1
|
Talens-Perales D, Sánchez-Torres P, Marín-Navarro J, Polaina J. In silico screening and experimental analysis of family GH11 xylanases for applications under conditions of alkaline pH and high temperature. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:198. [PMID: 33372612 PMCID: PMC7720462 DOI: 10.1186/s13068-020-01842-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
BACKGROUND Xylanases are one of the most extensively used enzymes for biomass digestion. However, in many instances, their use is limited by poor performance under the conditions of pH and temperature required by the industry. Therefore, the search for xylanases able to function efficiently at alkaline pH and high temperature is an important objective for different processes that use lignocellulosic substrates, such as the production of paper pulp and biofuels. RESULTS A comprehensive in silico analysis of family GH11 sequences from the CAZY database allowed their phylogenetic classification in a radial cladogram in which sequences of known or presumptive thermophilic and alkalophilic xylanases appeared in three clusters. Eight sequences from these clusters were selected for experimental analysis. The coding DNA was synthesized, cloned and the enzymes were produced in E. coli. Some of these showed high xylanolytic activity at pH values > 8.0 and temperature > 80 °C. The best enzymes corresponding to sequences from Dictyoglomus thermophilum (Xyn5) and Thermobifida fusca (Xyn8). The addition of a carbohydrate-binding module (CBM9) to Xyn5 increased 4 times its activity at 90 °C and pH > 9.0. The combination of Xyn5 and Xyn8 was proved to be efficient for the saccharification of alkali pretreated rice straw, yielding xylose and xylooligosaccharides. CONCLUSIONS This study provides a fruitful approach for the selection of enzymes with suitable properties from the information contained in extensive databases. We have characterized two xylanases able to hydrolyze xylan with high efficiency at pH > 8.0 and temperature > 80 °C.
Collapse
Affiliation(s)
- David Talens-Perales
- Department of Food Biotechnology. Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Paterna, Valencia, Spain
| | - Paloma Sánchez-Torres
- Department of Food Biotechnology. Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Paterna, Valencia, Spain
| | - Julia Marín-Navarro
- Department of Food Biotechnology. Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Paterna, Valencia, Spain
- Department of Biochemistry and Molecular Biology, University of Valencia, Valencia, Spain
| | - Julio Polaina
- Department of Food Biotechnology. Institute of Agrochemistry and Food Technology, Spanish National Research Council (IATA-CSIC), Paterna, Valencia, Spain.
| |
Collapse
|
2
|
Zhang F, You S, Huang T, Wang JZ, Zhu LL, Wang B, Ye WS, Herman RA, Luo H, Wang J. Dual promoter strategy enhances co-expression of α-L-rhamnosidase and enhanced fluorescent protein for whole-cell catalysis and bioresource valorization. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 722:137865. [PMID: 32192973 DOI: 10.1016/j.scitotenv.2020.137865] [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: 11/30/2019] [Revised: 02/17/2020] [Accepted: 03/10/2020] [Indexed: 06/10/2023]
Abstract
Developing circular economy is the only way to improve the efficiency of resource utilization. Whole-cell catalysis is an effective method to recycle enzymes, improve catalytic efficiency, and reduce production costs. The enzyme, α-L-rhamnosidase has considerable application prospects in the field of biocatalysis as it can hydrolyze a variety of α-L rhamnoses. In the present study, the genes for α-L-rhamnosidase (rhaB1) and enhanced fluorescent protein (EGFP) were co-expressed using a bi-promoter expression vector pRSFDuet1 and their enzymatic properties were evaluated. To our knowledge, this study has established an effective rhamnosidase-fluorescent indicator and whole-cell catalytic system for the first time. Moreover, we analyzed the change in the activity of the crude rhaB1-EGFP as well as its whole-cell during the biocatalysis process using fluorescence intensity. Recombinant rhaB1-EGFP as a product which contains rhaB1 and EGFP showed higher thermal stability, pH stability, and conversion efficiency than rhaB1, and its optimum temperature for rutin catalysis was ideal for industrial applications. Moreover, under the optimal conditions of a rutin concentration of 0.05 g/L, pH of 6.0, temperature of 40 °C, a yield of 92.5% was obtained. Furthermore, we demonstrated the relationship between the fluorescence intensity and enzyme activity. This study established a highly efficient whole-cell catalytic system whose activity can be evaluated by fluorescence intensity, providing a reference for enzyme recycling.
Collapse
Affiliation(s)
- Fan Zhang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China
| | - Shuai You
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China; Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, PR China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Zhenjiang 212018, PR China; Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, Zhenjiang 212018, PR China
| | - Ting Huang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China
| | - Jin-Zheng Wang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China
| | - Lin-Lin Zhu
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China
| | - Bo Wang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China
| | - Wang-Sheng Ye
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China
| | - Richard Ansah Herman
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China
| | - Heng Luo
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China; Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, PR China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Zhenjiang 212018, PR China; Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, Zhenjiang 212018, PR China
| | - Jun Wang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212018, PR China; Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, PR China; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Zhenjiang 212018, PR China; Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, Zhenjiang 212018, PR China.
| |
Collapse
|
3
|
Guillotin L, Kim H, Traore Y, Moreau P, Lafite P, Coquoin V, Nuccio S, de Vaumas R, Daniellou R. Biochemical Characterization of the α-l-Rhamnosidase DtRha from Dictyoglomus thermophilum: Application to the Selective Derhamnosylation of Natural Flavonoids. ACS OMEGA 2019; 4:1916-1922. [PMID: 31459445 PMCID: PMC6649072 DOI: 10.1021/acsomega.8b03186] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 01/10/2019] [Indexed: 05/25/2023]
Abstract
α-l-Rhamnosidases are catalysts of industrial tremendous interest, but their uses are still somewhat limited by their poor thermal stabilities and selectivities. The thermophilic DtRha from Dictyoglomus thermophilum was cloned, and the recombinant protein was easily purified to homogeneity to afford 4.5 mg/L culture of biocatalyst. Michaelis-Menten parameters demonstrated it to be fully specific for α-l-rhamnose. Most significantly, DtRha demonstrated to have a stronger preference for α(1 → 2) linkage rather than α(1 → 6) linkage when removing rhamnosyl moiety from natural flavonoids. This selectivity was fully explained by the difference of binding of the corresponding substrates in the active site of the protein.
Collapse
Affiliation(s)
- Laure Guillotin
- Université
d’Orléans, CNRS, ICOA, UMR 7311, Rue de Chartres, BP 6759, 45067 Orléans Cedex 2, France
| | - Hyuna Kim
- Université
d’Orléans, CNRS, ICOA, UMR 7311, Rue de Chartres, BP 6759, 45067 Orléans Cedex 2, France
| | - Yasmina Traore
- Université
d’Orléans, CNRS, ICOA, UMR 7311, Rue de Chartres, BP 6759, 45067 Orléans Cedex 2, France
| | - Philippe Moreau
- Université
d’Orléans, CNRS, ICOA, UMR 7311, Rue de Chartres, BP 6759, 45067 Orléans Cedex 2, France
| | - Pierre Lafite
- Université
d’Orléans, CNRS, ICOA, UMR 7311, Rue de Chartres, BP 6759, 45067 Orléans Cedex 2, France
| | - Véronique Coquoin
- Extrasynthese, CS 30062,
ZI Lyon Nord, Impasse
Jacquard, 69727 Genay Cedex, France
| | - Sylvie Nuccio
- Extrasynthese, CS 30062,
ZI Lyon Nord, Impasse
Jacquard, 69727 Genay Cedex, France
| | - René de Vaumas
- Extrasynthese, CS 30062,
ZI Lyon Nord, Impasse
Jacquard, 69727 Genay Cedex, France
| | - Richard Daniellou
- Université
d’Orléans, CNRS, ICOA, UMR 7311, Rue de Chartres, BP 6759, 45067 Orléans Cedex 2, France
| |
Collapse
|
4
|
Pachl P, Škerlová J, Šimčíková D, Kotik M, Křenková A, Mader P, Brynda J, Kapešová J, Křen V, Otwinowski Z, Řezáčová P. Crystal structure of native α-L-rhamnosidase from Aspergillus terreus. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:1078-1084. [DOI: 10.1107/s2059798318013049] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/14/2018] [Indexed: 11/10/2022]
Abstract
α-L-Rhamnosidases cleave terminal nonreducing α-L-rhamnosyl residues from many natural rhamnoglycosides. This makes them catalysts of interest for various biotechnological applications. The X-ray structure of the GH78 family α-L-rhamnosidase from Aspergillus terreus has been determined at 1.38 Å resolution using the sulfur single-wavelength anomalous dispersion phasing method. The protein was isolated from its natural source in the native glycosylated form, and the active site contained a glucose molecule, probably from the growth medium. In addition to its catalytic domain, the α-L-rhamnosidase from A. terreus contains four accessory domains of unknown function. The structural data suggest that two of these accessory domains, E and F, might play a role in stabilizing the aglycon portion of the bound substrate.
Collapse
|
5
|
Lei L, Huang B, Liu A, Lu YJ, Zhou JL, Zhang J, Wong WL. Enzymatic production of natural sweetener trilobatin from citrus flavanone naringin using immobilised α-l
-rhamnosidase as the catalyst. Int J Food Sci Technol 2018. [DOI: 10.1111/ijfs.13796] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Lin Lei
- School of Chemical Engineering and Light Industry; Guangdong University of Technology; Guangzhou 510006 China
| | - Baohua Huang
- School of Chemical Engineering and Light Industry; Guangdong University of Technology; Guangzhou 510006 China
- Goldenpomelo Biotechnology Co. Ltd.; Meizhou 514021 China
| | - Aolu Liu
- School of Chemical Engineering and Light Industry; Guangdong University of Technology; Guangzhou 510006 China
| | - Yu-Jing Lu
- School of Chemical Engineering and Light Industry; Guangdong University of Technology; Guangzhou 510006 China
- Goldenpomelo Biotechnology Co. Ltd.; Meizhou 514021 China
| | - Jin-Lin Zhou
- Goldenpomelo Biotechnology Co. Ltd.; Meizhou 514021 China
| | - Jinjin Zhang
- School of Chemical Engineering and Light Industry; Guangdong University of Technology; Guangzhou 510006 China
| | - Wing-Leung Wong
- School of Chemical and Environmental Engineering; International Healthcare Innovation Institute (Jiangmen); Wuyi University; Jiangmen 529020 China
- Centre for Education in Environmental Sustainability; The Education University of Hong Kong; 10 Lo Ping Road Tai Po Hong Kong China
| |
Collapse
|
6
|
Abstract
Glycosyltransferases offer the opportunity to glycosylate a variety of substrates including health beneficial molecules like flavonoids in a regiospecific manner. Flavonoids are plant secondary metabolites that have antimicrobial, antioxidative, and health beneficial effects. Glycosylation often has impact on these properties and furthermore enhances the water solubility, the stability, and the bioavailability of the molecules. To detect flavonoid glycosylating enzymes we established a metagenome screen for the discovery of modifying clones. This function based screening technique can furthermore detect other modifications like methylations. The method relies on analysis of the culture supernatant extracts from biotransformation reactions in a thin layer chromatography (TLC) approach.
Collapse
|
7
|
Li B, Ji Y, Li Y, Ding G. Characterization of a glycoside hydrolase family 78 α-l-rhamnosidase from Bacteroides thetaiotaomicron VPI-5482 and identification of functional residues. 3 Biotech 2018; 8:120. [PMID: 29430381 PMCID: PMC5805665 DOI: 10.1007/s13205-018-1139-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 01/29/2018] [Indexed: 11/27/2022] Open
Abstract
A putative glycoside hydrolase family 78 α-l-rhamnosidase BtRha78A from Bacteroides thetaiotaomicron VPI-5482 was heterologously over-expressed in Escherichia coli. Enzymatic properties of recombinant BtRha78A were characterized in detail. Recombinant BtRha78A might efficiently hydrolyze p-nitrophenyl α-l-rhamnopyranoside. BtRha78A displayed the highest activity at 60 °C in pH 6.5. BtRha78A exhibited a good pH stability and relatively high thermostability. BtRha78A could be tolerant of a low concentration of alcohols. These attractive advantages made it a promising alternative biocatalyst for industrial applications. The catalytic general acid Asp335 and general base Glu595 of BtRha78A were confirmed by site-directed mutagenesis. Alanine scanning mutagenesis based on sequence alignment and structural analysis revealed that the conserved residues Asp330, Arg334, Trp339, Asp342, Tyr383, Trp440, and His620 were crucial for enzyme catalysis. Most functional residues located at the conserved general acid motif (Asp330-Asp342) and were completely conserved in the subfamily I Rha78s.
Collapse
Affiliation(s)
- Binchun Li
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006 China
| | - Yaru Ji
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006 China
| | - Yanqin Li
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006 China
| | - Guobin Ding
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006 China
| |
Collapse
|
8
|
Berini F, Casciello C, Marcone GL, Marinelli F. Metagenomics: novel enzymes from non-culturable microbes. FEMS Microbiol Lett 2017; 364:4329276. [DOI: 10.1093/femsle/fnx211] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/02/2017] [Indexed: 01/02/2023] Open
|
9
|
Adesioye FA, Makhalanyane TP, Biely P, Cowan DA. Phylogeny, classification and metagenomic bioprospecting of microbial acetyl xylan esterases. Enzyme Microb Technol 2016; 93-94:79-91. [DOI: 10.1016/j.enzmictec.2016.07.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 06/18/2016] [Accepted: 07/01/2016] [Indexed: 02/06/2023]
|
10
|
Contemporary molecular tools in microbial ecology and their application to advancing biotechnology. Biotechnol Adv 2015; 33:1755-73. [DOI: 10.1016/j.biotechadv.2015.09.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 09/19/2015] [Accepted: 09/20/2015] [Indexed: 12/30/2022]
|