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Tran DM, Huynh TU, Nguyen TH, Do TO, Nguyen AD. Data on gene cloning, expression, purification, and characterization of the glycoside hydrolase family 11 from Bacillus velezensis. Data Brief 2024; 52:109834. [PMID: 38370019 PMCID: PMC10873866 DOI: 10.1016/j.dib.2023.109834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/11/2023] [Accepted: 11/15/2023] [Indexed: 02/20/2024] Open
Abstract
Bacillus velezensis RB.IBE29 is a chitinolytic bacterium originally isolated from the rhizospheric soil of black pepper grown in Vietnam. This bacterium is a strong biocontrol agent against plant pathogens and possesses a novel chitinase system. Genome sequences available in CAZy database revealed B. velezensis possesses one gene encoding xylanase belonging to glycoside hydrolase family 11; however, this enzyme has yet to be un-experimentally characterized. In this work, xyA gene was isolated from the genomic DNA of strain RB.IBE29 and cloned in Escherichia coli DH5α cells using the pUC19 vector. Sequencing analysis showed that the ORF of xyA contains 642 bp and encodes the deduced xylanase with 213 aa and 23.27 kDa. The domain structure of the enzyme has a signal peptide and a family 11 catalytic domain. xyA (without peptide sequence) was successfully expressed in E. coli BL21-CodonPlus (DE3)-RIPL cells using the pColdII vector and purified using the HisTrap FF column. Purified recombinant xylanase degraded xylan substrates, had the highest hydrolytic activity at 55°C in 20 mM sodium phosphate buffer (pH 6.0), and MgCl2, CoCl2, and MnCl2 enhanced the enzymatic activity. Nucleotide sequence of xyA was submitted to the DDBJ/GenBank/EMBL under accession number LC779040. This is the first data on the gene cloning, expression, purification, and characterization of the glycoside hydrolase family 11 from B. velezensis.
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Affiliation(s)
- Dinh Minh Tran
- Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot, Dak Lak 630000, Viet Nam
| | - To Uyen Huynh
- Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot, Dak Lak 630000, Viet Nam
| | - Thi Huyen Nguyen
- Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot, Dak Lak 630000, Viet Nam
| | - Tu Oanh Do
- Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot, Dak Lak 630000, Viet Nam
| | - Anh Dzung Nguyen
- Institute of Biotechnology and Environment, Tay Nguyen University, Buon Ma Thuot, Dak Lak 630000, Viet Nam
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Álvarez-Lagazzi AP, Cabrera N, Francis F, Ramírez CC. Bacillus subtilis (Bacillales, Bacillaceae) Spores Affect Survival and Population Growth in the Grain Aphid Sitobion avenae (Hemiptera, Aphididae) in Relation to the Presence of the Facultative Bacterial Endosymbiont Regiella insecticola (Enterobacteriales, Enterobacteriaceae). JOURNAL OF ECONOMIC ENTOMOLOGY 2021; 114:2043-2050. [PMID: 34463330 DOI: 10.1093/jee/toab164] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Indexed: 06/13/2023]
Abstract
The grain aphid Sitobion avenae (Fabricius) is one of the most important cereal pests, damaging crops through sap sucking and virus transmission. Sitobion avenae harbors the secondary endosymbiont Regiella insecticola, which is highly prevalent in populations in south-central Chile and other regions of the world. In order to develop ecological alternatives for biological control, we studied the effect of applying the spores of a strain of the bacterium Bacillus subtilis on the survival and fecundity of the most prevalent genotype of S. avenae in central Chile. The strain selected was one that in previous studies had shown the ability to outcompete other bacteria. Using clones of this aphid genotype infected and uninfected with R. insecticola, we found that applying B. subtilis spores through artificial diets and spraying on leaves decreased both adult survival and nymph production. The detection of spores within the aphid body was negatively correlated with nymph production and was lower in the presence of R. insecticola when applied in diets. B. subtilis spores applied on leaves reduced the number of aphids, an effect that was stronger on aphids harboring R. insecticola. A possible interaction between endosymbiotic bacteria and bacterial antagonists within the aphid body is discussed.
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Affiliation(s)
- Alan P Álvarez-Lagazzi
- Instituto de Ciencias Biológicas, Universidad de Talca, Campus Talca 3460000, Chile
- Centre for Molecular and Functional Ecology in Agroecosystems, Universidad de Talca, Campus Talca 3460000, Chile
| | - Nuri Cabrera
- Instituto de Ciencias Biológicas, Universidad de Talca, Campus Talca 3460000, Chile
- Centre for Molecular and Functional Ecology in Agroecosystems, Universidad de Talca, Campus Talca 3460000, Chile
| | - Frederic Francis
- Functional and Evolutionary Entomology, Gembloux Agro-Bio Tech, University of Liege, Passage des Déportés 2, B-5030 Gembloux, Belgium
| | - Claudio C Ramírez
- Instituto de Ciencias Biológicas, Universidad de Talca, Campus Talca 3460000, Chile
- Centre for Molecular and Functional Ecology in Agroecosystems, Universidad de Talca, Campus Talca 3460000, Chile
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3
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In vitro fermentation of arabinoxylan from oat ( Avena sativa L.) by Pekin duck intestinal microbiota. 3 Biotech 2019; 9:54. [PMID: 30729078 DOI: 10.1007/s13205-019-1571-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 01/03/2019] [Indexed: 10/27/2022] Open
Abstract
Arabinoxylan (AX) is abundant in cereal grains used as feed for ducks. However, the duck intestinal microbes responsible for the degradation of AX are not fully understood. In this study, oat AX was degraded and utilized by different duck intestinal microbiota in vitro. Changes in short-chain fatty acids (SCFAs), branch-chain fatty acids, and the pH resulted from a 72-h AX fermentation in intestinal samples were measured. The addition of AX increased the concentration of isobutyric acid and decreased the concentrations of SCFAs. The pH values decreased significantly in the intestinal samples. Gut microbiota were assessed using high-throughput sequencing of the 16S ribosomal RNA gene, and the results indicated that AX stimulated the growth of Megamonas and Bifidobacterium species, with Megamonas exhibiting the greatest stimulation. Overall, the results suggest that oat AX is utilized by specific bacteria in duck intestines, providing the theoretical basis for the impacts of AX on animal health.
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Zhou N, Sun YT, Chen DW, Du W, Yang H, Liu SJ. Harnessing microfluidic streak plate technique to investigate the gut microbiome of Reticulitermes chinensis. Microbiologyopen 2018; 8:e00654. [PMID: 29897677 PMCID: PMC6436436 DOI: 10.1002/mbo3.654] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Revised: 04/04/2018] [Accepted: 04/23/2018] [Indexed: 02/01/2023] Open
Abstract
The termite gut microbiome is a model system to investigate microbial interactions and their associations with host. For decades, extensive research with molecular tools and conventional cultivation method has been carried out to define the microbial diversity in termite gut. Yet, many bacterial groups of the termite gut microbiome have not been successfully cultivated in laboratory. In this study, we adapted the recently developed microfluidic streak plate (MSP) technique for cultivation of termite gut microbial communities at both aerobic and anaerobic conditions. We found that 99 operational taxonomic units (OTUs) were cultivable by MSP approach and 18 OTUs were documented first time for termite gut microbiota. Further analysis of the bacterial diversities derived by culture‐dependent MSP approach and culture‐independent 16S rRNA gene typing revealed that both methods have bias in recovery of gut microbiota. In total 396 strains were isolated with MSP technique, and potential new taxa at species and/or genus levels were obtained that were phylogenetically related to Burkholderia, Micrococcus, and Dysgonomonas. Results from this study indicate that MSP technique is applicable for cultivating previously unknown and new microbial groups of termite gut microbiota.
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Affiliation(s)
- Nan Zhou
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Tong Sun
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,College of Life Science, at Hebei University, Baoding, China
| | - Dong-Wei Chen
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Wenbin Du
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hong Yang
- School of Life Sciences at Central, China Normal University, Wuhan, China
| | - Shuang-Jiang Liu
- State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,College of Life Science, at Hebei University, Baoding, China
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Boucherba N, Gagaoua M, Bouanane-Darenfed A, Bouiche C, Bouacem K, Kerbous MY, Maafa Y, Benallaoua S. Biochemical properties of a new thermo- and solvent-stable xylanase recovered using three phase partitioning from the extract of Bacillus oceanisediminis strain SJ3. BIORESOUR BIOPROCESS 2017; 4:29. [PMID: 28736694 PMCID: PMC5498614 DOI: 10.1186/s40643-017-0161-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 07/01/2017] [Indexed: 11/29/2022] Open
Abstract
The present study investigates the production and partial biochemical characterization of an extracellular thermostable xylanase from the Bacillus oceanisediminis strain SJ3 newly recovered from Algerian soil using three phase partitioning (TPP). The maximum xylanase activity recorded after 2 days of incubation at 37 °C was 20.24 U/ml in the presence of oat spelt xylan. The results indicated that the enzyme recovered in the middle phase of TPP system using the optimum parameters were determined as 50% ammonium sulfate saturation with 1.0:1.5 ratio of crude extract: t-butanol at pH and temperature of 8.0 and 10 °C, respectively. The xylanase was recovered with 3.48 purification fold and 107% activity recovery. The enzyme was optimally active at pH 7.0 and was stable over a broad pH range of 5.0–10. The optimum temperature for xylanase activity was 55 °C and the half-life time at this temperature was of 6 h. At this time point the enzyme retained 50% of its activity after incubation for 2 h at 95 °C. The crude enzyme resist to sodium dodecyl sulfate and β-mercaptoethanol, while all the tested ions do not affect the activity of the enzyme. The recovered enzyme is, at least, stable in tested organic solvents except in propanol where a reduction of 46.5% was observed. Further, the stability of the xylanase was higher in hydrophobic solvents where a maximum stability was observed with cyclohexane. These properties make this enzyme to be highly thermostable and may be suggested as a potential candidate for application in some industrial processes. To the best of our knowledge, this is the first report of xylanase activity and recoverey using three phase partitioning from B. oceanisediminis.
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Affiliation(s)
- Nawel Boucherba
- Laboratory of Applied Microbiology, Faculty of Nature Science and Life, University of Bejaia, 06000 Bejaia, Algeria
| | - Mohammed Gagaoua
- INATAA, Université des Frères Mentouri Constantine 1, Route de Ain El-Bey, 25000 Constantine, Algeria.,UMR1213 Herbivores, INRA, VetAgro Sup, Clermont Université, Université de Lyon, 63122 Saint-Genès-Champanelle, France
| | - Amel Bouanane-Darenfed
- Laboratory of Cellular and Molecular Biology, Microbiology Team, Faculty of Biological Sciences, University of Sciences, Technology of Houari Boumediene (USTHB), PO Box 32, El Alia, Bab Ezzouar, 16111 Algiers, Algeria
| | - Cilia Bouiche
- Laboratory of Applied Microbiology, Faculty of Nature Science and Life, University of Bejaia, 06000 Bejaia, Algeria
| | - Khelifa Bouacem
- Laboratory of Cellular and Molecular Biology, Microbiology Team, Faculty of Biological Sciences, University of Sciences, Technology of Houari Boumediene (USTHB), PO Box 32, El Alia, Bab Ezzouar, 16111 Algiers, Algeria
| | - Mohamed Yacine Kerbous
- Laboratory of Applied Microbiology, Faculty of Nature Science and Life, University of Bejaia, 06000 Bejaia, Algeria
| | - Yacine Maafa
- Laboratory of Applied Microbiology, Faculty of Nature Science and Life, University of Bejaia, 06000 Bejaia, Algeria
| | - Said Benallaoua
- Laboratory of Applied Microbiology, Faculty of Nature Science and Life, University of Bejaia, 06000 Bejaia, Algeria
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GC×GC-TOFMS for the Analysis of Metabolites Produced by Termites (Reticulitermes flavipes) Bred on Different Carbon Sources. SEPARATIONS 2016. [DOI: 10.3390/separations3020019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Tarayre C, Bauwens J, Brasseur C, Mattéotti C, Millet C, Guiot PA, Destain J, Vandenbol M, Portetelle D, De Pauw E, Haubruge E, Francis F, Thonart P. Isolation and cultivation of xylanolytic and cellulolytic Sarocladium kiliense and Trichoderma virens from the gut of the termite Reticulitermes santonensis. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:4369-4382. [PMID: 25300185 DOI: 10.1007/s11356-014-3681-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 10/01/2014] [Indexed: 06/04/2023]
Abstract
The purpose of this work was the isolation and cultivation of cellulolytic and xylanolytic microorganisms extracted from the gut of the lower termite Reticulitermes santonensis. Microcrystalline cellulose (with and without lignin) and beech wood xylan were used as diets instead of poplar wood in order to select cellulose and hemicellulose-degrading fungi. The strain Sarocladium kiliense (Acremonium kiliense) CTGxxyl was isolated from the termites fed on xylan, while the strain Trichoderma virens CTGxAviL was isolated from the termites fed on cellulose (with and without lignin). Both molds were cultivated in liquid media containing different substrates: agro-residues or purified polymers. S. kiliense produced maximal β-glucosidase, endo-1,4-β-D-glucanase, exo-1,4-β-D-glucanase and endo-1,4-β-D-xylanase activities of 0.103, 3.99, 0.53, and 40.8 IU/ml, respectively. T. virens produced maximal β-xylosidase, endo-1,4-β-D-glucanase, exo-1,4-β-D-glucanase, and endo-1,4-β-D-xylanase activities of 0.38, 1.48, 0.69, and 426 IU/ml. The cellulase and the xylanase of S. kiliense, less common than T. virens, were further investigated. The optimal activity of the xylanase was observed at pH 9-10 at 60 °C. The cellulase showed its maximal activity at pH 10, 70 °C. Zymography identified different xylanases produced by both molds, and some fragment sizes were highlighted: 35, 100, and 170 kDa for S. kiliense and 20, 40, 80, and 170 kDa for T. virens. In both cases, endo-1,4-β-D-xylanase activities were confirmed through mass spectrometry.
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Affiliation(s)
- Cédric Tarayre
- Unit of Bio-Industries, Gembloux Agro-Bio Tech, University of Liège, 5030, Gembloux, Belgium,
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Microbial Exo-xylanases: A Mini Review. Appl Biochem Biotechnol 2014; 174:81-92. [DOI: 10.1007/s12010-014-1042-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 06/29/2014] [Indexed: 10/25/2022]
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Kashyap R, Monika, Subudhi E. A novel thermoalkaliphilic xylanase fromGordoniasp. is salt, solvent and surfactant tolerant. J Basic Microbiol 2014; 54:1342-9. [DOI: 10.1002/jobm.201400097] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 05/11/2014] [Indexed: 11/12/2022]
Affiliation(s)
- Radhika Kashyap
- Department of Biotechnology; National Institute of Medical Sciences (NIMS) University; Jaipur India
| | - Monika
- Department of Biotechnology; Mata Gujri College; Fatehgarh Sahib Punjab India
| | - Enketeswara Subudhi
- Center of Biotechnology; Siksha 'O' Anusandhan University; Kalinganagar Ghatikia Bhubaneswar Orissa India
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MALDI-TOF MS analysis of cellodextrins and xylo-oligosaccharides produced by hindgut homogenates of Reticulitermes santonensis. Molecules 2014; 19:4578-94. [PMID: 24731986 PMCID: PMC6270808 DOI: 10.3390/molecules19044578] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 04/02/2014] [Accepted: 04/04/2014] [Indexed: 12/03/2022] Open
Abstract
Hindgut homogenates of the termite Reticulitermes santonensis were incubated with carboxymethyl cellulose (CMC), crystalline celluloses or xylan substrates. Hydrolysates were analyzed with matrix-assisted laser desorption/ionization coupled to time-of-flight mass spectrometry (MALDI-TOF MS). The method was first set up using acid hydrolysis analysis to characterize non-enzymatic profiles. Commercial enzymes of Trichoderma reesei or T. longibrachiatum were also tested to validate the enzymatic hydrolysis analysis. For CMC hydrolysis, data processing and visual display were optimized to obtain comprehensive profiles and allow rapid comparison and evaluation of enzymatic selectivity, according to the number of substituents of each hydrolysis product. Oligosaccharides with degrees of polymerization (DPs) ranging from three to 12 were measured from CMC and the enzymatic selectivity was demonstrated. Neutral and acidic xylo-oligosaccharides with DPs ranging from three to 11 were measured from xylan substrate. These results are of interest for lignocellulose biomass valorization and demonstrated the potential of termites and their symbiotic microbiota as a source of interesting enzymes for oligosaccharides production.
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Isolation of amylolytic, xylanolytic, and cellulolytic microorganisms extracted from the gut of the termite Reticulitermes santonensis by means of a micro-aerobic atmosphere. World J Microbiol Biotechnol 2013; 30:1655-60. [PMID: 24353041 DOI: 10.1007/s11274-013-1585-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 12/14/2013] [Indexed: 10/25/2022]
Abstract
The aim of this work was to isolate enzyme-producing microorganisms from the tract of the termite Reticulitermes santonensis. The microorganisms were extracted from the guts and anaerobic (CO₂ or CO₂/H₂) and micro-aerobic atmospheres were used to stimulate growth. Three different strategies were tried out. First, the sample was spread on Petri dishes containing solid media with carboxymethylcellulose, microcrystalline cellulose or cellobiose. This technique allowed us to isolate two bacteria: Streptomyces sp. strain ABGxAviA1 and Pseudomonas sp. strain ABGxCellA. The second strategy consisted in inoculating a specific liquid medium containing carboxymethylcellulose, microcrystalline cellulose, or cellobiose. The samples were then spread on Petri dishes with the same specific medium containing carboxymethylcellulose, microcrystalline cellulose, or cellobiose. This led to the isolation of the mold Aspergillus sp. strain ABGxAviA2. Finally, the third strategy consisted in heating the first culture and spreading samples on agar plates containing rich medium. This led to the isolation of the bacterium Bacillus subtilis strain ABGx. All those steps were achieved in controlled atmospheres. The four enzyme-producing strains which were isolated were obtained by using a micro-aerobic atmosphere. Later, enzymatic assays were performed on the four strains. Streptomyces sp. strain ABGxAviA1 was found to produce only amylase, while Pseudomonas sp. strain ABGxCellA was found to produce β-glucosidase as well. Aspergillus sp. strain ABGxAviA2 showed β-glucosidase, amylase, cellulase, and xylanase activities. Finally, B. subtilis strain ABGx produced xylanase and amylase.
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