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Palit K, Das S. Cellulolytic potential of mangrove bacteria Bacillus haynesii DS7010 and the effect of anthropogenic and environmental stressors on bacterial survivability and cellulose metabolism. ENVIRONMENTAL RESEARCH 2024; 252:118774. [PMID: 38552827 DOI: 10.1016/j.envres.2024.118774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 04/02/2024]
Abstract
Cellulose degrading bacterial diversity of Bhitarkanika mangrove ecosystem, India, was uncovered and the cellulose degradation mechanism in Bacillus haynesii DS7010 under the modifiers such as pH (pCO2), salinity and lead (Pb) was elucidated in the present study. The abundance of cellulose degrading heterotrophic bacteria was found to be higher in mangrove sediment than in water. The most potential strain, B. haynesii DS7010 showed the presence of endoglucanase, exoglucanase and β-glucosidase with the maximum degradation recorded at 48 h of incubation, with 1% substrate concentration at 41 °C incubation temperature. Two glycoside hydrolase genes, celA and celB were confirmed in this bacterium. 3D structure prediction of the translated CelA and CelB proteins showed maximum similarities with glycoside hydrolase 48 (GH48) and glycoside hydrolase 5 (GH5) respectively. Native PAGE followed by zymogram assay unveiled the presence of eight isoforms of cellulase ranged from 78 kDa to 245 kDa. Among the stressors, most adverse effect was observed under Pb stress at 1400 ppm concentration, followed by pH at pH 4. This was indicated by prolonged lag phase growth, higher reactive oxygen species (ROS) production, lower enzyme activity and downregulation of celA and celB gene expressions. Salinity augmented bacterial metabolism up to 3% NaCl concentration. Mangrove leaf litter degradation by B. haynesii DS7010 indicated a substantial reduction in cellulolytic potential of the bacterium in response to the synergistic effect of the stressors. Microcosm set up with the stressors exhibited 0.97% decrease in total carbon (C%) and 0.02% increase in total nitrogen (N%) after 35 d of degradation while under natural conditions, the reduction in C and the increase in N were 4.05% and 0.2%, respectively. The findings of the study suggest the cellulose degradation mechanism of a mangrove bacterium and its resilience to the future consequences of environmental pollution and climate change.
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Affiliation(s)
- Krishna Palit
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, 769008, Odisha, India.
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Kim DY, Kim J, Lee YM, Byeon SM, Gwak JH, Lee JS, Shin DH, Park HY. Novel, acidic, and cold-adapted glycoside hydrolase family 8 endo-β-1,4-glucanase from an Antarctic lichen-associated bacterium, Lichenicola cladoniae PAMC 26568. Front Microbiol 2022; 13:935497. [PMID: 35910630 PMCID: PMC9329076 DOI: 10.3389/fmicb.2022.935497] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
Endo-β-1,4-glucanase is a crucial glycoside hydrolase (GH) involved in the decomposition of cellulosic materials. In this study, to discover a novel cold-adapted β-1,4-D-glucan-degrading enzyme, the gene coding for an extracellular endo-β-1,4-glucanase (GluL) from Lichenicola cladoniae PAMC 26568, an Antarctic lichen (Cladonia borealis)-associated bacterium, was identified and recombinantly expressed in Escherichia coli BL21. The GluL gene (1044-bp) encoded a non-modular polypeptide consisting of a single catalytic GH8 domain, which shared the highest sequence identity of 55% with that of an uncharacterized protein from Gluconacetobacter takamatsuzukensis (WP_182950054). The recombinant endo-β-1,4-glucanase (rGluL: 38.0 kDa) most efficiently degraded sodium carboxymethylcellulose (CMC) at pH 4.0 and 45°C, and showed approximately 23% of its maximum degradation activity even at 3°C. The biocatalytic activity of rGluL was noticeably enhanced by >1.3-fold in the presence of 1 mM Mn2+ or NaCl at concentrations between 0.1 and 0.5 M, whereas the enzyme was considerably downregulated by 1 mM Hg2+ and Fe2+ together with 5 mM N-bromosuccinimide and 0.5% sodium dodecyl sulfate. rGluL is a true endo-β-1,4-glucanase, which could preferentially decompose D-cellooligosaccharides consisting of 3 to 6 D-glucose, CMC, and barley β-glucan, without other additional glycoside hydrolase activities. The specific activity (15.1 U mg–1) and kcat/Km value (6.35 mg–1 s–1mL) of rGluL toward barley β-glucan were approximately 1.8- and 2.2-fold higher, respectively, compared to its specific activity (8.3 U mg–1) and kcat/Km value (2.83 mg–1 s–1mL) toward CMC. The enzymatic hydrolysis of CMC, D-cellotetraose, and D-cellohexaose yielded primarily D-cellobiose, accompanied by D-glucose, D-cellotriose, and D-cellotetraose. However, the cleavage of D-cellopentaose by rGluL resulted in the production of only D-cellobiose and D-cellotriose. The findings of the present study imply that rGluL is a novel, acidic, and cold-adapted GH8 endo-β-1,4-glucanase with high specific activity, which can be exploited as a promising candidate in low-temperature processes including textile and food processes.
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Affiliation(s)
- Do Young Kim
- Industrial Bio-Materials Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- *Correspondence: Do Young Kim,
| | - Jonghoon Kim
- Industrial Bio-Materials Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Yung Mi Lee
- Division of Life Sciences, Korea Polar Research Institute, Incheon, South Korea
| | - Soo Min Byeon
- Industrial Bio-Materials Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- Department of Biological Science, Daejeon University, Daejeon, South Korea
| | - Jeong Hae Gwak
- Industrial Bio-Materials Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Jong Suk Lee
- Biocenter, Gyeonggido Business and Science Accelerator (GBSA), Suwon, South Korea
| | | | - Ho-Yong Park
- Industrial Bio-Materials Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
- Ho-Yong Park,
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Cai LN, Xu SN, Lu T, Lin DQ, Yao SJ. Salt-tolerant and thermostable mechanisms of an endoglucanase from marine Aspergillus niger. BIORESOUR BIOPROCESS 2022; 9:44. [PMID: 38647856 PMCID: PMC10991132 DOI: 10.1186/s40643-022-00533-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/31/2022] [Indexed: 11/10/2022] Open
Abstract
The cellulase cocktail of marine Aspergillus niger exhibited salt-tolerant and thermostable properties, which is of great potential in industrial application. In order to excavate the single tolerant cellulase components from complex cellulase cocktail, constitutive homologous expression was employed for direct obtainment of the endoglucanase (AnEGL). Enzymatic property study revealed that AnEGL exhibited a property of salt tolerance and a strong thermostability in high salinity environment. Significantly, its activity increased to 129% and the half-life at 65 °C increased to 27.7-fold with the presence of 4.5 M NaCl. Molecular dynamics simulation revealed that Na+ and Cl- could form salt bridges with charged residues, and then influenced the activity of loops and the stability of substrate binding pocket, which accounted for the salt tolerance and thermostability. Further, site-specific mutagenesis study proved that the residues Asp95 and Asp99 in the pocket were of great concern for the tolerant properties. The salt-tolerant and thermostable AnEGL was of great value in lignocellulosic utilization and the conjectural mechanisms were of referential significance for other tolerant enzymes.
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Affiliation(s)
- Li-Nian Cai
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Sheng-Nan Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Dong-Qiang Lin
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Shan-Jing Yao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
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Huang Z, Ni G, Zhao X, Wang F, Qu M. Characterization of a GH8 β-1,4-Glucanase from Bacillus subtilis B111 and Its Saccharification Potential for Agricultural Straws. J Microbiol Biotechnol 2021; 31:1446-1454. [PMID: 34409950 PMCID: PMC9705894 DOI: 10.4014/jmb.2105.05026] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/11/2021] [Accepted: 08/19/2021] [Indexed: 12/15/2022]
Abstract
Herein, we cloned and expressed an endo-β-1,4-glucanase gene (celA1805) from Bacillus subtilis B111 in Escherichia coli. The recombinant celA1805 contains a glycosyl hydrolase (GH) family 8 domain and shared 76.8% identity with endo-1,4-β-glucanase from Bacillus sp. KSM-330. Results showed that the optimal pH and temperature of celA1805 were 6.0 and 50°C, respectively, and it was stable at pH 3-9 and temperature ≤50°C. Metal ions slightly affected enzyme activity, but chemical agents generally inhibited enzyme activity. Moreover, celA1805 showed a wide substrate specificity to CMC, barley β-glucan, lichenin, chitosan, PASC and avicel. The Km and Vmax values of celA1805 were 1.78 mg/ml and 50.09 μmol/min/mg. When incubated with cellooligosaccharides ranging from cellotriose to cellopentose, celA1805 mainly hydrolyzed cellotetrose (G4) and cellopentose (G5) to cellose (G2) and cellotriose (G3), but hardly hydrolyzed cellotriose. The concentrations of reducing sugars saccharified by celA1805 from wheat straw, rape straw, rice straw, peanut straw, and corn straw were increased by 0.21, 0.51, 0.26, 0.36, and 0.66 mg/ml, respectively. The results obtained in this study suggest potential applications of celA1805 in biomass saccharification.
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Affiliation(s)
- Zhen Huang
- Key Laboratory of Animal Nutrition of Jiangxi Province, Nutritional Feed Development Engineering Research Center, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R. China
| | - Guorong Ni
- College of Land Resources and Environment, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R. China
| | - Xiaoyan Zhao
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R. China
| | - Fei Wang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R. China,Corresponding author F. Wang Phone/Fax: +86 791 83813459 E-mail:
| | - Mingren Qu
- Key Laboratory of Animal Nutrition of Jiangxi Province, Nutritional Feed Development Engineering Research Center, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R. China,
M. Qu E-mail:
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Lekakarn H, Bunterngsook B, Laothanachareon T, Champreda V. Functional characterization of endoglucanase (CelB) isolated from lignocellulose-degrading microbial consortium for biomass saccharification. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2020.101888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Şafak H, Otur Ç, Kurt-Kızıldoğan A. Molecular and biochemical characterization of a recombinant endoglucanase rCKT3eng, from an extreme halophilic Haloarcula sp. strain CKT3. Int J Biol Macromol 2020; 151:1173-1180. [PMID: 31751744 DOI: 10.1016/j.ijbiomac.2019.10.161] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 10/18/2019] [Accepted: 10/18/2019] [Indexed: 10/25/2022]
Abstract
Halophilic cellulases are indispensable enzymes of heavy industrial processes as resistant biocatalysts due to high level activity at extreme conditions. In this study, crude cellulase from an extreme halophilic Haloarcula sp. CKT3 was characterized. Then, recombinant expression of putative endo-1,4-β-glucanase gene, of CKT3 strain, in E. coli BL21(DE3) was performed with the aim of obtaining highly pure, active and robust industrial enzyme for such industrial aplications. The crude cellulase had optimal activity (16.9 U/mg) at 70 °C, pH 7.0 and 4 M NaCl exhibiting good thermostability, high pH and halotolerance. Indeed, it is very stable in water-insoluble organic solvents with log Po/w ≥ 2.13 and highly resistant to SDS (10%). Recombinant CKT3eng has a molecular weight of 36.9 kDa and 99% aminoacid identity to endo-l,4-β-D-glucanase from Haloarcula argentinensis. Its 3D structure was predicted using Phyre2 and I-TASSER. rCKT3eng enzyme provided 31.6 U/mg activity at optimal 50 °C, pH 7.0 and 3 M NaCl. In addition to its quite similar stability values and resistance to organic solvents and SDS, rCKT3eng has superiority over crude enzyme with 1.87-fold higher specific activity. Therefore, rCKT3eng offers a promising enzyme for industrial use with its valuable activity and stability in extreme conditions.
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Affiliation(s)
- Haktan Şafak
- Enzyme and Microbial Biotechnology Section, Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, Samsun 55139, Turkey
| | - Çiğdem Otur
- Enzyme and Microbial Biotechnology Section, Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, Samsun 55139, Turkey
| | - Aslıhan Kurt-Kızıldoğan
- Enzyme and Microbial Biotechnology Section, Department of Agricultural Biotechnology, Faculty of Agriculture, Ondokuz Mayıs University, Samsun 55139, Turkey.
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7
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Engineering of a highly thermostable endoglucanase from the GH7 family of Bipolaris sorokiniana for higher catalytic efficiency. Appl Microbiol Biotechnol 2020; 104:3935-3945. [DOI: 10.1007/s00253-020-10515-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/15/2020] [Accepted: 03/01/2020] [Indexed: 11/26/2022]
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Xu D, Xu L, Zhou F, Wang B, Wang S, Lu M, Sun J. Gut Bacterial Communities of Dendroctonus valens and Monoterpenes and Carbohydrates of Pinus tabuliformis at Different Attack Densities to Host Pines. Front Microbiol 2018; 9:1251. [PMID: 29963021 PMCID: PMC6011813 DOI: 10.3389/fmicb.2018.01251] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 05/23/2018] [Indexed: 01/03/2023] Open
Abstract
Insects harbor a community of gut bacteria, ranging from pathogenic to obligate mutualistic organisms. Both biotic and abiotic factors can influence species composition and structure of the insect gut bacterial communities. Dendroctonus valens is a destructive forest pest in China. To overcome host pine defenses, beetles mass-attack the pine to a threshold density that can exhaust pine defenses. The intensity of pine chemical defenses and carbohydrate concentrations of pines can be influenced by beetle attack, both of which are known factors that modify beetle's gut microbiota. However, little is known to what extent variation exists in the beetle's gut communities, and host monoterpenes and carbohydrates at different attack densities. In this study, the gut bacterial microbiota of D. valens at low and high attack densities were analyzed, and monoterpenes and carbohydrates in host pine phloem were assayed in parallel. The results showed that no significant changes of gut bacterial communities of the beetles and concentrations of D-glucose, D-pinitol, and D-fructose in pine phloem were found between low and high attack densities. The concentrations of α-pinene, β-pinene, limonene at high attack densities were significantly higher than those at low attack densities. Our results suggested that different attack densities of D. valens influence monoterpenes concentration of host pines' phloem but have no significant impact on gut bacterial community structures of D. valens and carbohydrate concentration of host trees' phloem in early attack phase. Similar gut bacterial community structures of D. valens between low and high attack densities might be due to the quick adaptation of gut microbiota to high monoterpenes concentrations.
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Affiliation(s)
- Dandan Xu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Letian Xu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, College of Life Science, Hubei University, Wuhan, China
| | - Fangyuan Zhou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Bo Wang
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, China
| | - Shanshan Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute of Health Sciences, Anhui University, Hefei, China
| | - Min Lu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jianghua Sun
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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Ruginescu RM, Cojoc R, Enache M, Lazăr V. Preliminary Characterization of a Cellulase Producing Bacterial Strain Isolated from a Romanian Hypersaline Lake. ACTA ACUST UNITED AC 2018. [DOI: 10.4236/jep.2018.910066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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10
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Debez A, Belghith I, Friesen J, Montzka C, Elleuche S. Facing the challenge of sustainable bioenergy production: Could halophytes be part of the solution? J Biol Eng 2017; 11:27. [PMID: 28883890 PMCID: PMC5580303 DOI: 10.1186/s13036-017-0069-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 06/18/2017] [Indexed: 11/17/2022] Open
Abstract
Due to steadily growing population and economic transitions in the more populous countries, renewable sources of energy are needed more than ever. Plant biomass as a raw source of bioenergy and biofuel products may meet the demand for sustainable energy; however, such plants typically compete with food crops, which should not be wasted for producing energy and chemicals. Second-generation or advanced biofuels that are based on renewable and non-edible biomass resources are processed to produce cellulosic ethanol, which could be further used for producing energy, but also bio-based chemicals including higher alcohols, organic acids, and bulk chemicals. Halophytes do not compete with conventional crops for arable areas and freshwater resources, since they grow naturally in saline ecosystems, mostly in semi-arid and arid areas. Using halophytes for biofuel production may provide a mid-term economically feasible and environmentally sustainable solution to producing bioenergy, contributing, at the same time, to making saline areas – which have been considered unproductive for a long time – more valuable. This review emphasises on halophyte definition, global distribution, and environmental requirements. It also examines their enzymatic valorization, focusing on salt-tolerant enzymes from halophilic microbial species that may be deployed with greater advantage compared to their conventional mesophilic counterparts for faster degradation of halophyte biomass.
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Affiliation(s)
- Ahmed Debez
- Laboratoire des Plantes Extrêmophiles (LPE), Centre de Biotechnologie de Borj-Cedria (CBBC), BP 901, 2050 Hammam-Lif, Tunisia.,Arab German Young Academy of Sciences and Humanities (AGYA), Working group "Energy, Water and Environment", at the Berlin-Brandenburg Academy of Sciences and Humanities, Berlin, Germany
| | - Ikram Belghith
- Laboratoire des Plantes Extrêmophiles (LPE), Centre de Biotechnologie de Borj-Cedria (CBBC), BP 901, 2050 Hammam-Lif, Tunisia
| | - Jan Friesen
- Arab German Young Academy of Sciences and Humanities (AGYA), Working group "Energy, Water and Environment", at the Berlin-Brandenburg Academy of Sciences and Humanities, Berlin, Germany.,Department of Catchment Hydrology, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Carsten Montzka
- Arab German Young Academy of Sciences and Humanities (AGYA), Working group "Energy, Water and Environment", at the Berlin-Brandenburg Academy of Sciences and Humanities, Berlin, Germany.,Institute of Bio- and Geosciences: Agrosphere (IBG-3), Forschungszentrum Jülich GmbH, Leo-Brandt-Str, 52425 Jülich, Germany
| | - Skander Elleuche
- Arab German Young Academy of Sciences and Humanities (AGYA), Working group "Energy, Water and Environment", at the Berlin-Brandenburg Academy of Sciences and Humanities, Berlin, Germany.,Institute of Technical Microbiology, Hamburg University of Technology (TUHH), Kasernenstr. 12, 21073 Hamburg, Germany.,Present address: Miltenyi Biotec GmbH, Friedrich-Ebert-Straße 68, 51429 Bergisch Gladbach, Germany
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11
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Scapin SMN, Souza FHM, Zanphorlin LM, de Almeida TS, Sade YB, Cardoso AM, Pinheiro GL, Murakami MT. Structure and function of a novel GH8 endoglucanase from the bacterial cellulose synthase complex of Raoultella ornithinolytica. PLoS One 2017; 12:e0176550. [PMID: 28448629 PMCID: PMC5407803 DOI: 10.1371/journal.pone.0176550] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/12/2017] [Indexed: 02/02/2023] Open
Abstract
Cellulose synthesis in bacteria is a complex process involving the concerted action of several enzymes whose genes are often organized in operons. This process influences many fundamental physiological aspects such as bacteria and host interaction, biofilm formation, among others. Although it might sound contradictory, the participation of cellulose-degrading enzymes is critical to this process. The presence of endoglucanases from family 8 of glycosyl hydrolases (GH8) in bacterial cellulose synthase (Bcs) complex has been described in different bacteria, including the model organism Komagataeibacter xylinus; however, their role in this process is not completely understood. In this study, we describe the biochemical characterization and three-dimensional structure of a novel GH8 member from Raoultella ornithinolytica, named AfmE1, which was previously identified by our group from the metagenomic analysis of the giant snail Achatina fulica. Our results demonstrated that AfmE1 is an endo-β-1,4-glucanase, with maximum activity in acidic to neutral pH over a wide temperature range. This enzyme cleaves cello-oligosaccharides with a degree of polymerization ≥ 5 and presents six glucosyl-binding subsites. The structural comparison of AfmE1 with other GH8 endoglucanases showed significant structural dissimilarities in the catalytic cleft, particularly in the subsite +3, which correlate with different functional mechanisms, such as the recognition of substrate molecules having different arrangements and crystallinities. Together, these findings provide new insights into molecular and structural features of evolutionarily conserved endoglucanases from the bacterial cellulose biosynthetic machinery.
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Affiliation(s)
- Sandra Mara Naressi Scapin
- Division of Metrology Applied to Life Sciences, National Institute of Metrology, Quality and Technology, Duque de Caxias, Rio de Janeiro, Brazil
- * E-mail: (SMNS); (MTM)
| | - Flavio Henrique Moreira Souza
- Brazilian Bioethanol Science and Technology Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Leticia Maria Zanphorlin
- Brazilian Bioethanol Science and Technology Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Thamyres Silva de Almeida
- Division of Metrology Applied to Life Sciences, National Institute of Metrology, Quality and Technology, Duque de Caxias, Rio de Janeiro, Brazil
| | - Youssef Bacila Sade
- Division of Metrology Applied to Life Sciences, National Institute of Metrology, Quality and Technology, Duque de Caxias, Rio de Janeiro, Brazil
| | - Alexander Machado Cardoso
- Division of Metrology Applied to Life Sciences, National Institute of Metrology, Quality and Technology, Duque de Caxias, Rio de Janeiro, Brazil
| | - Guilherme Luiz Pinheiro
- Division of Metrology Applied to Life Sciences, National Institute of Metrology, Quality and Technology, Duque de Caxias, Rio de Janeiro, Brazil
| | - Mario Tyago Murakami
- Brazilian Bioethanol Science and Technology Laboratory, National Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
- * E-mail: (SMNS); (MTM)
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Mühlmann M, Kunze M, Ribeiro J, Geinitz B, Lehmann C, Schwaneberg U, Commandeur U, Büchs J. Cellulolytic RoboLector - towards an automated high-throughput screening platform for recombinant cellulase expression. J Biol Eng 2017; 11:1. [PMID: 28074108 PMCID: PMC5219752 DOI: 10.1186/s13036-016-0043-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 12/14/2016] [Indexed: 11/20/2022] Open
Abstract
Background Cellulases are key player in the hydrolyzation of cellulose. Unfortunately, this reaction is slow and a bottleneck in the process chain from biomass to intermediates and biofuels due to low activities of the enzymes. To overcome this draw back, a lot of effort is put into the area of protein engineering, to modify these enzymes by directed evolution or rational design. Huge clone libraries are constructed and have to be screened for improved variants. High-throughput screening is the method of choice to tackle this experimental effort, but up to now only a few process steps are adapted to automated platforms and little attention has been turned to the reproducibility of clone rankings. Results In this study, an extended robotic platform is presented to conduct automated high-throughput screenings of clone libraries including preculture synchronization and biomass specific induction. Automated upstream, downstream and analytical process steps are described and evaluated using E. coli and K. lactis as model organisms. Conventional protocols for media preparation, cell lysis, Azo-CMC assay and PAHBAH assay are successfully adapted to automatable high-throughput protocols. Finally, a recombinant E. coli celA2 clone library was screened and a reliable clone ranking could be realized. Conclusion The RoboLector device is a suitable platform to perform all process steps of an automated high-throughput clone library screening for improved cellulases. On-line biomass growth measurement controlling liquid handling actions enables fair comparison of clone variants. Electronic supplementary material The online version of this article (doi:10.1186/s13036-016-0043-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Martina Mühlmann
- AVT-Chair for Biochemical Engineering, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Martin Kunze
- AVT-Chair for Biochemical Engineering, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Joaquim Ribeiro
- AVT-Chair for Biochemical Engineering, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Bertram Geinitz
- AVT-Chair for Biochemical Engineering, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Christian Lehmann
- Chair for Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Ulrich Schwaneberg
- Chair for Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Ulrich Commandeur
- Chair for Molecular Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Jochen Büchs
- AVT-Chair for Biochemical Engineering, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
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A novel pH-stable, endoglucanase (JqCel5A) isolated from a salt-lake microorganism, Jonesia quinghaiensis. ELECTRON J BIOTECHN 2016. [DOI: 10.1016/j.ejbt.2016.09.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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14
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Bai X, Yuan X, Wen A, Li J, Bai Y, Shao T. Efficient expression and characterization of a cold-active endo-1, 4-β-glucanase from Citrobacter farmeri by co-expression of Myxococcus xanthus protein S. ELECTRON J BIOTECHN 2016. [DOI: 10.1016/j.ejbt.2016.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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15
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Alves M, Pereira A, Matos P, Henriques J, Vicente C, Aikawa T, Hasegawa K, Nascimento F, Mota M, Correia A, Henriques I. Bacterial community associated to the pine wilt disease insect vectors Monochamus galloprovincialis and Monochamus alternatus. Sci Rep 2016; 6:23908. [PMID: 27045340 PMCID: PMC4820700 DOI: 10.1038/srep23908] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 03/10/2016] [Indexed: 11/25/2022] Open
Abstract
Monochamus beetles are the dispersing vectors of the nematode Bursaphelenchus xylophilus, the causative agent of pine wilt disease (PWD). PWD inflicts significant damages in Eurasian pine forests. Symbiotic microorganisms have a large influence in insect survival. The aim of this study was to characterize the bacterial community associated to PWD vectors in Europe and East Asia using a culture-independent approach. Twenty-three Monochamus galloprovincialis were collected in Portugal (two different locations); twelve Monochamus alternatus were collected in Japan. DNA was extracted from the insects’ tracheas for 16S rDNA analysis through denaturing gradient gel electrophoresis and barcoded pyrosequencing. Enterobacteriales, Pseudomonadales, Vibrionales and Oceanospirilales were present in all samples. Enterobacteriaceae was represented by 52.2% of the total number of reads. Twenty-three OTUs were present in all locations. Significant differences existed between the microbiomes of the two insect species while for M. galloprovincialis there were no significant differences between samples from different Portuguese locations. This study presents a detailed description of the bacterial community colonizing the Monochamus insects’ tracheas. Several of the identified bacterial groups were described previously in association with pine trees and B. xylophilus, and their previously described functions suggest that they may play a relevant role in PWD.
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Affiliation(s)
- Marta Alves
- Departamento de Biologia e Centro de Estudos do Ambiente e do Mar (CESAM), Universidade de Aveiro, Aveiro, 3810-193, Portugal.,Departamento de Biologia e Instituto de Biomedicina (iBiMED), Universidade de Aveiro, Aveiro, 3810-193, Portugal
| | - Anabela Pereira
- Departamento de Biologia e Centro de Estudos do Ambiente e do Mar (CESAM), Universidade de Aveiro, Aveiro, 3810-193, Portugal
| | - Patrícia Matos
- Departamento de Biologia e Centro de Estudos do Ambiente e do Mar (CESAM), Universidade de Aveiro, Aveiro, 3810-193, Portugal
| | - Joana Henriques
- INIAV/Unidade Estratégica de Investigação e Serviços de Sistemas Agrários e Florestais e Sanidade Vegetal, Av. da República, Quinta do Marquês, Oeiras, 2780-157, Portugal
| | - Cláudia Vicente
- NemaLab-ICAAM, Universidade de Évora, Núcleo da Mitra, Ap. 94, Évora, 7002-554, Portugal.,Environmental Biology Department, Chubu University, Kasugai, Japan
| | - Takuya Aikawa
- FFPRI - Forestry and Forest Products Research Institute, Tohuku, Japan
| | - Koichi Hasegawa
- Environmental Biology Department, Chubu University, Kasugai, Japan
| | - Francisco Nascimento
- NemaLab-ICAAM, Universidade de Évora, Núcleo da Mitra, Ap. 94, Évora, 7002-554, Portugal
| | - Manuel Mota
- NemaLab-ICAAM, Universidade de Évora, Núcleo da Mitra, Ap. 94, Évora, 7002-554, Portugal.,Dep. Ciências da Vida, EPCV, Universidade Lusófona de Humanidades e Tecnologias (ULHT), Av. Campo Grande 376, 1749-024 Lisboa, Portugal
| | - António Correia
- Departamento de Biologia e Centro de Estudos do Ambiente e do Mar (CESAM), Universidade de Aveiro, Aveiro, 3810-193, Portugal
| | - Isabel Henriques
- Departamento de Biologia e Centro de Estudos do Ambiente e do Mar (CESAM), Universidade de Aveiro, Aveiro, 3810-193, Portugal.,Departamento de Biologia e Instituto de Biomedicina (iBiMED), Universidade de Aveiro, Aveiro, 3810-193, Portugal
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16
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Deep K, Poddar A, Das SK. Cloning, Overexpression, and Characterization of Halostable, Solvent-Tolerant Novel β-Endoglucanase from a Marine Bacterium Photobacterium panuliri LBS5T (DSM 27646T). Appl Biochem Biotechnol 2015; 178:695-709. [DOI: 10.1007/s12010-015-1903-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 10/15/2015] [Indexed: 11/28/2022]
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17
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Geethu C, Nair RA. Purification and biochemical characterization of an extracellular endoglucanase from the necrotrophic oomycete,Pythium myriotylumDreschler. J Basic Microbiol 2014; 54:1322-30. [DOI: 10.1002/jobm.201400323] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 07/05/2014] [Indexed: 12/24/2022]
Affiliation(s)
- C. Geethu
- School of Biotechnology; National Institute of Technology Calicut (NITC); Calicut Kerala India
| | - R. Aswati Nair
- School of Biotechnology; National Institute of Technology Calicut (NITC); Calicut Kerala India
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18
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Piñar G, Kraková L, Pangallo D, Piombino-Mascali D, Maixner F, Zink A, Sterflinger K. Halophilic bacteria are colonizing the exhibition areas of the Capuchin Catacombs in Palermo, Italy. Extremophiles 2014; 18:677-91. [PMID: 24863363 PMCID: PMC4065341 DOI: 10.1007/s00792-014-0649-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 04/27/2014] [Indexed: 01/11/2023]
Abstract
The Capuchin Catacombs of Palermo, Italy, contain over 1800 mummies dating from the 16th to 20th centuries AD. Their environment is not conducive to the conservation of the remains due to, among other factors, water infiltration, which is producing salt efflorescences on the walls. A multiphasic approach was applied to investigate the halophilic microbiota present in the Catacombs. Enrichment cultures were conducted on media containing different NaCl concentrations, ranging from 3 to 20 %. For screening of the strains, the following two PCR-based methods were used and compared: fluorescence internal transcribed spacer PCR (f-ITS) and random amplification of polymorphic DNA (RAPD) analyses. Results derived from RAPD profiles were shown to be slightly more discriminative than those derived from f-ITS. In addition, the proteolytic and cellulolytic abilities were screened through the use of plate assays, gelatin agar and Ostazin Brilliant Red H-3B (OBR-HEC), respectively. Many of the strains isolated from the wall samples displayed proteolytic activities, such as all strains belonging to the genera Bacillus, Virgibacillus and Arthrobacter, as well as some strains related to the genera Oceanobacillus, Halobacillus and Idiomarina. In addition, many of the strains isolated from materials employed to stuff the mummies showed cellulolytic activities, such as those related to species of the genera Chromohalobacter and Nesterenkonia, as well as those identified as Staphylococcus equorum and Halomonas sp. Furthermore, many of the strains were pigmented ranging from yellow to a strong pink color, being directly related to the discoloration displayed by the materials.
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Affiliation(s)
- G Piñar
- VIBT-Vienna Institute of BioTechnology, Department of Biotechnology, University of Natural Resources and Life Sciences, Muthgasse 11, 1190, Vienna, Austria,
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Abstract
α-Glucuronidase enzymes play an essential role in the full enzymatic hydrolysis of hemicellulose. Up to this point, all genes encoding α-glucuronidase enzymes have been cloned from individual, pure culture strains. Using a high-throughput screening strategy, we have isolated the first α-glucuronidase gene (rum630-AG) from a mixed population of microorganisms. The gene was subcloned into a prokaryotic vector, and the enzyme was overexpressed and biochemically characterized. The RUM630-AG enzyme had optimum activity at pH 6.5 and 40 °C. When birchwood xylan was used as substrate, the RUM630-AG functioned synergistically with an endoxylanase enzyme to hydrolyze the substrate.
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20
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Liu D, Zhang R, Yang X, Xu Y, Tang Z, Tian W, Shen Q. Expression, purification and characterization of two thermostable endoglucanases cloned from a lignocellulosic decomposing fungi Aspergillus fumigatus Z5 isolated from compost. Protein Expr Purif 2011; 79:176-86. [DOI: 10.1016/j.pep.2011.06.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Revised: 06/08/2011] [Accepted: 06/09/2011] [Indexed: 11/27/2022]
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