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Sürmeli Y, Şanlı-Mohamed G. Engineering of xylanases for the development of biotechnologically important characteristics. Biotechnol Bioeng 2023; 120:1171-1188. [PMID: 36715367 DOI: 10.1002/bit.28339] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/19/2022] [Accepted: 01/26/2023] [Indexed: 01/31/2023]
Abstract
Xylanases are the main biocatalysts used for the reduction of the xylan backbone from hemicellulose, randomly splitting off β-1,4-glycosidic linkages between xylopyranosyl residues. Xylanase market has been annually estimated at 500 million US Dollars and they are potentially used in broad industrial process ranges such as paper pulp biobleaching, xylo-oligosaccharide production, and biofuel manufacture from lignocellulose. The highly stable xylanases are preferred in the downstream procedure of industrial processes because they can tolerate severe conditions. Almost all native xylanases can not endure adverse conditions thus they are industrially not proper to be utilized. Protein engineering is a powerful technology for developing xylanases, which can effectively work in adverse conditions and can meet requirements for industrial processes. This study considered state-of-the-art strategies of protein engineering for creating the xylanase gene diversity, high-throughput screening systems toward upgraded traits of the xylanases, and the prediction and comprehensive analysis of the target mutations in xylanases by in silico methods. Also, key molecular factors have been elucidated for industrial characteristics (alkaliphilic enhancement, thermal stability, and catalytic performance) of GH11 family xylanases. The present review explores industrial characteristics improved by directed evolution, rational design, and semi-rational design as protein engineering approaches for pulp bleaching process, xylooligosaccharides production, and biorefinery & bioenergy production.
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Affiliation(s)
- Yusuf Sürmeli
- Department of Agricultural Biotechnology, Tekirdağ Namık Kemal University, Tekirdağ, Turkey
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Cayetano-Cruz M, Caro-Gómez LA, Plascencia-Espinosa M, Santiago-Hernández A, Benítez-Cardoza CG, Campos JE, Hidalgo-Lara ME, Zamorano-Carrillo A. Effect of the single mutation N9Y on the catalytical properties of xylanase Xyn11A from Cellulomonas uda: a biochemical and molecular dynamic simulation analysis. Biosci Biotechnol Biochem 2021; 85:1971-1985. [PMID: 34232281 DOI: 10.1093/bbb/zbab124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 06/29/2021] [Indexed: 11/12/2022]
Abstract
Cellulomonas uda produces Xyn11A, moderately thermostable xylanase, with optimal activity at 50 °C and pH 6.5. An improvement in the biochemical properties of Xyn11A was achieved by site-directed mutagenesis approach. Wild-type xylanase, Xyn11A-WT, and its mutant Xyn11A-N9Y were expressed in Escherichia coli, and then both enzymes were purified and characterized. Xyn11A-N9Y displayed optimal activity at 60 °C and pH 7.5, an upward shift of 10 ºC in the optimum temperature, and an upward shift of one unit in optimum pH; also, it manifested an 11-fold increase in thermal stability at 60 ºC, compared to that displayed by Xyn11A-WT. Molecular dynamics (MD) simulations of Xyn11A-WT and Xyn11A-N9Y suggest the substitution N9Y leads to an array of secondary structure changes at the N-terminal end and an increase in the number of hydrogen bonds in Xyn11A-N9Y. Based on the significant improvements, Xyn11A-N9Y may be considered as a candidate for several biotechnological applications.
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Affiliation(s)
- Maribel Cayetano-Cruz
- Departamento de Biotecnología y Bioingeniería, CINVESTAV, Av. Instituto Politécnico Nacional No. 2508, D.F. CP 07360, México
| | - Luis A Caro-Gómez
- Laboratorio de Investigación Bioquímica y Biofísica Computacional, Doctorado en Ciencias en Biotecnología, ENMH, Instituto Politécnico Nacional, Guillermo Massieu Helguera, México, D.F. 07320, México
| | - Miguel Plascencia-Espinosa
- CIBA-Instituto Politécnico Nacional, Km 1.5 Carretera Estatal Tecuexcomac-Tepetitla, 90700, Tepetitla, Tlaxcala, México
| | - Alejandro Santiago-Hernández
- Departamento de Biotecnología y Bioingeniería, CINVESTAV, Av. Instituto Politécnico Nacional No. 2508, D.F. CP 07360, México
| | - Claudia G Benítez-Cardoza
- Laboratorio de Investigación Bioquímica y Biofísica Computacional, Doctorado en Ciencias en Biotecnología, ENMH, Instituto Politécnico Nacional, Guillermo Massieu Helguera, México, D.F. 07320, México
| | - Jorge E Campos
- Laboratorio de Bioquímica Molecular, UBIPRO, FES Iztacala, UNAM, Av. de los Barrios No. 1, Los Reyes Iztacala, CP 54090, Tlalnepantla de Baz, Estado de México, México
| | - María Eugenia Hidalgo-Lara
- Departamento de Biotecnología y Bioingeniería, CINVESTAV, Av. Instituto Politécnico Nacional No. 2508, D.F. CP 07360, México
| | - Absalom Zamorano-Carrillo
- Laboratorio de Investigación Bioquímica y Biofísica Computacional, Doctorado en Ciencias en Biotecnología, ENMH, Instituto Politécnico Nacional, Guillermo Massieu Helguera, México, D.F. 07320, México
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Gagné D, Narayanan C, Nguyen-Thi N, Roux LD, Bernard DN, Brunzelle JS, Couture JF, Agarwal PK, Doucet N. Ligand Binding Enhances Millisecond Conformational Exchange in Xylanase B2 from Streptomyces lividans. Biochemistry 2016; 55:4184-96. [PMID: 27387012 DOI: 10.1021/acs.biochem.6b00130] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Xylanases catalyze the hydrolysis of xylan, an abundant carbon and energy source with important commercial ramifications. Despite tremendous efforts devoted to the catalytic improvement of xylanases, success remains limited because of our relatively poor understanding of their molecular properties. Previous reports suggested the potential role of atomic-scale residue dynamics in modulating the catalytic activity of GH11 xylanases; however, dynamics in these studies was probed on time scales orders of magnitude faster than the catalytic time frame. Here, we used nuclear magnetic resonance titration and relaxation dispersion experiments ((15)N-CPMG) in combination with X-ray crystallography and computational simulations to probe conformational motions occurring on the catalytically relevant millisecond time frame in xylanase B2 (XlnB2) and its catalytically impaired mutant E87A from Streptomyces lividans 66. Our results show distinct dynamical properties for the apo and ligand-bound states of the enzymes. The apo form of XlnB2 experiences conformational exchange for residues in the fingers and palm regions of the catalytic cleft, while the catalytically impaired E87A variant displays millisecond dynamics only in the fingers, demonstrating the long-range effect of the mutation on flexibility. Ligand binding induces enhanced conformational exchange of residues interacting with the ligand in the fingers and thumb loop regions, emphasizing the potential role of residue motions in the fingers and thumb loop regions for recognition, positioning, processivity, and/or stabilization of ligands in XlnB2. To the best of our knowledge, this work represents the first experimental characterization of millisecond dynamics in a GH11 xylanase family member. These results offer new insights into the potential role of conformational exchange in GH11 enzymes, providing essential dynamic information to help improve protein engineering and design applications.
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Affiliation(s)
- Donald Gagné
- INRS-Institut Armand-Frappier, Université du Québec , 531 Boul. des Prairies, Laval, Québec H7V 1B7, Canada
| | - Chitra Narayanan
- INRS-Institut Armand-Frappier, Université du Québec , 531 Boul. des Prairies, Laval, Québec H7V 1B7, Canada
| | - Nhung Nguyen-Thi
- INRS-Institut Armand-Frappier, Université du Québec , 531 Boul. des Prairies, Laval, Québec H7V 1B7, Canada
| | - Louise D Roux
- INRS-Institut Armand-Frappier, Université du Québec , 531 Boul. des Prairies, Laval, Québec H7V 1B7, Canada
| | - David N Bernard
- INRS-Institut Armand-Frappier, Université du Québec , 531 Boul. des Prairies, Laval, Québec H7V 1B7, Canada
| | - Joseph S Brunzelle
- Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University , 320 East Superior Street, Chicago, Illinois 60611, United States
| | - Jean-François Couture
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa , 451 Smyth Road, Ottawa, Ontario K1H 8M5, Canada.,PROTEO, Québec Network for Research on Protein Function, Engineering, and Applications, Université Laval , 1045 Avenue de la Médecine, Québec, Québec G1V 0A6, Canada.,GRASP, Groupe de Recherche Axé sur la Structure des Protéines, McGill University , 3649 Promenade Sir William Osler, Montréal, Québec H3G 0B1, Canada
| | - Pratul K Agarwal
- Computational Biology Institute and Computer Science and Mathematics Division, Oak Ridge National Laboratory , 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States.,Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Nicolas Doucet
- INRS-Institut Armand-Frappier, Université du Québec , 531 Boul. des Prairies, Laval, Québec H7V 1B7, Canada.,PROTEO, Québec Network for Research on Protein Function, Engineering, and Applications, Université Laval , 1045 Avenue de la Médecine, Québec, Québec G1V 0A6, Canada.,GRASP, Groupe de Recherche Axé sur la Structure des Protéines, McGill University , 3649 Promenade Sir William Osler, Montréal, Québec H3G 0B1, Canada
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Verma D, Satyanarayana T. Molecular approaches for ameliorating microbial xylanases. BIORESOURCE TECHNOLOGY 2012; 117:360-367. [PMID: 22595098 DOI: 10.1016/j.biortech.2012.04.034] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Revised: 04/09/2012] [Accepted: 04/11/2012] [Indexed: 05/31/2023]
Abstract
In industrial processes, chemical catalysis is being replaced by enzyme catalysis, since the latter is environmentally benign, non-persistent and cost effective. Microbial xylanases have significant applications in textile, baking, food and feed industries, and in paper and pulp industries for reducing the chlorine requirement. The hazardous chlorine required for bleaching can be reduced up to 25-30% by including an enzymatic step in the pulp bleaching process. The paper pulp bleaching requires xylanases that are active at alkaline pH and elevated temperatures. The enzymes from the cultured microbes do not perform optimally in the paper industry due to their inadequate stability under the process conditions of high temperature and alkaline pH. This review, therefore, deals with the rationale of molecular approaches such as protein engineering for designing xylanases with improved characteristics to suit the process conditions in industries, and prospects and problems.
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Affiliation(s)
- Digvijay Verma
- Department of Microbiology, University of Delhi South Campus, New Delhi 110 021, India
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Li Y, Zhang B, Chen X, Chen Y, Cao Y. Improvement of Aspergillus sulphureus endo-beta-1,4-xylanase expression in Pichia pastoris by codon optimization and analysis of the enzymic characterization. Appl Biochem Biotechnol 2009; 160:1321-31. [PMID: 19412581 DOI: 10.1007/s12010-009-8621-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2009] [Accepted: 03/18/2009] [Indexed: 11/26/2022]
Abstract
The gene xynB from Aspergillus sulphureus encoding the endo-beta-1,4-xylanase was de novo synthesized by splicing overlap extension polymerase chain reaction according to Pichia pastoris protein's codon bias. The synthetic DNA and wild-type DNA were placed under the control of a glyceraldehyde-3-phosphate dehydrogenase gene promoter (GAP) in the constitutive expression vector plasmid pGAPzalphaA and electrotransformed into the P. pastoris X-33 strain, respectively. The transformants screened by Zeocin were able to constitutively secrete the xylanase in YPD liquid medium. The maximum yield of the recombinant xylanase produced by the synthetic DNA was 105 U ml(-1), which was about 5-fold higher than that by wild-type DNA under the flask culture at 28 degrees Celsius for 3 days. The enzyme showed optimal activity at 50 degrees Celsius and pH 5.0. The residual activity remained above 90% after the recombinant xylanase was pretreated in Na(2)HPO(4)-citric acid buffer (pH 2.4) for 2 h. The xylanase activity was significantly improved by Zn(2+). These biochemical characteristics suggest that the recombinant xylanase has a prospective application in feed industry as an additive.
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Affiliation(s)
- Yihang Li
- National Key Laboratory of Animal Nutrition, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, People's Republic of China
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