 and 82 located at the end of the inner β-barrel was prone to unfold. The rigidified main chain and filling of a groove by the mutations on the bottom of the active site canyon may stabilize the mutants and thus improve their thermostability.
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30
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Lu H, Luo H, Shi P, Huang H, Meng K, Yang P, Yao B. A novel thermophilic endo-β-1,4-mannanase from Aspergillus nidulans XZ3: functional roles of carbohydrate-binding module and Thr/Ser-rich linker region. Appl Microbiol Biotechnol 2013; 98:2155-63. [DOI: 10.1007/s00253-013-5112-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Revised: 07/08/2013] [Accepted: 07/09/2013] [Indexed: 10/26/2022]
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31
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Du Y, Shi P, Huang H, Zhang X, Luo H, Wang Y, Yao B. Characterization of three novel thermophilic xylanases from Humicola insolens Y1 with application potentials in the brewing industry. BIORESOURCE TECHNOLOGY 2013; 130:161-167. [PMID: 23306124 DOI: 10.1016/j.biortech.2012.12.067] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 12/08/2012] [Accepted: 12/10/2012] [Indexed: 06/01/2023]
Abstract
Three xylanase genes (xynA, xynB, xynC) of glycosyl hydrolase family 10 were identified in Humicola insolens Y1. The deduced protein sequences showed the highest identity of ⩽83% to known fungal xylanases and of ⩽38% with each other. Recombinant XynA-C produced in Pichia pastoris showed optimal activities at pH 6.0-7.0 and at high temperature (70-80°C), and exhibited good stability over a broad pH range and temperatures at 60°C. The gene xynC produced by H. insolens Y1 (named XynW) was similar in enzyme properties with XynC expressed by Pichia. XynA exhibited better alkaline adaptation and thermostability, and had higher catalytic efficiency and wider substrate specificity. Under simulated mashing conditions, addition of XynA-C showed better performance on filtration acceleration (37.4%) and viscosity reduction (13.5%) than Ultraflo from Novozyme. Thus the three xylanases represent good candidates for application in the brewing industry.
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Affiliation(s)
- Yanlong Du
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
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32
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Wang Y, Fu Z, Huang H, Zhang H, Yao B, Xiong H, Turunen O. Improved thermal performance of Thermomyces lanuginosus GH11 xylanase by engineering of an N-terminal disulfide bridge. BIORESOURCE TECHNOLOGY 2012; 112:275-279. [PMID: 22425398 DOI: 10.1016/j.biortech.2012.02.092] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 02/15/2012] [Accepted: 02/17/2012] [Indexed: 05/31/2023]
Abstract
In order to increase the stability of thermophilic Thermomyces lanuginosus GH11 xylanase, TLX, a disulfide bridge Q1C-Q24C was introduced into the N-terminal region of the enzyme. The apparent temperature optimum shifted upwards at pH 6.5 by about 10°C to 75°C. The resistance to thermal inactivation also increased by about 10°C. The melting temperature measured by CD spectroscopy increased from 66 to 74°C. Therefore the N-terminal disulfide bridge increased both kinetic and thermodynamic stability almost equally. At pH 8 and 70°C, the disulfide bridge increased the enzyme half-life 20-fold in the presence of substrate. In contrast to the situation in acidic-neutral pH, the substrate decreased the thermostability of xylanases in alkaline pH. The upper limit for the performance of the disulfide bridge mutant at pH 9 was 75°C. This study showed that N-terminal disulfide bridges can stabilize even thermostable family GH11 xylanases.
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Affiliation(s)
- Yawei Wang
- Engineering Research Centre of Bioresources in Southern China, College of Life Science, South-central University for Nationalities, Wuhan 430074, China
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33
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Hosing AS, Valerie NCK, Dziegielewski J, Brautigan DL, Larner JM. PP6 regulatory subunit R1 is bidentate anchor for targeting protein phosphatase-6 to DNA-dependent protein kinase. J Biol Chem 2012; 287:9230-9. [PMID: 22298787 DOI: 10.1074/jbc.m111.333708] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA-dependent protein kinase (DNA-PK) becomes activated in response to DNA double strand breaks, initiating repair by the non-homologous end joining pathway. DNA·PK complexes with the regulatory subunit SAPSR1 (R1) of protein phosphatase-6 (PP6). Knockdown of either R1 or PP6c prevents DNA-PK activation in response to ionizing radiation-induced DNA damage and radiosensitizes glioblastoma cells. Here, we demonstrate that R1 is necessary for and bridges the interaction between DNA-PK and PP6c. Using R1 deletion mutants, DNA-PK binding was mapped to two distinct regions of R1 spanning residues 1-326 and 522-700. Either region expressed alone was sufficient to bind DNA-PK, but only deletion of residues 1-326, not 522-700, eliminated interaction of R1 with DNA-PK. We assign 1-326 as the dominant domain and 522-700 as the supporting region. These results demonstrate that R1 acts as a bidentate anchor to DNA-PK and recruits PP6c. Targeting the dominant interface with small molecule or peptidomimetic inhibitors could specifically prevent activation of DNA-PK and thereby sensitize cells to ionizing radiation and other genotoxic agents.
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Affiliation(s)
- Amol S Hosing
- Department of Radiation Oncology, University of Virginia Health System, Charlottesville, Virginia 22908, USA
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34
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Metagenomic cellulases highly tolerant towards the presence of ionic liquids—linking thermostability and halotolerance. Appl Microbiol Biotechnol 2011; 95:135-46. [DOI: 10.1007/s00253-011-3732-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 10/30/2011] [Accepted: 11/15/2011] [Indexed: 10/15/2022]
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35
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Cheng CL, Lo YC, Lee KS, Lee DJ, Lin CY, Chang JS. Biohydrogen production from lignocellulosic feedstock. BIORESOURCE TECHNOLOGY 2011; 102:8514-23. [PMID: 21570833 DOI: 10.1016/j.biortech.2011.04.059] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2011] [Revised: 04/18/2011] [Accepted: 04/19/2011] [Indexed: 05/16/2023]
Abstract
Due to the recent energy crisis and rising concern over climate change, the development of clean alternative energy sources is of significant interest. Biohydrogen produced from cellulosic feedstock, such as second generation feedstock (lignocellulosic biomass) and third generation feedstock (carbohydrate-rich microalgae), is a promising candidate as a clean, CO2-neutral, non-polluting and high efficiency energy carrier to meet the future needs. This article reviews state-of-the-art technology on lignocellulosic biohydrogen production in terms of feedstock pretreatment, saccharification strategy, and fermentation technology. Future developments of integrated biohydrogen processes leading to efficient waste reduction, low CO2 emission and high overall hydrogen yield is discussed.
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Affiliation(s)
- Chieh-Lun Cheng
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan
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36
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López G, Bañares-Hidalgo A, Estrada P. Xylanase II from Trichoderma reesei QM 9414: conformational and catalytic stability to Chaotropes, Trifluoroethanol, and pH changes. J Ind Microbiol Biotechnol 2010; 38:113-25. [DOI: 10.1007/s10295-010-0836-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Accepted: 07/26/2010] [Indexed: 11/24/2022]
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