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Zhang K, Qi X, Feng N, Wang Y, Wei H, Liu M. Antioxidant capacity of xylooligosaccharides generated from beechwood xylan by recombinant family GH10 Aspergillus niger xylanase A and insights into the enzyme's competitive inhibition by riceXIP. Enzyme Microb Technol 2024; 179:110456. [PMID: 38754147 DOI: 10.1016/j.enzmictec.2024.110456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/21/2024] [Accepted: 05/08/2024] [Indexed: 05/18/2024]
Abstract
In this study, the family GH10 xylanase AnXylA10 derived from Aspergillus niger JL15 strain was expressed in Pichia pastoris X33. The recombinant xylanase, reAnXylA10 exhibited optimal activity at 40 ℃ and pH 5.0. The hydrolysates generated from beechwood xylan using reAnXylA10 primarily consisted of xylobiose (X2) to xylohexaose (X6) and demonstrated remarkable antioxidant capacity. Furthermore, the rice xylanase inhibitory protein (riceXIP) was observed to competitively inhibit reAnXylA10, exhibiting an inhibition constant (Ki) of 140.6 nM. Molecular dynamics (MD) simulations of AnXylA10-riceXIP complex revealed that the α-7 helix (Q225-S238) of riceXIP intruded into the catalytic pocket of AnXylA10, thereby obstructing substrate access to the active site. Specifically, residue K226 of riceXIP formed robust interactions with E136 and E242, the two catalytic sites of AnXylA10, predominantly through high-occupied hydrogen bonds. Based on QTAIM, electron densities for the atom pairs K226riceXIP@HZ1-E136AnXylA10@OE2 and K226riceXIP@HZ3-E242AnXylA10@OE1 were determined to be 0.04628 and 0.02914 a.u., respectively. Binding free energy of AnXylA10-riceXIP complex was -59.0±7.6 kcal/mol, significantly driven by electrostatic and van der Waals forces. Gaining insights into the interaction between xylanase and its inhibitors, and mining the inhibition mechanism in depth, will facilitate the design of innovative GH10 family xylanases that are both highly efficient and resistant to inhibitors.
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Affiliation(s)
- Keer Zhang
- Key Laboratory of Specialty Agri-product Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Xinyu Qi
- Key Laboratory of Specialty Agri-product Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Ningxin Feng
- Key Laboratory of Specialty Agri-product Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Yuzhu Wang
- Key Laboratory of Specialty Agri-product Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Huiwen Wei
- Key Laboratory of Specialty Agri-product Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Mingqi Liu
- Key Laboratory of Specialty Agri-product Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou 310018, China.
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2
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Li P, Hu C, Li Y, Ge L, Wu G, Lv B, Jiang W, Xi D. The cold - resistance mechanism of a mutagenic Volvariella volvacea strain VH3 with outstanding traits revealed by transcriptome profiling. BMC Microbiol 2021; 21:336. [PMID: 34876003 PMCID: PMC8653554 DOI: 10.1186/s12866-021-02396-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Accepted: 11/22/2021] [Indexed: 11/14/2022] Open
Abstract
Background The straw mushroom (Volvariella volvacea) is one of the important vegetables that is popular for its delicious taste. However, the straw mushroom is sensitive to low temperature, resulting in economic loss during transportation and storage. We obtained a novel straw mushroom strain, named VH3, via ultraviolet mutagenesis. Results Our study revealed that VH3 exhibited high cold resistance compared to an ordinary straw mushroom cultivar, V23. We found that the electrolyte leakages of VH3 were always significantly lower than that of V23 treated with 4 °C for 0 h, 2 h,4 h, 8 h, 16 h, and 24 h. Before cold treatment (0 h), there were no difference of MDA contents, SOD activities, and CAT activities between VH3 and V23. At the late stage (8 h, 26 h, and 24 h) of cold treatment, the MDA contents of VH3 were lower while both the SOD and CAT activities were higher than those of V23. To investigate the potential mechanisms of VH3 cold resistance, we performed transcriptome sequencing to detect the transcriptome profiling of VH3 and V23 after 0 h and 4 h cold treatment. Transcriptome sequencing revealed that 111 differentially expressed genes (DEG) between V23 (0 h) and VH3 (0 h) (V23–0_vs_VH3–0), consisting 50 up-regulated and 61 down-regulated DEGs. A total of 117 DEGs were obtained between V23 (4 h) and VH3(4 h) (V23–4_vs_VH3–4), containing 94 up-regulated and 23 down-regulated DEGs. Among these DEGs, VVO_00021 and VVO_00017 were up-regulated while VVO_00003, VVO_00004, VVO_00010, and VVO_00030 were down-regulated in V23–0_vs_VH3–0 and VH3–4_vs_V23–4. KEGG and GO analysis revealed that the 6 DEGs were annotated to pathways related to cold stress. Besides, the GA3 content was also decreased in VH3. Conclusions Collectively, our study first revealed that the increased cold resistance of VH3 might be caused by the expression change of VVO_00003, VVO_00004, VVO_00017, VVO_00021, and VVO_00030, and decreased GA3. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02396-8.
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Affiliation(s)
- Peng Li
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Cong Hu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Yujie Li
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Lei Ge
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Guogan Wu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Beibei Lv
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Wei Jiang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
| | - Dandan Xi
- Shanghai Key Laboratory of Protected Horticultural Technology, Protected Horticultural Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China.
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Koeksoy E, Bezuidt OM, Bayer T, Chan CS, Emerson D. Zetaproteobacteria Pan-Genome Reveals Candidate Gene Cluster for Twisted Stalk Biosynthesis and Export. Front Microbiol 2021; 12:679409. [PMID: 34220764 PMCID: PMC8250860 DOI: 10.3389/fmicb.2021.679409] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/06/2021] [Indexed: 12/15/2022] Open
Abstract
Twisted stalks are morphologically unique bacterial extracellular organo-metallic structures containing Fe(III) oxyhydroxides that are produced by microaerophilic Fe(II)-oxidizers belonging to the Betaproteobacteria and Zetaproteobacteria. Understanding the underlying genetic and physiological mechanisms of stalk formation is of great interest based on their potential as novel biogenic nanomaterials and their relevance as putative biomarkers for microbial Fe(II) oxidation on ancient Earth. Despite the recognition of these special biominerals for over 150 years, the genetic foundation for the stalk phenotype has remained unresolved. Here we present a candidate gene cluster for the biosynthesis and secretion of the stalk organic matrix that we identified with a trait-based analyses of a pan-genome comprising 16 Zetaproteobacteria isolate genomes. The “stalk formation in Zetaproteobacteria” (sfz) cluster comprises six genes (sfz1-sfz6), of which sfz1 and sfz2 were predicted with functions in exopolysaccharide synthesis, regulation, and export, sfz4 and sfz6 with functions in cell wall synthesis manipulation and carbohydrate hydrolysis, and sfz3 and sfz5 with unknown functions. The stalk-forming Betaproteobacteria Ferriphaselus R-1 and OYT-1, as well as dread-forming Zetaproteobacteria Mariprofundus aestuarium CP-5 and Mariprofundus ferrinatatus CP-8 contain distant sfz gene homologs, whereas stalk-less Zetaproteobacteria and Betaproteobacteria lack the entire gene cluster. Our pan-genome analysis further revealed a significant enrichment of clusters of orthologous groups (COGs) across all Zetaproteobacteria isolate genomes that are associated with the regulation of a switch between sessile and motile growth controlled by the intracellular signaling molecule c-di-GMP. Potential interactions between stalk-former unique transcription factor genes, sfz genes, and c-di-GMP point toward a c-di-GMP regulated surface attachment function of stalks during sessile growth.
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Affiliation(s)
- Elif Koeksoy
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States.,Leibniz Institute DSMZ (German Collection of Microorganisms and Cell Cultures), Braunschweig, Germany
| | - Oliver M Bezuidt
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
| | - Timm Bayer
- Geomicrobiology Group, Center for Applied Geoscience, University of Tübingen, Tübingen, Germany
| | - Clara S Chan
- Department of Earth Sciences, University of Delaware, Newark, DE, United States.,School of Marine Sciences and Policy, University of Delaware, Newark, DE, United States
| | - David Emerson
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, United States
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Azzouz Z, Bettache A, Boucherba N, Prieto A, Martinez MJ, Benallaoua S, de Eugenio LI. Optimization of β-1,4-Endoxylanase Production by an Aspergillus niger Strain Growing on Wheat Straw and Application in Xylooligosaccharides Production. Molecules 2021; 26:molecules26092527. [PMID: 33926080 PMCID: PMC8123676 DOI: 10.3390/molecules26092527] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/16/2021] [Accepted: 04/23/2021] [Indexed: 11/24/2022] Open
Abstract
Plant biomass constitutes the main source of renewable carbon on the planet. Its valorization has traditionally been focused on the use of cellulose, although hemicellulose is the second most abundant group of polysaccharides on Earth. The main enzymes involved in plant biomass degradation are glycosyl hydrolases, and filamentous fungi are good producers of these enzymes. In this study, a new strain of Aspergillus niger was used for hemicellulase production under solid-state fermentation using wheat straw as single-carbon source. Physicochemical parameters for the production of an endoxylanase were optimized by using a One-Factor-at-a-Time (OFAT) approach and response surface methodology (RSM). Maximum xylanase yield after RSM optimization was increased 3-fold, and 1.41- fold purification was achieved after ultrafiltration and ion-exchange chromatography, with about 6.2% yield. The highest activity of the purified xylanase was observed at 50 °C and pH 6. The enzyme displayed high thermal and pH stability, with more than 90% residual activity between pH 3.0–9.0 and between 30–40 °C, after 24 h of incubation, with half-lives of 30 min at 50 and 60 °C. The enzyme was mostly active against wheat arabinoxylan, and its kinetic parameters were analyzed (Km = 26.06 mg·mL−1 and Vmax = 5.647 U·mg−1). Wheat straw xylan hydrolysis with the purified β-1,4 endoxylanase showed that it was able to release xylooligosaccharides, making it suitable for different applications in food technology.
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Affiliation(s)
- Zahra Azzouz
- Laboratoire de Microbiologie Appliquée (LMA), Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, 06000 Bejaia, Algeria; (Z.A.); (A.B.); (N.B.)
| | - Azzeddine Bettache
- Laboratoire de Microbiologie Appliquée (LMA), Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, 06000 Bejaia, Algeria; (Z.A.); (A.B.); (N.B.)
| | - Nawel Boucherba
- Laboratoire de Microbiologie Appliquée (LMA), Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, 06000 Bejaia, Algeria; (Z.A.); (A.B.); (N.B.)
| | - Alicia Prieto
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas (CIB-CSIC), C/Ramiro de Maeztu 9, 28040 Madrid, Spain; (A.P.); (M.J.M.)
| | - Maria Jesus Martinez
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas (CIB-CSIC), C/Ramiro de Maeztu 9, 28040 Madrid, Spain; (A.P.); (M.J.M.)
| | - Said Benallaoua
- Laboratoire de Microbiologie Appliquée (LMA), Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, 06000 Bejaia, Algeria; (Z.A.); (A.B.); (N.B.)
- Correspondence: (S.B.); (L.I.d.E.)
| | - Laura Isabel de Eugenio
- Biotechnology for Lignocellulosic Biomass Group, Centro de Investigaciones Biológicas (CIB-CSIC), C/Ramiro de Maeztu 9, 28040 Madrid, Spain; (A.P.); (M.J.M.)
- Correspondence: (S.B.); (L.I.d.E.)
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Cloning, Expression, and Characterization of Xylanase G2 from Aspergillus oryzae VTCC-F187 in Aspergillus niger VTCC-F017. BIOMED RESEARCH INTERNATIONAL 2021. [DOI: 10.1155/2021/8840038] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The study focuses on engineering of recombinant Aspergillus niger to produce highly active xylanase. The xylanase G2 encoding gene originating from Aspergillus oryzae VTCC-F187 was cloned, amplified, and inserted into the pAN7.1GluA vector with specific primers possessing BamHI. The recombinant plasmid was introduced into Aspergillus niger VTCC-F017 by chemical methods. The recombinant strain was checked by polymerase chain reaction method and Southern blot. Next, the recombinant protein was expressed and purified by His-tag column. The molecular mass of the purified xylanase G2, as determined by sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE), was 21 kDa with a specific activity of 1025 IU/mg towards 0.5% (w/v) of birchwood xylan. The optimal temperature and pH were 55°C and pH 6.5, respectively. The enzyme was stable in a temperature ranges 25–40°C and a pH ranges 5–7. The presence of Tween 80 enhanced xylanase activity. Triton X-100, however, had no impact on the function of the enzyme. The xylanase activity was reduced by Tween 20, SDS, and organic solvents. The enzyme was completely inhibited by Hg2+ and partially by Zn2+, Fe2+, and Ag+, while it was slightly stimulated by K+ and EDTA.
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Velasco J, Oliva B, Mulinari EJ, Quintero LP, da Silva Lima A, Gonçalves AL, Gonçalves TA, Damasio A, Squina FM, Ferreira Milagres AM, Abdella A, Wilkins MR, Segato F. Heterologous expression and functional characterization of a GH10 endoxylanase from Aspergillus fumigatus var. niveus with potential biotechnological application. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2019; 24:e00382. [PMID: 31799141 PMCID: PMC6881608 DOI: 10.1016/j.btre.2019.e00382] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 08/26/2019] [Accepted: 09/26/2019] [Indexed: 10/25/2022]
Abstract
Xylanases decrease the xylan content in pretreated biomass releasing it from hemicellulose, thus improving the accessibility of cellulose for cellulases. In this work, an endo-β-1,4-xylanase from Aspergillus fumigatus var. niveus (AFUMN-GH10) was successfully expressed. The structural analysis and biochemical characterization showed this AFUMN-GH10 does not contain a carbohydrate-binding module. The enzyme retained its activity in a pH range from 4.5 to 7.0, with an optimal temperature at 60 °C. AFUMN-GH10 showed the highest activity in beechwood xylan. The mode of action of AFUMN-GH10 was investigated by hydrolysis of APTS-labeled xylohexaose, which resulted in xylotriose and xylobiose as the main products. AFUMN-GH10 released 27% of residual xylan from hydrothermally-pretreated corn stover and 14% of residual xylan from hydrothermally-pretreated sugarcane bagasse. The results showed that environmentally friendly pretreatment followed by enzymatic hydrolysis with AFUMN-GH10 in low concentration is a suitable method to remove part of residual and recalcitrant hemicellulose from biomass.
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Affiliation(s)
- Josman Velasco
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Bianca Oliva
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Evandro José Mulinari
- Department of Physics and Applied Sciences, São Carlos Institute of Physics, University of São Paulo, São Carlos, SP, Brazil
| | - Leidy Patricia Quintero
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Awana da Silva Lima
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Aline Larissa Gonçalves
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
| | - Thiago Augusto Gonçalves
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, SP, Brazil
| | - André Damasio
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil
| | - Fabio Marcio Squina
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil
- Programa de Processos Tecnológicos e Ambientais, Universidade de Sorocaba, Sorocaba, SP, Brazil
| | | | - Asmaa Abdella
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA
- Industrial Agricultural Products Center, University of Nebraska-Lincoln, Lincoln, NE, USA
- Department of Industrial Biotechnology, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Egypt
| | - Mark R. Wilkins
- Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA
- Industrial Agricultural Products Center, University of Nebraska-Lincoln, Lincoln, NE, USA
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Fernando Segato
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena, SP, Brazil
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Wu Z. Mixed fermentation of Aspergillus niger and Candida shehatae to produce bioethanol with ionic-liquid-pretreated bagasse. 3 Biotech 2019; 9:41. [PMID: 30675451 PMCID: PMC6328811 DOI: 10.1007/s13205-019-1570-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 01/03/2019] [Indexed: 10/27/2022] Open
Abstract
In this study, bagasse was pretreated with ionic liquid (IL) 1-butyl-3-methylimidazolium chloride ([Bmim]Cl) and 1% NaOH solution for initial activation of bagasse. A mixed fermentation of treated bagasse by Aspergillus niger and Candida shehatae showed the optimal conditions with the addition of C. shehatae 12 h later at a 1:1 proportion to A. niger. To further improve the ethanol production and obtain optimal fermentation conditions, a Plackett-Burman design was applied to screen the significant formulation and process variables. The optimal ethanol fermentation conditions with IL pretreated bagasse were determined using response surface methodology by Box-Behnken design. Three variables "initial pH, (NH4)2SO4, fermentation time" were regarded as significant factors in the optimization study. The resulting optimum fermentation conditions for bioethanol was identified as: initial pH of 5.89, (NH4)2SO4 concentration of 0.40 g/50 mL, and fermentation time of 3.60 days. The verification experimental ethanol concentration was 8.14 g/L, which agreed with the predicted value. An enhancement of approximately 153.58% compared with initial fermentation conditions in ethanol production was found using optimized conditions. It demonstrated that optimization methodology had a positive effect on the improvement of ethanol production. Under the optimal fermentation medium and conditions, the ethanol production with IL-pretreated bagasse and untreated bagasse was 8.14 g/L and 5.03 g/L, respectively, which exhibited 62% increase, compared to initial conditions with production of 3.21 g/L and 2.67 g/L, respectively, which displayed 20% increase. Both under optimal and original fermentation conditions, compared to the fermentation medium with untreated bagasse, all the results indicated that IL-pretreated bagasse resulted in higher ethanol production than untreated bagasse, demonstrating that IL-pretreated bagasse successfully increased the ethanol production in the mixed fermentation by A. niger and C. shehatae.
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Affiliation(s)
- Zaiqiang Wu
- Center for Molecular Metabolism, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, 210094 China
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Parvizpour S, Razmara J, Shamsir MS. Temperature adaptation analysis of a psychrophilic mannanase through structural, functional and molecular dynamics simulation. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1492721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Sepideh Parvizpour
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jafar Razmara
- Department of Computer Science, Faculty of Mathematical Sciences, University of Tabriz, Tabriz, Iran
| | - Mohd Shahir Shamsir
- Bioinformatics Research Group, Faculty of Bioscience and Medical Engineering, Universiti Teknologi Malaysia, Johor, Malaysia
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9
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Sharma S, Sharma V, Nargotra P, Bajaj BK. Process desired functional attributes of an endoxylanase of GH10 family from a new strain of Aspergillus terreus S9. Int J Biol Macromol 2018; 115:663-671. [DOI: 10.1016/j.ijbiomac.2018.04.096] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 04/14/2018] [Accepted: 04/18/2018] [Indexed: 10/17/2022]
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10
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Patel S, Rauf A, Meher BR. In silico analysis of ChtBD3 domain to find its role in bacterial pathogenesis and beyond. Microb Pathog 2017; 110:519-526. [PMID: 28760454 DOI: 10.1016/j.micpath.2017.07.047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 07/24/2017] [Accepted: 07/27/2017] [Indexed: 12/12/2022]
Abstract
Chitin binding domain 3, known by the acronym ChtBD3, is a domain in the enzymes and proteins of several pathogenic virus, bacteria and fungi. As this domain is evolutionarily-conserved in virulence factors of these infectious agents, its detailed investigation is of clinical interest. In this regard, the current in silico study analyzed ChtBD3 domain distribution in bacterial proteins present in publicly-available SMART (simple modular architecture research tool) database. Also, the co-occurring domains of ChtBD3 in the studied proteins were mapped to understand positional rearrangement of the domain and consequent functional diversity. Custom-made scripts were used to interpret the data and to derive patterns. As expected, interesting results were obtained. ChtBD3 domain co-occurred with other critical domains like peptidase, glycol_hydrolase, kinase, hemagglutinin-acting, collagen-binding, among others. The findings are expected to be of clinical relevance.
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Affiliation(s)
- Seema Patel
- Bioinformatics and Medical Informatics Research Center, San Diego State University, San Diego, 92182, USA.
| | - Abdur Rauf
- Department of Chemistry, University of Swabi, Anbar, 23561, Khyber Pakhtunkhwa, Pakistan.
| | - Biswa Ranjan Meher
- Centre for Life Sciences, Central University of Jharkhand, Brambe, Ranchi, 835205, Jharkhand, India
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11
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van Munster JM, Thomas B, Riese M, Davis AL, Gray CJ, Archer DB, Flitsch SL. Application of carbohydrate arrays coupled with mass spectrometry to detect activity of plant-polysaccharide degradative enzymes from the fungus Aspergillus niger. Sci Rep 2017; 7:43117. [PMID: 28220903 PMCID: PMC5318901 DOI: 10.1038/srep43117] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 01/19/2017] [Indexed: 01/25/2023] Open
Abstract
Renewables-based biotechnology depends on enzymes to degrade plant lignocellulose to simple sugars that are converted to fuels or high-value products. Identification and characterization of such lignocellulose degradative enzymes could be fast-tracked by availability of an enzyme activity measurement method that is fast, label-free, uses minimal resources and allows direct identification of generated products. We developed such a method by applying carbohydrate arrays coupled with MALDI-ToF mass spectrometry to identify reaction products of carbohydrate active enzymes (CAZymes) of the filamentous fungus Aspergillus niger. We describe the production and characterization of plant polysaccharide-derived oligosaccharides and their attachment to hydrophobic self-assembling monolayers on a gold target. We verify effectiveness of this array for detecting exo- and endo-acting glycoside hydrolase activity using commercial enzymes, and demonstrate how this platform is suitable for detection of enzyme activity in relevant biological samples, the culture filtrate of A. niger grown on wheat straw. In conclusion, this versatile method is broadly applicable in screening and characterisation of activity of CAZymes, such as fungal enzymes for plant lignocellulose degradation with relevance to biotechnological applications as biofuel production, the food and animal feed industry.
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Affiliation(s)
- Jolanda M van Munster
- Fungal Biology and Genetics, School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Baptiste Thomas
- Chemical Biology, Manchester Institute for Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Michel Riese
- Chemical Biology, Manchester Institute for Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Adrienne L Davis
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Christopher J Gray
- Chemical Biology, Manchester Institute for Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - David B Archer
- Fungal Biology and Genetics, School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Sabine L Flitsch
- Chemical Biology, Manchester Institute for Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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12
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Yang P, Zhang H, Cao L, Zheng Z, Jiang S. Construction of Aspergillus niger integrated with cellulase gene from Ampullaria gigas Spix for improved enzyme production and saccharification of alkaline-pretreated rice straw. 3 Biotech 2016; 6:236. [PMID: 28330308 PMCID: PMC5095100 DOI: 10.1007/s13205-016-0545-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Accepted: 10/07/2016] [Indexed: 11/27/2022] Open
Abstract
Aspergillus niger is an important microorganism that has been used for decades to produce extracellular enzymes. In this study, a novel Aspergillus niger strain integrated with a eukaryotic expression vector harboring the gpd-Shi promoter of shiitake mushrooms and cellulase gene of Ampullaria gigas Spix was engineered to improve cellulase production for the achievement of highly efficient saccharification of agricultural residues. In one strain, designated ACShi27, which exhibited the highest total cellulase expression, total cellulase, endoglucanase, exoglucanase, and xylanase expression levels were 1.73, 16.23, 17.73, and 150.83 U ml−1, respectively; these values were 14.5, 22.3, 24.6, and 17.3% higher than those of the wild-type Aspergillus niger M85 using wheat bran as an induction substrate. Production of cellulases and xylanase by solid-state fermentation followed by in situ saccharification of ACShi27 was investigated with alkaline-pretreated rice straw as a substrate. After 2 days of enzyme induction at 30 °C, followed by 48 h of saccharification at 50 °C, the conversion rate of carbon polymers into reducing sugar reached 293.2 mg g−1, which was 1.23-fold higher than that of the wild-type strain. The expression of sestc in Aspergillus niger can improve the total cellulase and xylanase activity and synergism, thereby enhancing the lignocellulose in situ saccharification.
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Affiliation(s)
- Peizhou Yang
- College of Food Science and Engineering, Hefei University of Technology, Hefei, 230009, China.
- Anhui Key Laboratory of Intensive Processing of Agricultural Products, Hefei University of Technology, Hefei, 230009, China.
| | - Haifeng Zhang
- College of Food Science and Engineering, Hefei University of Technology, Hefei, 230009, China
- Anhui Key Laboratory of Intensive Processing of Agricultural Products, Hefei University of Technology, Hefei, 230009, China
| | - Lili Cao
- College of Food Science and Engineering, Hefei University of Technology, Hefei, 230009, China
- Anhui Key Laboratory of Intensive Processing of Agricultural Products, Hefei University of Technology, Hefei, 230009, China
| | - Zhi Zheng
- College of Food Science and Engineering, Hefei University of Technology, Hefei, 230009, China
- Anhui Key Laboratory of Intensive Processing of Agricultural Products, Hefei University of Technology, Hefei, 230009, China
| | - Shaotong Jiang
- College of Food Science and Engineering, Hefei University of Technology, Hefei, 230009, China
- Anhui Key Laboratory of Intensive Processing of Agricultural Products, Hefei University of Technology, Hefei, 230009, China
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Zhang Q, Li H, Zhu X, Lai F, Zhai Z, Wang Y. Exploration of the key functional proteins from an efficient cellulolytic microbial consortium using dilution-to-extinction approach. J Environ Sci (China) 2016; 43:199-207. [PMID: 27155425 DOI: 10.1016/j.jes.2015.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/21/2015] [Accepted: 09/23/2015] [Indexed: 06/05/2023]
Abstract
In the present study, the cellulose binding proteins (CBPs) secreted by a putative cellulolytic microbial consortium were isolated and purified by affinity digestion. The purified CBPs were subsequently separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Using mass spectrometric analyses, eight CBPs were identified and annotated to be similar to known proteins secreted by Clostridium clariflavum DSM 19732 and Paenibacillus sp. W-61. In addition, in combination with dilution-to-extinction approach and zymogram analysis technique, CBPs 6 (97kDa) and 12 (52kDa) were confirmed to be the key functional proteins that influence cellulolytic activities. Moreover, structural domain analyses and enzymatic activity detection indicated that CBPs 6 and 12 contained glycoside hydrolase families (GH) 9 and 48 catalytic modules, which both revealed endoglucandase and xylanase activities. It was suggested that the coexistence of GH9 and GH48 catalytic domains present in these two proteins could synergistically promote the efficient degradation of cellulose.
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Affiliation(s)
- Qinghua Zhang
- College of Bioscience and Engineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China.
| | - Hanguang Li
- College of Bioscience and Engineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China.
| | - Xiangdong Zhu
- College of Bioscience and Engineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Fenju Lai
- College of Bioscience and Engineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Zhijun Zhai
- College of Bioscience and Engineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yuanxiu Wang
- College of Bioscience and Engineering, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
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Bhattacharya AS, Bhattacharya A, Pletschke BI. Synergism of fungal and bacterial cellulases and hemicellulases: a novel perspective for enhanced bio-ethanol production. Biotechnol Lett 2015; 37:1117-29. [DOI: 10.1007/s10529-015-1779-3] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 01/21/2015] [Indexed: 12/15/2022]
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15
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Fan G, Yang S, Yan Q, Guo Y, Li Y, Jiang Z. Characterization of a highly thermostable glycoside hydrolase family 10 xylanase from Malbranchea cinnamomea. Int J Biol Macromol 2014; 70:482-9. [DOI: 10.1016/j.ijbiomac.2014.07.025] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 07/06/2014] [Accepted: 07/07/2014] [Indexed: 11/24/2022]
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16
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High-level soluble expression of a thermostable xylanase from thermophilic fungus Thermomyces lanuginosus in Escherichia coli via fusion with OsmY protein. Protein Expr Purif 2014; 99:1-5. [DOI: 10.1016/j.pep.2014.03.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 03/07/2014] [Accepted: 03/08/2014] [Indexed: 11/19/2022]
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17
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Extractive Fermentation of Xylanase from Aspergillus tamarii URM 4634 in a Bioreactor. Appl Biochem Biotechnol 2014; 173:1652-66. [DOI: 10.1007/s12010-014-0953-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 05/06/2014] [Indexed: 10/25/2022]
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18
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Wang J, Zeng D, Mai G, Liu G, Yu S. Homologous constitutive expression of Xyn III in Trichoderma reesei QM9414 and its characterization. Folia Microbiol (Praha) 2013; 59:229-33. [PMID: 24178623 DOI: 10.1007/s12223-013-0288-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 10/15/2013] [Indexed: 11/25/2022]
Abstract
Xylanase III (Xyn III), a specific endoxylanase that belongs to family 10 of the glycoside hydrolases, was overexpressed in Trichoderma reesei QM9414 using a constitutive strong promoter of the gene encoding pyruvate decarboxylase (pdc). The maximum recombinant xylanase activity achieved was 817.2 ± 65.2 U/mL in the transformant fermentation liquid. The productivities of Xyn III accounted for approximately 53% of the total protein secreted by the recombinant. The enzyme was optimally active at 60 °C and pH 6. The recombinant Xyn III was stable at pH 5-8. This is the first report on the homologous expression of xyn3 in T. reesei QM9414. The properties of Xyn III make it promising in a variety of industrial use.
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Affiliation(s)
- Juan Wang
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences, Shenzhen University, Shenzhen, Guangdong, 518060, People's Republic of China,
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