1
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Komp E, Phillips C, Lee LM, Fallin SM, Alanzi HN, Zorman M, McCully ME, Beck DAC. Neural network conditioned to produce thermophilic protein sequences can increase thermal stability. Sci Rep 2025; 15:14124. [PMID: 40268970 PMCID: PMC12019596 DOI: 10.1038/s41598-025-90828-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2024] [Accepted: 02/17/2025] [Indexed: 04/25/2025] Open
Abstract
This work presents Neural Optimization for Melting-temperature Enabled by Leveraging Translation (NOMELT), a novel approach for designing and ranking high-temperature stable proteins using neural machine translation. The model, trained on over 4 million protein homologous pairs from organisms adapted to different temperatures, demonstrates promising capability in targeting thermal stability. A designed variant of the Drosophila melanogaster Engrailed Homeodomain shows a melting temperature increase of 15.5 K. Furthermore, NOMELT achieves zero-shot predictive capabilities in ranking experimental melting and half-activation temperatures across a number of protein families. It achieves this without requiring extensive homology data or massive training datasets as do existing zero-shot predictors by specifically learning thermophilicity, as opposed to all natural variation. These findings underscore the potential of leveraging organismal growth temperatures in context-dependent design of proteins for enhanced thermal stability.
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Affiliation(s)
- Evan Komp
- Chemical Engineering, University of Washington, Seattle, WA, USA.
| | | | - Lauren M Lee
- Department of Biology, Santa Clara University, Santa Clara, CA, USA
| | - Shayna M Fallin
- Department of Biology, Santa Clara University, Santa Clara, CA, USA
| | - Humood N Alanzi
- Chemical Engineering, University of Washington, Seattle, WA, USA
| | - Marlo Zorman
- Chemical Engineering, University of Washington, Seattle, WA, USA
| | | | - David A C Beck
- Chemical Engineering, University of Washington, Seattle, WA, USA.
- eScience Institute, University of Washington, Seattle, WA, USA.
- Computer Science, University of Washington, Seattle, WA, USA.
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2
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Yang Y, Liu X, He X, Ren W, Gu H, Wang R, Li X. Genomic analysis and synergistic effect with cellulase by Streptomyces thermocarboxydus 12219. Int J Biol Macromol 2025; 296:139675. [PMID: 39793796 DOI: 10.1016/j.ijbiomac.2025.139675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2024] [Revised: 12/24/2024] [Accepted: 01/07/2025] [Indexed: 01/13/2025]
Abstract
In this study, we fully sequenced and analyzed the genome of strain 12219 and identified it as Streptomyces thermocarboxydus. The genome contained a single linear chromosome, 6,950,031 bp in size, with a GC content of 72.21 %. This study predicted a total of 6295 genes, including 128 glycoside hydrolase genes, 21 carbohydrate esterase genes, and 54 carbohydrate-binding module genes. When corncob was used as inducer, strain 12219 secreted cellulases and hemicellulases, with xylanase activity reaching 31.15 U/mL. During the hydrolysis of sodium hydroxide treated corn stover, a notable synergistic effect between the 12219 enzyme cocktail and commercial cellulase was observed. And the maximum degree of synergism reached 1.60. When the amount of the 12219 enzyme cocktail added to the commercial cellulase was 5 mg/g, the release of glucose, xylose, and cellobiose increased by 121.35 %, 178.58 %, and 29.33 %, respectively. These findings suggested that the 12219 enzyme cocktail held great potential for industrial applications.
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Affiliation(s)
- Yi Yang
- College of Forestry, Henan Agricultural University, Zhengzhou 450046, China.
| | - Xiaoyu Liu
- College of Forestry, Henan Agricultural University, Zhengzhou 450046, China.
| | - Xinyu He
- International Education College, Henan Agricultural University, Zhengzhou 450046, China.
| | - Weizheng Ren
- College of Forestry, Henan Agricultural University, Zhengzhou 450046, China.
| | - Haiping Gu
- College of Forestry, Henan Agricultural University, Zhengzhou 450046, China.
| | - Ruonan Wang
- College of Life Science, Luoyang Normal University, Luoyang 471934, China.
| | - Xuanzhen Li
- College of Forestry, Henan Agricultural University, Zhengzhou 450046, China.
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3
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Singh YR, Thakur A, Fontes CMGA, Goyal A. A novel thermophilic recombinant obligate xylobiohydrolase (AcGH30A) from Acetivibrio clariflavus orchestrates the deconstruction of xylan polysaccharides. Carbohydr Polym 2024; 340:122295. [PMID: 38858006 DOI: 10.1016/j.carbpol.2024.122295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/15/2024] [Accepted: 05/18/2024] [Indexed: 06/12/2024]
Abstract
GH30 xylobiohydrolases, an expanding enzyme category, need deeper insights for optimal use. The primary aim of this study was to characterize a new xylobiohydrolase, AcGH30A of GH30 family from Acetivibrio clariflavus. The gene encoding AcGH30A was cloned using pET28a(+) vector and expressed in E. coli BL21(DE3) cells. AcGH30A was purified by immobilized metal-ion affinity chromatography. SDS-PAGE analysis of AcGH30A showed molecular mass of ~58 kDa. AcGH30A showed optimum temperature 80 °C and optimum pH 7.0. AcGH30A was stable (maintaining >80 % of control activity) in pH range, 4-7 and temperature range, 30 °C -70 °C when incubated for 90 min. AcGH30A displayed melting temperature, 72 °C and half-life, 21 days at 4 °C. The enzyme activity of AcGH30A was enhanced by 10 mM Ca2+ and Mg2+ ions by 25 % and 21 %, respectively, whereas 10 mM Co2+, Zn2+, Fe2+, and Cu2+ ions significantly reduced it. AcGH30A showed activity against various xylan polysaccharides displaying highest Vmax, 139 U.mg-1 and KM, 0.71 mg.ml-1 against 4-O-methyl glucuronoxylan under optimum conditions. TLC, HPLC and LC-MS analyses of AcGH30A hydrolyzed products from xylan substrates revealed the release of sole product, xylobiose, confirming it as an obligate xylobiohydrolase. AcGH30A being a highly thermostable enzyme can be potentially utlilized in various biotechnological applications.
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Affiliation(s)
- Yumnam Robinson Singh
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati, Guwahati, Assam 781039, India
| | - Abhijeet Thakur
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati, Guwahati, Assam 781039, India
| | - Carlos M G A Fontes
- NZYTech - Genes & Enzymes, Estrada do Paço do Lumiar, Campus do Lumiar, Edifício E - R/C, 1649-038 Lisbon, Portugal; CIISA - Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisbon, Portugal
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology, Guwahati, Guwahati, Assam 781039, India.
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Lisov AV, Belova OV, Belov AA, Lisova ZA, Nagel AS, Shadrin AM, Andreeva-Kovalevskaya ZI, Nagornykh MO, Zakharova MV, Leontievsky AA. Expression in Pichia pastoris of Thermostable Endo-1,4-β-xylanase from the Actinobacterium Nocardiopsis halotolerans: Properties and Use for Saccharification of Xylan-Containing Products. Int J Mol Sci 2024; 25:9121. [PMID: 39201806 PMCID: PMC11355003 DOI: 10.3390/ijms25169121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 08/19/2024] [Accepted: 08/21/2024] [Indexed: 09/03/2024] Open
Abstract
A gene encoding a polysaccharide-degrading enzyme was cloned from the genome of the bacterium Nocardiopsis halotolerans. Analysis of the amino acid sequence of the protein showed the presence of the catalytic domain of the endo-1,4-β-xylanases of the GH11 family. The gene was amplified by PCR and ligated into the pPic9m vector. A recombinant producer based on Pichia pastoria was obtained. The production of the enzyme, which we called NhX1, was carried out in a 10 L fermenter. Enzyme production was 10.4 g/L with an activity of 927 U/mL. Purification of NhX1 was carried out using Ni-NTA affinity chromatography. The purified enzyme catalyzed the hydrolysis of xylan but not other polysaccharides. Endo-1,4-β-xylanase NhX1 showed maximum activity and stability at pH 6.0-7.0. The enzyme showed high thermal stability, remaining active at 90 °C for 20 min. With beechwood xylan, the enzyme showed Km 2.16 mg/mL and Vmax 96.3 U/mg. The products of xylan hydrolysis under the action of NhX1 were xylobiose, xylotriose, xylopentaose, and xylohexaose. Endo-1,4-β-xylanase NhX1 effectively saccharified xylan-containing products used for the production of animal feed. The xylanase described herein is a thermostable enzyme with biotechnological potential produced in large quantities by P. pastoria.
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Affiliation(s)
- Alexander V. Lisov
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Oksana V. Belova
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Andrey A. Belov
- Faculty of Soil Science, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Zoya A. Lisova
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Alexey S. Nagel
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Andrey M. Shadrin
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Zhanna I. Andreeva-Kovalevskaya
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Maxim O. Nagornykh
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Marina V. Zakharova
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 142290 Pushchino, Russia
| | - Alexey A. Leontievsky
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, 142290 Pushchino, Russia
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Pasin TM, Lucas RC, de Oliveira TB, McLeish MJ, Polizeli MDLTM. A new halotolerant xylanase from Aspergillus clavatus expressed in Escherichia coli with catalytic efficiency improved by site-directed mutagenesis. 3 Biotech 2024; 14:178. [PMID: 38855145 PMCID: PMC11156621 DOI: 10.1007/s13205-024-04021-7] [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: 03/07/2024] [Accepted: 05/27/2024] [Indexed: 06/11/2024] Open
Abstract
Daily agro-industrial waste, primarily cellulose, lignin, and hemicellulose, poses a significant environmental challenge. Harnessing lignocellulolytic enzymes, particularly endo-1,4-β-xylanases, for efficient saccharification is a cost-effective strategy, transforming biomass into high-value products. This study focuses on the cloning, expression, site-directed mutagenesis, purification, three-dimensional modeling, and characterization of the recombinant endo-1,4-β-xylanase (XlnA) from Aspergillus clavatus in Escherichia coli. This work includes evaluation of the stability at varied NaCl concentrations, determining kinetic constants, and presenting the heterologous expression of XlnAΔ36 using pET22b(+). The expression led to purified enzymes with robust stability across diverse pH levels, exceptional thermostability at 50 °C, and 96-100% relative stability after 24 h in 3.0 M NaCl. Three-dimensional modeling reveals a GH11 architecture with catalytic residues Glu 132 and 22. XlnAΔ36 demonstrates outstanding kinetic parameters compared to other endo-1,4-β-xylanases, indicating its potential for industrial enzymatic cocktails, enhancing saccharification. Moreover, its ability to yield high-value compounds, such as sugars, suggests a promising and ecologically positive alternative for the food and biotechnology industries.
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Affiliation(s)
- Thiago M. Pasin
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900 Brazil
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202 USA
- Department of Chemistry, University of Texas at San Antonio, One UTSA Circle, San Antonio, TX 78249 USA
| | - Rosymar C. Lucas
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900 Brazil
- Department of Biochemistry, Institute of Biomedical Sciences, Federal University of Alfenas, Alfenas, MG 37130-001 Brazil
| | - Tássio B. de Oliveira
- Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP 14040-901 Brazil
- Department of Systematics and Ecology, Center for Exact and Nature Sciences, Federal University of Paraíba, João Pessoa, PB 58051-900 Brazil
| | - Michael J. McLeish
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202 USA
| | - Maria de Lourdes T. M. Polizeli
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP 14049-900 Brazil
- Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP 14040-901 Brazil
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Cabrera-Villamizar LA, Ebrahimi M, Martínez-Abad A, Talens-Perales D, López-Rubio A, Fabra MJ. Order matters: Methods for extracting cellulose from rice straw by coupling alkaline, ozone and enzymatic treatments. Carbohydr Polym 2024; 328:121746. [PMID: 38220332 DOI: 10.1016/j.carbpol.2023.121746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/20/2023] [Accepted: 12/26/2023] [Indexed: 01/16/2024]
Abstract
Rice straw is a widely produced residue that can be converted into value-added products. This work aimed at using greener processes combining mild alkali (A), ozone (O) and enzymatic (engineered xylanase) (E) treatments to extract cellulose and other value-added compounds from rice straw and to evaluate the effects of the order of the treatments. Solid (S) and liquid (L) fractions from the process were collected for physicochemical characterization. AOE treatment showed the best capacity to extract high purity cellulose and other valuable compounds. The lignin content was significantly decreased independently of the order of the treatments and, its content in the extract obtained after the AOE process was lower than the one obtained after the OAE process. Moreover, thermal stability of the samples increased after the enzymatic process, being higher in SAOE. The alkaline treatment increased the hemicellulose and polyphenol content (antioxidant activity) in the liquid fractions (LA and LOA). In contrast, the ozonized liquid fractions had lower polyphenol content. Therefore, alkali was fundamental in the process. In conclusion, the AOE strategy could be a more environmentally friendly method for extracting cellulose and other valuable compounds, which could be used to develop active materials in the future.
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Affiliation(s)
- Laura Andrea Cabrera-Villamizar
- Food Safety and Preservation Department, Institute of Agrochemistry and Food Technology (IATA), CSIC, 46980, Valencia, Spain.
| | - Mahrokh Ebrahimi
- Food Safety and Preservation Department, Institute of Agrochemistry and Food Technology (IATA), CSIC, 46980, Valencia, Spain; Institut Polytechnique UniLaSalle, Université d'Artois, ULR 7519, 19 rue Pierre Waguet, BP 30313, 60026 Beauvais Cédex, France.
| | - Antonio Martínez-Abad
- Food Safety and Preservation Department, Institute of Agrochemistry and Food Technology (IATA), CSIC, 46980, Valencia, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast), CSIC, 28006 Madrid, Spain.
| | - David Talens-Perales
- Food Biotechnology Department, Institute of Agrochemistry and Food Technology (IATA), CSIC, 46980, Valencia, Spain.
| | - Amparo López-Rubio
- Food Safety and Preservation Department, Institute of Agrochemistry and Food Technology (IATA), CSIC, 46980, Valencia, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast), CSIC, 28006 Madrid, Spain.
| | - María José Fabra
- Food Safety and Preservation Department, Institute of Agrochemistry and Food Technology (IATA), CSIC, 46980, Valencia, Spain; Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast), CSIC, 28006 Madrid, Spain.
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7
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Gupta GK, Kapoor RK. Recent advances in eco-friendly technology for decontamination of pulp and paper mill industrial effluent: a review. ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:275. [PMID: 38363444 DOI: 10.1007/s10661-024-12399-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/29/2024] [Indexed: 02/17/2024]
Abstract
The economic development of a country directly depends upon industries. But this economic development should not be at the cost of our natural environment. A substantial amount of water is spent during paper production, creating water scarcity and generating wastewater. Therefore, the Pollution Control Board classifies this industry into red category. Water is used in different papermaking stages such as debarking, pulping or bleaching, washing, and finishing. The wastewater thus generated contains lignin and xenobiotic compounds such as resin acids, chlorinated lignin, phenols, furans, dioxins, chlorophenols, adsorbable organic halogens (AOX), extractable organic halogens (EOCs), polychlorinated biphenyls, plasticizers, and polychlorinated dibenzodioxins. Nowadays, several microorganisms are used in the detoxification of these hazardous effluents. Researchers have found that microbial degradation is the most promising treatment method to remove high biological oxygen demand (BOD) and chemical oxygen demand (COD) from wastewater. Microorganisms also remove AOX toxicity, chlorinated compounds, suspended solids, color, lignin, derivatives, etc. from the pulp and paper mill effluents. But in the current scenario, mill effluents are known to deteriorate the environment and therefore it is highly desirable to deploy advanced technologies for effluent treatment. This review summarizes the eco-friendly advanced treatment technologies for effluents generated from pulp and paper mills.
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Affiliation(s)
- Guddu Kumar Gupta
- Enzyme and Fermentation Technology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, 124001, Haryana, India
| | - Rajeev Kumar Kapoor
- Enzyme and Fermentation Technology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, 124001, Haryana, India.
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Matos JMS, Evtuguin DV, de Sousa APM, Carvalho MGVS. Xylanase treatment of eucalypt kraft pulps: effect of carryover. Appl Microbiol Biotechnol 2024; 108:210. [PMID: 38355912 PMCID: PMC10867044 DOI: 10.1007/s00253-024-13027-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 01/03/2024] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
Abstract
The influence of pulp carryover on the efficiency of the xylanase (X) treatment of industrial unbleached and oxygen-delignified eucalypt kraft pulps (A1 and A2 pulps, with kappa number (KN) values of 16 and 10, respectively), collected at the same pulp mill, was studied regarding the consumption of bleaching chemicals and pulp bleachability. Another non-oxygen-delignified eucalyptus kraft pulp of KN 13 was received after the extended cooking from a different pulp mill (pulp B). The assays were performed with both lab-washed (carryover-free) and unwashed (carryover-rich) pulps. Both lab-washed and unwashed pulps with carryover were subjected to X treatment, the former being demonstrating considerably higher ClO2 savings than the pulps containing carryover. The savings of bleaching reagents were higher when the X stage was applied to the A1 pulp than to the A2 pulp. This advantage of A1 pulp, however, was not confirmed when using unwashed pulps. In contrast, the gains obtained from the X treatment of unwashed pulp A2 were practically as high as those observed for the lab-washed A2 pulp. Furthermore, a similar effect in X stage was recorded for unwashed pulps having close KN: oxygen-delignified A2 pulp and non-oxygen-delignified B pulp. The results suggest that pulp carryover and initial pH were the key factors relating to the effectiveness of X treatment. The application of X treatment to the A2 unwashed pulp (after the oxygen stage) not only saved 20% of the ClO2 and 10% of the sodium hydroxide, but also improved the brightness stability of the bleached pulp without affecting its papermaking properties. KEY POINTS: • Xylanase treatment boosts kraft pulp bleaching • Pulp carryover hinders the xylanase treatment • Nearly 20% of ClO2 and 10% NaOH savings can be reached using xylanase.
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Affiliation(s)
- José M S Matos
- CERES, Department of Chemical Engineering, University of Coimbra, 3030-790, Coimbra, Portugal
| | - Dmitry V Evtuguin
- CICECO/Department of Chemistry, University of Aveiro, 3810-193, Aveiro, Portugal.
| | | | - M Graça V S Carvalho
- CERES, Department of Chemical Engineering, University of Coimbra, 3030-790, Coimbra, Portugal
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Komp E, Alanzi HN, Francis R, Vuong C, Roberts L, Mosallanejad A, Beck DAC. Homologous Pairs of Low and High Temperature Originating Proteins Spanning the Known Prokaryotic Universe. Sci Data 2023; 10:682. [PMID: 37805601 PMCID: PMC10560248 DOI: 10.1038/s41597-023-02553-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/08/2023] [Indexed: 10/09/2023] Open
Abstract
Stability of proteins at high temperature has been a topic of interest for many years, as this attribute is favourable for applications ranging from therapeutics to industrial chemical manufacturing. Our current understanding and methods for designing high-temperature stability into target proteins are inadequate. To drive innovation in this space, we have curated a large dataset, learn2thermDB, of protein-temperature examples, totalling 24 million instances, and paired proteins across temperatures based on homology, yielding 69 million protein pairs - orders of magnitude larger than the current largest. This important step of pairing allows for study of high-temperature stability in a sequence-dependent manner in the big data era. The data pipeline is parameterized and open, allowing it to be tuned by downstream users. We further show that the data contains signal for deep learning. This data offers a new doorway towards thermal stability design models.
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Affiliation(s)
- Evan Komp
- Department of Chemical Engineering, University of Washington, Seattle, USA.
| | - Humood N Alanzi
- Department of Chemical Engineering, University of Washington, Seattle, USA
| | - Ryan Francis
- Department of Chemical Engineering, University of Washington, Seattle, USA
| | - Chau Vuong
- Department of Biochemistry, University of Washington, Seattle, USA
| | - Logan Roberts
- Department of Chemical Engineering, University of Washington, Seattle, USA
| | - Amin Mosallanejad
- Department of Chemical Engineering, University of Washington, Seattle, USA
| | - David A C Beck
- Department of Chemical Engineering, University of Washington, Seattle, USA.
- eScience Institute, University of Washington, Seattle, USA.
- Paul G. Allen School of Computer Science, University of Washington, Seattle, USA.
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10
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Kyomuhimbo HD, Feleni U, Haneklaus NH, Brink H. Recent Advances in Applications of Oxidases and Peroxidases Polymer-Based Enzyme Biocatalysts in Sensing and Wastewater Treatment: A Review. Polymers (Basel) 2023; 15:3492. [PMID: 37631549 PMCID: PMC10460086 DOI: 10.3390/polym15163492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/10/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
Oxidase and peroxidase enzymes have attracted attention in various biotechnological industries due to their ease of synthesis, wide range of applications, and operation under mild conditions. Their applicability, however, is limited by their poor stability in harsher conditions and their non-reusability. As a result, several approaches such as enzyme engineering, medium engineering, and enzyme immobilization have been used to improve the enzyme properties. Several materials have been used as supports for these enzymes to increase their stability and reusability. This review focusses on the immobilization of oxidase and peroxidase enzymes on metal and metal oxide nanoparticle-polymer composite supports and the different methods used to achieve the immobilization. The application of the enzyme-metal/metal oxide-polymer biocatalysts in biosensing of hydrogen peroxide, glucose, pesticides, and herbicides as well as blood components such as cholesterol, urea, dopamine, and xanthine have been extensively reviewed. The application of the biocatalysts in wastewater treatment through degradation of dyes, pesticides, and other organic compounds has also been discussed.
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Affiliation(s)
- Hilda Dinah Kyomuhimbo
- Department of Chemical Engineering, University of Pretoria, Pretoria 0028, South Africa;
| | - Usisipho Feleni
- Institute for Nanotechnology and Water Sustainability (iNanoWS), College of Science, Engineering and Technology, University of South Africa, Florida Campus, Roodepoort, Johannesburg 1710, South Africa;
| | - Nils H. Haneklaus
- Transdisciplinarity Laboratory Sustainable Mineral Resources, University for Continuing Education Krems, 3500 Krems, Austria;
| | - Hendrik Brink
- Department of Chemical Engineering, University of Pretoria, Pretoria 0028, South Africa;
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11
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Sarma RK, Gohain A, Ahmed TH, Yadav A, Saikia R. An environment-benign approach of bamboo pulp bleaching using extracellular xylanase of strain Bacillus stratosphericus EB-11 isolated from elephant dung. Folia Microbiol (Praha) 2023; 68:135-149. [PMID: 36048323 DOI: 10.1007/s12223-022-01003-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 08/23/2022] [Indexed: 11/30/2022]
Abstract
The use of microbial enzymes is highly encouraged in paper and pulp industries to reduce the excessive use of hazardous chemicals. During the study, xylanase of Bacillus stratosphericus EB-11 was characterized for pulp bleaching applications. The extracellular xylanase was produced under submerged fermentation using bamboo waste as a natural carbon source. There was fast cell division and enzyme production under optimized fermentation conditions in the bioreactor. The highest activity was 91,200U after 30 h of growth with Km and Vmax of 3.52 mg/mL and 391.5 μmol/min per mg respectively. The purified enzyme with molecular mass ~ 60 kDa had conferred positive activity on native PAGE. The strong inhibition by ethylenediaminetetraacetate and SDS showed the metallo-xylanase nature of the purified enzyme. The bacterial xylanase reduces the use of hydrogen peroxide by 0.4%. Similarly, biological oxygen demand and chemical oxygen demand were reduced by 42.6 and 35.2%. The xylanase-hydrogen peroxide combined treatment and conventional chlorine dioxide-alkaline (CDE1D1D2) bleaching showed almost similar improvement in physicochemical properties of bamboo pulp. Xylanase-peroxide bleaching reduces the lignin content to 4.95% from 13.32% unbleached pulp. This content after CDE1D1D2 treatment was 4.21%. The kappa number decreased from 15.2 to 9.46 with increasing the burst factor (15.51), crystallinity index (60.25%), viscosity (20.1 cp), and brightness (65.4%). The overall finding will encourage the development of new cleaner methods of bleaching in the paper and pulp industry.
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Affiliation(s)
| | - Anwesha Gohain
- Department of Botany, Arunachal University of Studies, PIN-792013, Namsai, India
| | - Tobiul Hussain Ahmed
- Chemical Engineering Group, Engineering Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat-785006, Assam, India
| | - Archana Yadav
- Biotechnology Group, Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat-785006, Assam, India
| | - Ratul Saikia
- Biotechnology Group, Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology, Jorhat-785006, Assam, India
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12
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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: 10] [Impact Index Per Article: 5.0] [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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13
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Biochemical characterization of a thermally stable, acidophilic and surfactant-tolerant xylanase from Aspergillus awamori AFE1 and hydrolytic efficiency of its immobilized form. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.06.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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14
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Singh R, Pal DB, Alkhanani MF, Almalki AH, Areeshi MY, Haque S, Srivastava N. Prospects of soil microbiome application for lignocellulosic biomass degradation: An overview. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:155966. [PMID: 35584752 DOI: 10.1016/j.scitotenv.2022.155966] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/04/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
Sustainable and practically viable biofuels production technology using lignocellulosic biomass is still seeking its way of implementation owing to some major issues involved therein. Unavailability of efficient microbial sources for the degradation of cellulosic biomass is one of the major roadblocks in biomass to biofuels production technology. In this context, utilization of microbiomes to degrade lignocellulaosic biomass is emerging as a rapid and effective approach that can fulfill the requirements of biomass based biofuels production technology. Therefore, the present review is targeted to explore soil metagenomic approach to improve the lignocellulosic biomass degradation processing for the cost-effective and eco-friendly application. Soil microbiomes consist of rich microbial community along with high probability of cellulolytic microbes, and can be identified by culture independent metagenomics method which can be structurally and functionally explored via genomic library. Therefore, in depth analysis and discussion have also been made via structural & functional metagenomics tools along with their contribution to genomic library. Additionally, the present review highlights currently existing bottlenecks along with their feasible solutions. This review will help to understand the basic research as well as industrial concept for the process improvement based on soil microbiome mediated lignocellulosic biomass degradation, and this may likely to implement for the low-cost commercial biofuels production technology.
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Affiliation(s)
- Rajeev Singh
- Department of Environmental Studies, Satyawati College, University of Delhi, Delhi, 110052, India
| | - Dan Bahadur Pal
- Department of Chemical Engineering, Birla Institute of Technology, Mesra, Ranchi 835215, Jharkhand, India
| | - Mustfa F Alkhanani
- Emergency Service Department, College of Applied Sciences, AlMaarefa University, Riyadh 11597, Saudi Arabia
| | - Atiah H Almalki
- Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia; Addiction and Neuroscience Research Unit, College of Pharmacy, Taif University, Al-Hawiah, Taif 21944, Saudi Arabia
| | - Mohammed Yahya Areeshi
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Jazan University, Jazan 45142, Saudi Arabia; Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan 45142, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan 45142, Saudi Arabia; Bursa Uludağ University, Faculty of Medicine, Görükle Campus, 16059 Nilüfer, Bursa, Turkey
| | - Neha Srivastava
- Department of Chemical Engineering and Technology, Indian Institute of Technology (BHU), Varanasi 221005, India.
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15
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Wu X, Shi Z, Tian W, Liu M, Huang S, Liu X, Yin H, Wang L. A thermostable and CBM2-linked GH10 xylanase from Thermobifida fusca for paper bleaching. Front Bioeng Biotechnol 2022; 10:939550. [PMID: 36091429 PMCID: PMC9459120 DOI: 10.3389/fbioe.2022.939550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/02/2022] [Indexed: 11/25/2022] Open
Abstract
Xylanases have the potential to be used as bio-deinking and bio-bleaching materials and their application will decrease the consumption of the chlorine-based chemicals currently used for this purpose. However, xylanases with specific properties could act effectively, such as having significant thermostability and alkali resistance, etc. In this study, we found that TfXyl10A, a xylanase from Thermobifida fusca, was greatly induced to transcript by microcrystalline cellulose (MCC) substrate. Biochemical characterization showed that TfXyl10A is optimally effective at temperature of 80 °C and pH of 9.0. After removing the carbohydrate-binding module (CBM) and linker regions, the optimum temperature of TfXyl10A-CD was reduced by 10°C (to 70°C), at which the enzyme’s temperature tolerance was also weakened. While truncating only the CBM domain (TfXyl10AdC) had no significant effect on its thermostability. Importantly, polysaccharide-binding experiment showed that the auxiliary domain CBM2 could specifically bind to cellulose substrates, which endowed xylanase TfXyl10A with the ability to degrade xylan surrounding cellulose. These results indicated that TfXyl10A might be an excellent candidate in bio-bleaching processes of paper industry. In addition, the features of active-site architecture of TfXyl10A in GH10 family were further analyzed. By mutating each residue at the -2 and -1 subsites to alanine, the binding force and enzyme activity of mutants were observably decreased. Interestingly, the mutant E51A, locating at the distal -3 subsite, exhibited 90% increase in relative activity compared with wild-type (WT) enzyme TfXyl10A-CD (the catalytic domain of TfXyl110A). This study explored the function of a GH10 xylanase containing a CBM2 domain and the contribution of amino acids in active-site architecture to catalytic activity. The results obtained provide guidance for the rational design of xylanases for industrial applications under high heat and alkali-based operating conditions, such as paper bleaching.
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Affiliation(s)
- Xiuyun Wu
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China
- State Key Laboratory of Biological Fermentation Engineering of Beer, Qingdao, China
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Zelu Shi
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Wenya Tian
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Mengyu Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Shuxia Huang
- State Key Laboratory of Biological Fermentation Engineering of Beer, Qingdao, China
| | - Xinli Liu
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China
| | - Hua Yin
- State Key Laboratory of Biological Fermentation Engineering of Beer, Qingdao, China
- *Correspondence: Hua Yin, ; Lushan Wang,
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
- *Correspondence: Hua Yin, ; Lushan Wang,
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16
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Sohail M, Barzkar N, Michaud P, Tamadoni Jahromi S, Babich O, Sukhikh S, Das R, Nahavandi R. Cellulolytic and Xylanolytic Enzymes from Yeasts: Properties and Industrial Applications. Molecules 2022; 27:3783. [PMID: 35744909 PMCID: PMC9229053 DOI: 10.3390/molecules27123783] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 11/17/2022] Open
Abstract
Lignocellulose, the main component of plant cell walls, comprises polyaromatic lignin and fermentable materials, cellulose and hemicellulose. It is a plentiful and renewable feedstock for chemicals and energy. It can serve as a raw material for the production of various value-added products, including cellulase and xylanase. Cellulase is essentially required in lignocellulose-based biorefineries and is applied in many commercial processes. Likewise, xylanases are industrially important enzymes applied in papermaking and in the manufacture of prebiotics and pharmaceuticals. Owing to the widespread application of these enzymes, many prokaryotes and eukaryotes have been exploited to produce cellulase and xylanases in good yields, yet yeasts have rarely been explored for their plant-cell-wall-degrading activities. This review is focused on summarizing reports about cellulolytic and xylanolytic yeasts, their properties, and their biotechnological applications.
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Affiliation(s)
- Muhammad Sohail
- Department of Microbiology, University of Karachi, Karachi 75270, Pakistan;
| | - Noora Barzkar
- Department of Marine Biology, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas 3995, Iran
| | - Philippe Michaud
- Institute Pascal, Université Clermont Auvergne, CNRS, Clermont Auvergne INP, F-63000 Clermont-Ferrand, France;
| | - Saeid Tamadoni Jahromi
- Persian Gulf and Oman Sea Ecology Research Center, Iranian Fisheries Sciences Research Institute, Agricultural Research Education and Extension Organization (AREEO), Bandar Abbas 3995, Iran
| | - Olga Babich
- Institute of Living Systems, Immanuel Kant Baltic Federal University, 236016 Kaliningrad, Russia; (O.B.); (S.S.)
| | - Stanislav Sukhikh
- Institute of Living Systems, Immanuel Kant Baltic Federal University, 236016 Kaliningrad, Russia; (O.B.); (S.S.)
| | - Rakesh Das
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), 1433 Aas, Norway;
| | - Reza Nahavandi
- Animal Science Research Institute of Iran (ASRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj 8361, Iran;
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17
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Liu Z, Wen S, Wu G, Wu H. Heterologous expression and characterization of Anaeromyces robustus xylanase and its use in bread making. Eur Food Res Technol 2022. [DOI: 10.1007/s00217-022-04047-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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18
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Dong R, Liu X, Wang Y, Qin X, Wang X, Zhang H, Wang Y, Luo H, Yao B, Bai Y, Tu T. Fusion of a proline-rich oligopeptide to the C-terminus of a ruminal xylanase improves catalytic efficiency. Bioengineered 2022; 13:10482-10492. [PMID: 35441569 PMCID: PMC9161913 DOI: 10.1080/21655979.2022.2061290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Xylanases are widely used in the degradation of lignocellulose and are important industrial enzymes. Therefore, increasing the catalytic activity of xylanases can improve their efficiency and performance. In this study, we introduced the C-terminal proline-rich oligopeptide of the rumen-derived XynA into XylR, a GH10 family xylanase. The optimum temperature and pH of the fused enzyme (XylR-Fu) were consistent with those of XylR; however, its catalytic efficiency was 2.48-fold higher than that of XylR. Although the proline-rich oligopeptide did not change the enzyme hydrolysis mode, the amount of oligosaccharides released from beechwood xylan by XylR-Fu was 17% higher than that released by XylR. This increase may be due to the abundance of proline in the oligopeptide, which plays an important role in substrate binding. Furthermore, circular dichroism analysis indicated that the proline-rich oligopeptide might increase the rigidity of the overall structure, thereby enhancing the affinity to the substrate and catalytic activity of the enzyme. Our study shows that the proline-rich oligopeptide enhances the catalytic efficiency of GH10 xylanases and provides a better understanding of the C-terminal oligopeptide-function relationships. This knowledge can guide the rational design of GH10 xylanases to improve their catalytic activity and provides clues for further applications of xylanases in industry.
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Affiliation(s)
- Ruyue Dong
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoqing Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yaru Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xing Qin
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaolu Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Honglian Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuan Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yingguo Bai
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tao Tu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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19
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Revealing the Potential of Xylanase from a New Halophilic Microbulbifer sp. CL37 with Paper De-Inking Ability. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2021. [DOI: 10.1007/s13369-021-06400-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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20
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Unraveling Synergism between Various GH Family Xylanases and Debranching Enzymes during Hetero-Xylan Degradation. Molecules 2021; 26:molecules26226770. [PMID: 34833862 PMCID: PMC8618192 DOI: 10.3390/molecules26226770] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/15/2021] [Accepted: 10/27/2021] [Indexed: 11/20/2022] Open
Abstract
Enzymes classified with the same Enzyme Commission (EC) that are allotted in different glycoside hydrolase (GH) families can display different mechanisms of action and substrate specificities. Therefore, the combination of different enzyme classes may not yield synergism during biomass hydrolysis, as the GH family allocation of the enzymes influences their behavior. As a result, it is important to understand which GH family combinations are compatible to gain knowledge on how to efficiently depolymerize biomass into fermentable sugars. We evaluated GH10 (Xyn10D and XT6) and GH11 (XynA and Xyn2A) β-xylanase performance alone and in combination with various GH family α-l-arabinofuranosidases (GH43 AXH-d and GH51 Abf51A) and α-d-glucuronidases (GH4 Agu4B and GH67 AguA) during xylan depolymerization. No synergistic enhancement in reducing sugar, xylose and glucuronic acid released from beechwood xylan was observed when xylanases were supplemented with either one of the glucuronidases, except between Xyn2A and AguA (1.1-fold reducing sugar increase). However, overall sugar release was significantly improved (≥1.1-fold reducing sugar increase) when xylanases were supplemented with either one of the arabinofuranosidases during wheat arabinoxylan degradation. Synergism appeared to result from the xylanases liberating xylo-oligomers, which are the preferred substrates of the terminal arabinofuranosyl-substituent debranching enzyme, Abf51A, allowing the exolytic β-xylosidase, SXA, to have access to the generated unbranched xylo-oligomers. Here, it was shown that arabinofuranosidases are key enzymes in the efficient saccharification of hetero-xylan into xylose. This study demonstrated that consideration of GH family affiliations of the carbohydrate-active enzymes (CAZymes) used to formulate synergistic enzyme cocktails is crucial for achieving efficient biomass saccharification.
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21
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Gupta GK, Dixit M, Kapoor RK, Shukla P. Xylanolytic Enzymes in Pulp and Paper Industry: New Technologies and Perspectives. Mol Biotechnol 2021; 64:130-143. [PMID: 34580813 DOI: 10.1007/s12033-021-00396-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/08/2021] [Indexed: 11/26/2022]
Abstract
The pulp and paper industry discharges massive amount of wastewater containing hazardous organochlorine compounds released during different processing stages. Therefore, some cost-effective and nonpolluting practices such as enzymatic treatments are required for the potential mitigation of effluents released in the environment. Various xylanolytic enzymes such as xylanases, laccases, cellulases and hemicellulases are used to hydrolyse raw materials in the paper manufacturing industry. These enzymes are used either individually or in combination, which has the efficient potential to be considered for bio-deinking and bio-bleaching components. They are highly dynamic, renewable, and high in specificity for enhancing paper quality. The xylanase act on the xylan and cellulases act on the cellulose fibers, and thus increase the bleaching efficacy of paper. Similarly, hemicellulase enzyme like endo-xylanases, arabinofuranosidase and β-D-xylosidases have been described as functional properties towards the biodegradation of biomass. In contrast, laccase enzymes act as multi-copper oxidoreductases, bleaching the paper by the oxidation and reduction process. Laccases possess low redox potential compared to other enzymes, which need some redox mediators to catalyze. The enzymatic process can be affected by various factors such as pH, temperature, metal ions, incubation periods, etc. These factors can either increase or decrease the efficiency of the enzymes. This review draws attention to the xylanolytic enzyme-based advanced technologies for pulp bleaching in the paper industry.
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Affiliation(s)
- Guddu Kumar Gupta
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Mandeep Dixit
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Rajeev Kumar Kapoor
- Enzyme and Fermentation Technology Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India.
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, 221005, India.
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22
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Expression of an alkaline feruloyl esterases from thermophilic Chaetomium thermophilum and its boosting effect on delignification of pulp. Enzyme Microb Technol 2021; 150:109859. [PMID: 34489049 DOI: 10.1016/j.enzmictec.2021.109859] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/20/2021] [Accepted: 06/23/2021] [Indexed: 11/23/2022]
Abstract
Exploration of feruloyl esterase (FAE) with the resistance to heat and alkali conditions in biobleaching process to improve the separation efficiency of lignocellulose is the key to achieving green papermaking. Herein, we expressed FAEB of C. thermophilum and obtained a thermostable alkaline FAE that can effectively promote the removal of lignin from pulp. The faeB gene was successfully obtained through genomic Blast strategy and high-efficiency expressed under the control of strong alcohol oxidase promoter in Pichia pastoris. The recombinant CtFAEB has an optimal temperature of 65 °C and pH of 7.0. After treated at 65 °C for 1 h, CtFAEB can still retain 63.21 % of its maximum activity, showing a good thermal stability. In addition, the recombinant CtFAEB has broad pH stability and can retain about 56 % of the maximum activity even at pH 11.0. Compared with the effect of mesophilic FAE, pretreatment with thermostable CtFAEB can promote the delignification by laccase and alkaline hydrogen peroxide from the pulp at 70 °C and pH 9.0. Alignment of the protein sequences of CtFAEB and mesophilic FAE suggested that the percentage of amino acids that easily form alpha helix in CtFAEB increases, which enhances its structural rigidity and thereby improves its thermal stability and alkali tolerance. Our study provides an effective method to obtain thermostable and alkaline FAEs, which will promote its application in biobleaching and other biorefining industries.
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Dube S, Rawtani D. Understanding intricacies of bioinspired organic-inorganic hybrid nanoflowers: A quest to achieve enhanced biomolecules immobilization for biocatalytic, biosensing and bioremediation applications. Adv Colloid Interface Sci 2021; 295:102484. [PMID: 34358991 DOI: 10.1016/j.cis.2021.102484] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 06/29/2021] [Accepted: 07/02/2021] [Indexed: 01/10/2023]
Abstract
The immobilization of biomolecules has been a subject of interest for scientists for a long time. The organic-inorganic hybrid nanoflowers are a new class of nanostructures that act as a host platform for the immobilization of such biomolecules. It provides better practical applicability to these functional biomolecules while also providing superior activity and reusability when catalysis is involved. These nanostructures have a versatile and straightforward synthesis process and also exhibit enzyme mimicking activity in many cases. However, this facile synthesis involves many intricacies that require in-depth analysis to fully attain its potential as an immobilization technique. A complete account of all the factors involving the synthesis process optimisation is essential to be studied to make it commercially viable. This paper explores all the different aspects of hybrid nanoflowers which sets them apart from the conventional immobilization techniques while also giving an overview of its wide range of applications in industries.
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Thermostable cellulose saccharifying microbial enzymes: Characteristics, recent advances and biotechnological applications. Int J Biol Macromol 2021; 188:226-244. [PMID: 34371052 DOI: 10.1016/j.ijbiomac.2021.08.024] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/19/2021] [Accepted: 08/03/2021] [Indexed: 12/12/2022]
Abstract
Cellulases play a promising role in the bioconversion of renewable lignocellulosic biomass into fermentable sugars which are subsequently fermented to biofuels and other value-added chemicals. Besides biofuel industries, they are also in huge demand in textile, detergent, and paper and pulp industries. Low titres of cellulase production and processing are the main issues that contribute to high enzyme cost. The success of ethanol-based biorefinery depends on high production titres and the catalytic efficiency of cellulases functional at elevated temperatures with acid/alkali tolerance and the low cost. In view of their wider application in various industrial processes, stable cellulases that are active at elevated temperatures in the acidic-alkaline pH ranges, and organic solvents and salt tolerance would be useful. This review provides a recent update on the advances made in thermostable cellulases. Developments in their sources, characteristics and mechanisms are updated. Various methods such as rational design, directed evolution, synthetic & system biology and immobilization techniques adopted in evolving cellulases with ameliorated thermostability and characteristics are also discussed. The wide range of applications of thermostable cellulases in various industrial sectors is described.
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25
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Nagpal R, Bhardwaj NK, Mahajan R. Eco-friendly bleaching of sugarcane bagasse with crude xylanase and pectinase enzymes to reduce the bleaching effluent toxicity. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:42990-42998. [PMID: 34218371 DOI: 10.1007/s11356-021-15122-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Abstract
Bio-bleaching effect on bagasse pulp using xylano-pectinolytic enzymes produced by a bacterial species was studied in order to evaluate the potential of these enzymes in paper industry. In this study, action of enzymes was maximum with xylanase/pectinase dose 7/1.75 IU/g, pulp consistency 1:12.5 g/L, pH 8.5, temperature 50° C and 180 min of treatment time. Under the optimized bio-bleaching conditions, removal of reducing sugars (6.15±0.05 mg/L), brightness (16.08%), whiteness (25.54%) and release of chromophores (hydrophobic and phenolic compounds and lignin impurities) were maximum, along with decrease in kappa number (26.28%), and yellowness (27.88%) values were obtained. Improvement in the various physical properties like breaking length (10.28%), burst index (29.55%), tear index (5.02%), double fold (14.89%), Gurley porosity (15%) and viscosity (8.6%), along with the reduction of chlorine dioxide dose by 27%, was also observed. There is also reduction in COD and BOD values of bio-bleached effluents by 27.62% and 20.52%, respectively. This is the first report on bio-bleaching of bagasse pulp using xylano-pectinolytic enzymes.
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Affiliation(s)
- Raksha Nagpal
- Department of Biotechnology, Kurukshetra University, Kurukshetra, India
| | - Nishi K Bhardwaj
- Avantha Center for Industrial Research and Development, Paper Mill Campus, Yamuna Nagar, India
| | - Ritu Mahajan
- Department of Biotechnology, Kurukshetra University, Kurukshetra, India.
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Xie W, Yu Q, Zhang R, Liu Y, Cao R, Wang S, Zhan R, Liu Z, Wang K, Wang C. Insights into the Catalytic Mechanism of a Novel XynA and Structure-Based Engineering for Improving Bifunctional Activities. Biochemistry 2021; 60:2071-2083. [PMID: 34156819 DOI: 10.1021/acs.biochem.1c00134] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Xylan and cellulose are the two major constituents of numerous types of lignocellulose. The bifunctional enzyme that exhibits xylanase/cellulase activity has attracted a great deal of attention in biofuel production. Previously, a thermostable GH10 family enzyme (XynA) from Bacillus sp. KW1 was found to degrade both xylan and cellulose. To improve bifunctional activity on the basis of structure, we first determined the crystal structure of XynA at 2.3 Å. Via molecular docking and activity assays, we revealed that Gln250 and His252 were indispensable to bifunctionality, because they could interact with two conserved catalytic residues, Glu182 and Glu280, while bringing the substrate close to the activity pocket. Then we used a structure-based engineering strategy to improve xylanase/cellulase activity. Although no mutants with increased bifunctional activity were obtained after much screening, we found the answer in the N-terminal 36-amino acid truncation of XynA. The activities of XynA_ΔN36 toward beechwood xylan, wheat arabinoxylan, filter paper, and barley β-glucan were significantly increased by 0.47-, 0.53-, 2.46-, and 1.04-fold, respectively. Furthermore, upon application, this truncation released more reducing sugars than the wild type in the degradation of pretreated corn stover and sugar cane bagasse. These results showed the detailed molecular mechanism of the GH10 family bifunctional endoxylanase/cellulase. The basis of these catalytic performances and the screened XynA_ΔN36 provide clues for the further use of XynA in industrial applications.
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Affiliation(s)
- Wei Xie
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China
| | - Qi Yu
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China
| | - Ruiqing Zhang
- Research Center of Chinese Herbal Resource Science and Engineering, Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China
| | - Yun Liu
- Research Center of Chinese Herbal Resource Science and Engineering, Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China
| | - Ruoting Cao
- Research Center of Chinese Herbal Resource Science and Engineering, Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China
| | - Sidi Wang
- College of Fundamental Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Ruoting Zhan
- Research Center of Chinese Herbal Resource Science and Engineering, Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China
| | - Zhongqiu Liu
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China
| | - Kui Wang
- Research Center of Chinese Herbal Resource Science and Engineering, Key Laboratory of Chinese Medicinal Resource from Lingnan (Guangzhou University of Chinese Medicine), Ministry of Education, Joint Laboratory of National Engineering Research Center for the Pharmaceutics of Traditional Chinese Medicines, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China
| | - Caiyan Wang
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, China
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Balderas Hernández VE, Salas-Montantes CJ, Barba-De la Rosa AP, De Leon-Rodriguez A. Autodisplay of an endo-1,4-β-xylanase from Clostridium cellulovorans in Escherichia coli for xylans degradation. Enzyme Microb Technol 2021; 149:109834. [PMID: 34311879 DOI: 10.1016/j.enzmictec.2021.109834] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 05/10/2021] [Accepted: 05/22/2021] [Indexed: 11/29/2022]
Abstract
The goal of this work was the autodisplay of the endo β-1,4-xylanase (XynA) from Clostridium cellulovorans in Escherichia coli using the AIDA system to carry out whole-cell biocatalysis and hydrolysate xylans. For this, pAIDA-xynA vector containing a synthetic xynA gene was fused to the signal peptide of the toxin subunit B Vibro cholere (ctxB) and the auto-transporter of the synthetic aida gene, which encodes for the connector peptide and β-barrel of the auto-transporter (AT-AIDA). E. coli TOP10 cells were transformed and the biocatalyst was characterized using beechwood xylans as substrate. Optimal operational conditions were temperature of 55 °C and pH 6.5, and the Michaelis-Menten catalytic constants Vmax and Km were 149 U/gDCW and 6.01 mg/mL, respectively. Xylanase activity was inhibited by Cu2+, Zn2+ and Hg2+ as well as EDTA, detergents, and organic acids, and improved by Ca2+, Co2+ and Mn2+ ions. Ca2+ ion strongly enhanced the xylanolytic activity up to 2.4-fold when 5 mM CaCl2 were added. Also, Ca2+ improved enzyme stability at 60 and 70 °C. Results suggest that pAIDA-xynA vector has the ability to express functional xylanase to perform whole-cell biocatalysis in order to hydrolysate xylans from hemicellulose feedstock.
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Affiliation(s)
- Victor E Balderas Hernández
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), Camino a la Presa de San José 2055 Lomas 4ª. Sección, C.P. 78216, San Luis Potosí, Mexico
| | - Carlos J Salas-Montantes
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), Camino a la Presa de San José 2055 Lomas 4ª. Sección, C.P. 78216, San Luis Potosí, Mexico
| | - Ana P Barba-De la Rosa
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), Camino a la Presa de San José 2055 Lomas 4ª. Sección, C.P. 78216, San Luis Potosí, Mexico
| | - Antonio De Leon-Rodriguez
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), Camino a la Presa de San José 2055 Lomas 4ª. Sección, C.P. 78216, San Luis Potosí, Mexico.
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Zhang S, Zhao S, Shang W, Yan Z, Wu X, Li Y, Chen G, Liu X, Wang L. Synergistic mechanism of GH11 xylanases with different action modes from Aspergillus niger An76. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:118. [PMID: 33971954 PMCID: PMC8112042 DOI: 10.1186/s13068-021-01967-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/03/2021] [Indexed: 05/28/2023]
Abstract
BACKGROUND Xylan is the most abundant hemicellulose polysaccharide in nature, which can be converted into high value-added products. However, its recalcitrance to breakdown requires the synergistic action of multiple enzymes. Aspergillus niger, possessing numerous xylan degrading isozyme-encoding genes, are highly effective xylan degraders in xylan-rich habitats. Therefore, it is necessary to explore gene transcription, the mode of action and cooperation mechanism of different xylanase isozymes to further understand the efficient xylan-degradation by A. niger. RESULTS Aspergillus niger An76 encoded a comprehensive set of xylan-degrading enzymes, including five endo-xylanases (one GH10 and four GH11). Quantitative transcriptional analysis showed that three xylanase genes (xynA, xynB and xynC) were up-regulated by xylan substrates, and the order and amount of enzyme secretion differed. Specifically, GH11 xylanases XynA and XynB were initially secreted successively, followed by GH10 xylanase XynC. Biochemical analyses displayed that three GH11 xylanases (XynA, XynB and XynD) showed differences in catalytic performance and product profiles, possibly because of intricate hydrogen bonding between substrates and functional residues in the active site architectures impacted their binding capacity. Among these, XynB had the best performance in the degradation of xylan and XynE had no catalytic activity. Furthermore, XynA and XynB showed synergistic effects during xylan degradation. CONCLUSIONS The sequential secretion and different action modes of GH11 xylanases were essential for the efficient xylan degradation by A. niger An76. The elucidation of the degradation mechanisms of these xylanase isozymes further improved our understanding of GH-encoding genes amplification in filamentous fungi and may guide the design of the optimal enzyme cocktails in industrial applications.
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Affiliation(s)
- Shu Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 Shandong China
| | - Sha Zhao
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 Shandong China
- School of Life Sciences, Shandong University, Qingdao, 266237 Shandong China
| | - Weihao Shang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 Shandong China
| | - Zijuan Yan
- School of Life Sciences, Shandong University, Qingdao, 266237 Shandong China
| | - Xiuyun Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 Shandong China
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, 250353 Shandong China
| | - Yingjie Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 Shandong China
| | - Guanjun Chen
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 Shandong China
| | - Xinli Liu
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology, Shandong Academy of Sciences, Jinan, 250353 Shandong China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237 Shandong China
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Talens-Perales D, Jiménez-Ortega E, Sánchez-Torres P, Sanz-Aparicio J, Polaina J. Phylogenetic, functional and structural characterization of a GH10 xylanase active at extreme conditions of temperature and alkalinity. Comput Struct Biotechnol J 2021; 19:2676-2686. [PMID: 34093984 PMCID: PMC8148631 DOI: 10.1016/j.csbj.2021.05.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/29/2021] [Accepted: 05/01/2021] [Indexed: 01/31/2023] Open
Abstract
Endoxylanases active under extreme conditions of
temperature and alkalinity can replace the use of highly pollutant chemicals in
the pulp and paper industry. Searching for enzymes with these properties, we
carried out a comprehensive bioinformatics study of the GH10 family. The
phylogenetic analysis allowed the construction of a radial cladogram in which
protein sequences putatively ascribed as thermophilic and alkaliphilic appeared
grouped in a well-defined region of the cladogram, designated TAK Cluster. One
among five TAK sequences selected for experimental analysis (Xyn11) showed
extraordinary xylanolytic activity under simultaneous conditions of high
temperature (90 °C) and alkalinity (pH 10.5). Addition of a carbohydrate binding
domain (CBM2) at the C-terminus of the protein sequence further improved the
activity of the enzyme at high pH. Xyn11 structure, which has been solved at
1.8 Å resolution by X-ray crystallography, reveals an unusually high number of
hydrophobic, ionic and hydrogen bond atomic interactions that could account for
the enzyme’s extremophilic nature.
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Affiliation(s)
- David Talens-Perales
- Institute of Agrochemistry and Food Technology, Spanish National Research Council (CSIC), Paterna, Valencia, Spain
| | - Elena Jiménez-Ortega
- Institute of Physical-Chemistry Rocasolano, Spanish National Research Council (CSIC), Madrid, Spain
| | - Paloma Sánchez-Torres
- Institute of Agrochemistry and Food Technology, Spanish National Research Council (CSIC), Paterna, Valencia, Spain
| | - Julia Sanz-Aparicio
- Institute of Physical-Chemistry Rocasolano, Spanish National Research Council (CSIC), Madrid, Spain
| | - Julio Polaina
- Institute of Agrochemistry and Food Technology, Spanish National Research Council (CSIC), Paterna, Valencia, Spain
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Liu Y, Wang J, Bao C, Dong B, Cao Y. Characterization of a novel GH10 xylanase with a carbohydrate binding module from Aspergillus sulphureus and its synergistic hydrolysis activity with cellulase. Int J Biol Macromol 2021; 182:701-711. [PMID: 33862072 DOI: 10.1016/j.ijbiomac.2021.04.065] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/08/2021] [Accepted: 04/12/2021] [Indexed: 12/31/2022]
Abstract
A study was carried out to investigate the characterization of a novel Aspergillus sulphureus JCM01963 xylanase (AS-xyn10A) with a carbohydrate binding module (CBM) and its application in degrading alkali pretreated corncob, rapeseed meal and corn stover alone and in combination with a commercial cellulase. In this study, the 3D structure of AS-xyn10A, which contained a CBM at C-terminal. AS-xyn10A and its CBM-truncated variant (AS-xyn10A-dC) was codon-optimized and over-expressed in Komagaella phaffii X-33 (syn. Pichia pastoris) and characterized with optimal condition at 70 °C and pH 5.0, respectively. AS-xyn10A displayed high activity to xylan extracted from corn stover, corncob, and rapeseed meal. The concentration of hydrolyzed xylo-oligosaccharides (XOSs) reached 1592.26 μg/mL, 1149.92 μg/mL, and 621.86 μg/mL, respectively. Xylobiose was the main product (~70%) in the hydrolysis mixture. AS-xyn10A significantly synergized with cellulase to improve the hydrolysis efficiency of corn stover, corncob, and rapeseed meal to glucose. The degree of synergy (DS) was 1.32, 1.31, and 1.30, respectively. Simultaneously, XOSs hydrolyzed with AS-xyn10A and cellulase was improved by 46.48%, 66.13% and 141.45%, respectively. In addition, CBM variant decreased the yields of xylo-oligosaccharide and glucose in rapeseed meal degradation. This study provided a novel GH10 endo-xylanase, which has potential applications in hydrolysis of biomass.
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Affiliation(s)
- Yajing Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, People's Republic of China
| | - Jian Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, People's Republic of China
| | - Chengling Bao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, People's Republic of China
| | - Bing Dong
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, People's Republic of China
| | - Yunhe Cao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, People's Republic of China.
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PUL-Mediated Plant Cell Wall Polysaccharide Utilization in the Gut Bacteroidetes. Int J Mol Sci 2021; 22:ijms22063077. [PMID: 33802923 PMCID: PMC8002723 DOI: 10.3390/ijms22063077] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/07/2021] [Accepted: 03/11/2021] [Indexed: 01/16/2023] Open
Abstract
Plant cell wall polysaccharides (PCWP) are abundantly present in the food of humans and feed of livestock. Mammalians by themselves cannot degrade PCWP but rather depend on microbes resident in the gut intestine for deconstruction. The dominant Bacteroidetes in the gut microbial community are such bacteria with PCWP-degrading ability. The polysaccharide utilization systems (PUL) responsible for PCWP degradation and utilization are a prominent feature of Bacteroidetes. In recent years, there have been tremendous efforts in elucidating how PULs assist Bacteroidetes to assimilate carbon and acquire energy from PCWP. Here, we will review the PUL-mediated plant cell wall polysaccharides utilization in the gut Bacteroidetes focusing on cellulose, xylan, mannan, and pectin utilization and discuss how the mechanisms can be exploited to modulate the gut microbiota.
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Liu Z, Shao T, Li Y, Wu B, Jia H, Hao N. Expression, Characterization and Its Deinking Potential of a Thermostable Xylanase From Planomicrobium glaciei CHR43. Front Bioeng Biotechnol 2021; 9:618979. [PMID: 33681158 PMCID: PMC7928332 DOI: 10.3389/fbioe.2021.618979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/22/2021] [Indexed: 11/17/2022] Open
Abstract
Genome mining is more and more widely used in identifying new enzymes from database. In the present study, we reported a putative xylanase, Pg-Xyn (WP_053166147.1), which originated from a psychrotolerant strain Planomicrobium glaciei CHR 43, and was identified from Genbank by genome mining. Sequence analysis and homology modeling showed that Pg-Xyn belongs to glycosyl hydrolase family 10. On the basis of heterologous expression in E. coli and biochemical characterization, we found Pg-Xyn was most active at pH 9.0 and 80°C and exhibited good stability from pH 5.0 to 12.0 and below 90°C. Pg-Xyn was slightly activated in the presence of Ca2+ and Mg2+, while it was strongly inhibited by Mn2+. The analysis of hydrolysis products showed that Pg-Xyn was an endo-β-1,4-xylanase. In addition, Pg-Xyn performed good deinking ability in a paper deinking test. In consideration of its unique properties, Pg-Xyn might be a promising candidate for application in the paper and pulp industries.
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Affiliation(s)
- Zhaoxing Liu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Tingting Shao
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Yan Li
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Bin Wu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Honghua Jia
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Ning Hao
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
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Otero DM, Cavalcante Braga AR, Kalil SJ. Diversification of nitrogen sources as a tool to improve endo-xylanase enzyme activity produced by Cryptococcus laurentii. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.101941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Lai Z, Zhou C, Ma X, Xue Y, Ma Y. Enzymatic characterization of a novel thermostable and alkaline tolerant GH10 xylanase and activity improvement by multiple rational mutagenesis strategies. Int J Biol Macromol 2020; 170:164-177. [PMID: 33352153 DOI: 10.1016/j.ijbiomac.2020.12.137] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/08/2020] [Accepted: 12/17/2020] [Indexed: 11/15/2022]
Abstract
Thermo-alkaline xylanases are widely applied in paper pulping industry. In this study, a novel thermostable and alkaline tolerant GH10 xylanase (Xyn30Y5) gene from alkaliphilic Bacillus sp. 30Y5 was cloned and the surface-layer homology (SLH) domains truncated enzyme (Xyn30Y5-SLH) was expressed in Escherichia coli. The purified Xyn30Y5-SLH was most active at 70 °C and pH 7.0 and showed the highest specific activity of 349.4 U mg-1. It retained more than 90% activity between pH 6.0 to 9.5 and was stable at pH 6.0-10.0. To improve the activity, 47 mutants were designed based on eight rational strategies and 21 mutants showed higher activity. By combinatorial mutagenesis, the best mutant 3B demonstrated specific activity of 1016.8 U mg-1 with a doubled catalytic efficiency (kcat/Km) and RA601/2h value, accompanied by optimal pH shift to 8.0. The molecular dynamics simulation analysis indicated that the increase of flexibility of α5 helix and loop7 located near to the catalytic residues is likely responsible for its activity improvement. And the decrease of flexibility of the most unstable regions is vital for the thermostablity improvement. This work provided not only a novel thermostable and alkaline tolerant xylanase with industrial application potential but also an effective mutagenesis strategy for xylanase activity improvement.
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Affiliation(s)
- Zhihua Lai
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Cheng Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Xiaochen Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanfen Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanhe Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; National Engineering Laboratory for Industrial Enzymes, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
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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: 13] [Impact Index Per Article: 2.6] [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.
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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.
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Patel K, Dudhagara P. Optimization of xylanase production by Bacillus tequilensis strain UD-3 using economical agricultural substrate and its application in rice straw pulp bleaching. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101846] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Verma D, Satyanarayana T. Xylanolytic Extremozymes Retrieved From Environmental Metagenomes: Characteristics, Genetic Engineering, and Applications. Front Microbiol 2020; 11:551109. [PMID: 33042057 PMCID: PMC7527525 DOI: 10.3389/fmicb.2020.551109] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 08/21/2020] [Indexed: 01/29/2023] Open
Abstract
Xylanolytic enzymes have extensive applications in paper, food, and feed, pharmaceutical, and biofuel industries. These industries demand xylanases that are functional under extreme conditions, such as high temperature, acidic/alkaline pH, and others, which are prevailing in bioprocessing industries. Despite the availability of several xylan-hydrolyzing enzymes from cultured microbes, there is a huge gap between what is available and what industries require. DNA manipulations as well as protein-engineering techniques are also not quite satisfactory in generating xylan-hydrolyzing extremozymes. With a compound annual growth rate of 6.6% of xylan-hydrolyzing enzymes in the global market, there is a need for xylanolytic extremozymes. Therefore, metagenomic approaches have been employed to uncover hidden xylanolytic genes that were earlier inaccessible in culture-dependent approaches. Appreciable success has been achieved in retrieving several unusual xylanolytic enzymes with novel and desirable characteristics from different extreme environments using functional and sequence-based metagenomic approaches. Moreover, the Carbohydrate Active Enzymes database includes approximately 400 GH-10 and GH-11 unclassified xylanases. This review discusses sources, characteristics, and applications of xylanolytic enzymes obtained through metagenomic approaches and their amelioration by genetic engineering techniques.
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Affiliation(s)
- Digvijay Verma
- Department of Microbiology, Babasaheb Bhimrao Ambedkar (Central) University, Lucknow, India
| | - Tulasi Satyanarayana
- Department of Biological Sciences and Engineering, Netaji Subhas University of Technology, Dwarka, New Delhi, India
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Yang J, Ma T, Shang-Guan F, Han Z. Improving the catalytic activity of thermostable xylanase from Thermotoga maritima via mutagenesis of non-catalytic residues at glycone subsites. Enzyme Microb Technol 2020; 139:109579. [PMID: 32732029 DOI: 10.1016/j.enzmictec.2020.109579] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/31/2020] [Accepted: 04/14/2020] [Indexed: 10/24/2022]
Abstract
Endo-β-1,4-xylanase from Thermotoga maritima, TmxB, is an industrially attractive enzyme due to its extreme thermostability. To improve its application value, four variants were designed on the basis of multiple sequence and three-dimensional structure alignments. Wild-type TmxB (wt-TmxB) and its mutants were produced via a Pichia pastoris expression system. Among four single-site mutants, the tyrosine substitution of a threonine residue (T74Y) at putative -3/-4 subsite led to a 1.3-fold increase in specific activity at 40 °C - 100 °C and pH 5 for 5 min, with beechwood xylan as the substrate. T74Y had an improved catalytic efficiency (kcat/Km), being 1.6 times that of wt-TmxB. Variants DY (two amino acid insertions) and N68Q displayed a slight increase (1.2 fold) and dramatic decline (1.7 fold) in catalytic efficiency, respectively. Mutant E67Y was totally inactive under all test conditions. Structural modeling and docking simulation elucidated structural insights into the molecular mechanism of activity changes for these TmxB variants. This study helps in further understanding the roles of the non-catalytic amino acids at the glycone subsites of xylanases from glycoside hydrolase family 10.
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Affiliation(s)
- Jiangke Yang
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Tengfei Ma
- School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Fang Shang-Guan
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Zhenggang Han
- College of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan 430023, China.
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Efficient xylan-to-sugar biotransformation using an engineered xylanase in hyperthermic environment. Int J Biol Macromol 2020; 157:17-23. [DOI: 10.1016/j.ijbiomac.2020.04.145] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/11/2020] [Accepted: 04/18/2020] [Indexed: 11/30/2022]
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Single Residue Substitution at N-Terminal Affects Temperature Stability and Activity of L2 Lipase. Molecules 2020; 25:molecules25153433. [PMID: 32731608 PMCID: PMC7435863 DOI: 10.3390/molecules25153433] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/26/2020] [Accepted: 07/01/2020] [Indexed: 11/24/2022] Open
Abstract
Rational design is widely employed in protein engineering to tailor wild-type enzymes for industrial applications. The typical target region for mutation is a functional region like the catalytic site to improve stability and activity. However, few have explored the role of other regions which, in principle, have no evident functionality such as the N-terminal region. In this study, stability prediction software was used to identify the critical point in the non-functional N-terminal region of L2 lipase and the effects of the substitution towards temperature stability and activity were determined. The results showed 3 mutant lipases: A8V, A8P and A8E with 29% better thermostability, 4 h increase in half-life and 6.6 °C higher thermal denaturation point, respectively. A8V showed 1.6-fold enhancement in activity compared to wild-type. To conclude, the improvement in temperature stability upon substitution showed that the N-terminal region plays a role in temperature stability and activity of L2 lipase.
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Jacomini D, Bussler L, Corrêa JM, Kadowaki MK, Maller A, da-Conceição Silva JL, Simão RDCG. Cloning, expression and characterization of C. crescentus xynA2 gene and application of Xylanase II in the deconstruction of plant biomass. Mol Biol Rep 2020; 47:4427-4438. [PMID: 32424521 DOI: 10.1007/s11033-020-05507-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 05/08/2020] [Indexed: 11/24/2022]
Abstract
Biotechnology offers innovative alternatives for industrial bioprocesses mainly because it uses enzymes that biodegrade the hemicellulose releasing fermentable sugars. Caulobacter crescentus (C. crescentus) has seven genes responsible for xylanolytic cleavage, 5 to β-xylosidases (EC 3.2.1.37) and 2 for endoxylanases, like xynA2 (CCNA_03137) that encodes Xylanase II (EC 3.2.1.8) of the glycohydrolases-GH10 group. The xynA2 gene was amplified by PCR, cloned into the pTrcHisA vector e efficiently overexpressed in E. coli providing a His-tag fusion protein. Recombinant xylanase (XynA2) was purified by affinity chromatography using a nickel sepharose column and exhibited a single 43 kDa band on SDS-PAGE gel. XynA2 showed an optimum alkaline pH (8) and stability at alkaline pH for 24 h. Although C. crescentus is mesophilic, XynA2 has optimum temperature of 60 °C and is thermo-resistance at 65 °C. XynA maintains 66% of the enzymatic activity at high temperatures (90 °C) without being denatured.The enzyme displayed a xylanolitic activity free of cellulase to xylan from beechwood and it was not inhibited in the presence of 50 μmol mL-1 of xylose. In addition, dithiothreitol (DTT) induced XynA2 activity, as it improved its kinetic parameters by lowering the KM (5.78 μmol mL-1) and increasing the KCat/KM ratio (1.63 U s-1). Finally, C. crescentus XynA2 efficiently hydrolyzed corn straw with high release of reducing sugars that can be applied in different branches of the industry.
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Affiliation(s)
- Débora Jacomini
- Laboratório de Bioquímica Molecular, Centro de Ciências Exatas e Tecnológicas, Universidade Estadual do Oeste do Paraná, Cascavel,, Paraná, 85814-110, Brazil
| | - Larissa Bussler
- Laboratório de Bioquímica Molecular, Centro de Ciências Exatas e Tecnológicas, Universidade Estadual do Oeste do Paraná, Cascavel,, Paraná, 85814-110, Brazil
| | - Juliana Moço Corrêa
- Laboratório de Bioquímica Molecular, Centro de Ciências Médicas e Farmacêuticas, Universidade Estadual do Oeste do Paraná, Rua Universitária, 2069, Cascavel, PR, 85814-110, Brazil
| | - Marina Kimiko Kadowaki
- Laboratório de Bioquímica Molecular, Centro de Ciências Médicas e Farmacêuticas, Universidade Estadual do Oeste do Paraná, Rua Universitária, 2069, Cascavel, PR, 85814-110, Brazil
| | - Alexandre Maller
- Laboratório de Bioquímica Molecular, Centro de Ciências Médicas e Farmacêuticas, Universidade Estadual do Oeste do Paraná, Rua Universitária, 2069, Cascavel, PR, 85814-110, Brazil
| | - José Luis da-Conceição Silva
- Laboratório de Bioquímica Molecular, Centro de Ciências Médicas e Farmacêuticas, Universidade Estadual do Oeste do Paraná, Rua Universitária, 2069, Cascavel, PR, 85814-110, Brazil
| | - Rita de Cássia Garcia Simão
- Laboratório de Bioquímica Molecular, Centro de Ciências Exatas e Tecnológicas, Universidade Estadual do Oeste do Paraná, Cascavel,, Paraná, 85814-110, Brazil. .,Laboratório de Bioquímica Molecular, Centro de Ciências Médicas e Farmacêuticas, Universidade Estadual do Oeste do Paraná, Rua Universitária, 2069, Cascavel, PR, 85814-110, Brazil.
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42
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Wu X, Zhang Q, Zhang L, Liu S, Chen G, Zhang H, Wang L. Insights Into the Role of Exposed Surface Charged Residues in the Alkali-Tolerance of GH11 Xylanase. Front Microbiol 2020; 11:872. [PMID: 32457729 PMCID: PMC7225583 DOI: 10.3389/fmicb.2020.00872] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/14/2020] [Indexed: 11/29/2022] Open
Abstract
Thermostable and alkaline- or acid-stable xylanases are more advantageous in agricultural and industrial fields. In this study, a rational structure-based design was conducted based on a thermostable GH11 xylanase TlXynA from Thermomyces lanuginosus to improved pH-tolerance. Four mutant enzymes (P1, P2, P3, and P4) and five variants (N1, N2, N3, N4, and N5) were constructed by substituting surface charged residue combinations using site-directed mutagenesis. Compared to the native enzyme, two mutants P1 and P2 showed higher acid tolerance, especially at pH 3.0, presented 50 and 40% of their maximum activity, respectively. In addition, four mutants N1, N2, N3 and N4 had higher tolerance than the native enzyme to alkaline environments (pH 7.0-9.0). At pH 9.0, the residual activities of N1, N2, N3, and N4 were 86, 78, 77, and 66%, respectively. In summary, an improved pH-tolerance design principle is being reported.
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Affiliation(s)
- Xiuyun Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Qun Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Lanzeng Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Shijia Liu
- Taishan College, Shandong University, Jinan, China
| | - Guanjun Chen
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Huaiqiang Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, China
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43
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Isolation and Characterization of a Novel Cold-Active, Halotolerant Endoxylanase from Echinicola rosea sp. Nov. JL3085 T. Mar Drugs 2020; 18:md18050245. [PMID: 32384803 PMCID: PMC7281462 DOI: 10.3390/md18050245] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 05/01/2020] [Accepted: 05/03/2020] [Indexed: 11/24/2022] Open
Abstract
We cloned a xylanase gene (xynT) from marine bacterium Echinicola rosea sp. nov. JL3085T and recombinantly expressed it in Escherichia coli BL21. This gene encoded a polypeptide with 379 amino acid residues and a molecular weight of ~43 kDa. Its amino acid sequence shared 45.3% similarity with an endoxylanase from Cellvibrio mixtus that belongs to glycoside hydrolases family 10 (GH10). The XynT showed maximum activity at 40 °C and pH 7.0, and a maximum velocity of 62 μmoL min−1 mg−1. The XynT retained its maximum activity by more than 69%, 51%, and 26% at 10 °C, 5 °C, and 0 °C, respectively. It also exhibited the highest activity of 135% in the presence of 4 M NaCl and retained 76% of its activity after 24 h incubation with 4 M NaCl. This novel xylanase, XynT, is a cold-active and halotolerant enzyme that may have promising applications in drug, food, feed, and bioremediation industries.
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44
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Zarafeta D, Galanopoulou AP, Leni ME, Kaili SI, Chegkazi MS, Chrysina ED, Kolisis FN, Hatzinikolaou DG, Skretas G. XynDZ5: A New Thermostable GH10 Xylanase. Front Microbiol 2020; 11:545. [PMID: 32390953 PMCID: PMC7193231 DOI: 10.3389/fmicb.2020.00545] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 03/12/2020] [Indexed: 12/27/2022] Open
Abstract
Xylanolytic enzymes have a broad range of applications in industrial biotechnology as biocatalytic components of various processes and products, such as food additives, bakery products, coffee extraction, agricultural silage and functional foods. An increasing market demand has driven the growing interest for the discovery of xylanases with specific industrially relevant characteristics, such as stability at elevated temperatures and in the presence of other denaturing factors, which will facilitate their incorporation into industrial processes. In this work, we report the discovery and biochemical characterization of a new thermostable GH10 xylanase, termed XynDZ5, exhibiting only 26% amino acid sequence identity to the closest characterized xylanolytic enzyme. This new enzyme was discovered in an Icelandic hot spring enrichment culture of a Thermoanaerobacterium species using a recently developed bioinformatic analysis platform. XynDZ5 was produced recombinantly in Escherichia coli, purified and characterized biochemically. This analysis revealed that it acts as an endo-1,4-β-xylanase that performs optimally at 65–75°C and pH 7.5. The enzyme is capable of retaining high levels of catalytic efficiency after several hours of incubation at high temperatures, as well as in the presence of significant concentrations of a range of metal ions and denaturing agents. Interestingly, the XynDZ5 biochemical profile was found to be atypical, as it also exhibits significant exo-activity. Computational modeling of its three-dimensional structure predicted a (β/α)8 TIM barrel fold, which is very frequently encountered among family GH10 enzymes. This modeled structure has provided clues about structural features that may explain aspects of its catalytic performance. Our results suggest that XynDZ5 represents a promising new candidate biocatalyst appropriate for several high-temperature biotechnological applications in the pulp, paper, baking, animal-feed and biofuel industries.
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Affiliation(s)
- Dimitra Zarafeta
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Anastasia P Galanopoulou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece.,Department of Biology, Enzyme and Microbial Biotechnology Unit, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Evangelia Leni
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Stavroula I Kaili
- Department of Biology, Enzyme and Microbial Biotechnology Unit, National and Kapodistrian University of Athens, Athens, Greece
| | - Magda S Chegkazi
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Evangelia D Chrysina
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Fragiskos N Kolisis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Dimitris G Hatzinikolaou
- Department of Biology, Enzyme and Microbial Biotechnology Unit, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgios Skretas
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
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45
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Highly alkali-stable and cellulase-free xylanases from Fusarium sp. 21 and their application in clarification of orange juice. Int J Biol Macromol 2020; 155:572-580. [PMID: 32246958 DOI: 10.1016/j.ijbiomac.2020.03.249] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/27/2020] [Accepted: 03/30/2020] [Indexed: 11/21/2022]
Abstract
Xylanase is a versatile tool in the food, fiber biobleaching and biofuel industries. Here, to discover new enzyme with special properties, we cloned three xylanases (Xyn11A, Xyn11B, and Xyn11C) by mining the genome of the xylanase producing fungus strain Fusarium sp. 21, biochemically characterized these enzyme and explored their potential application in juice processing. Both Xyn11A and Xyn11B had an optimal pH of 6.0 and optimal temperature of 45 °C, and retained >90% of the residual activity at pH range of 5-10.5 for 24 h. Xyn11C displayed the maximum activity at pH 5.0 and 45 °C and outstanding pH stability with a minimal loss of activity in the pH range of 2.0-10.5. These three xylanases displayed a strong specificity towards beechwood and corncob xylan, with no activity for other substrates. Xyn11A showed much a higher activity against corncob xylan, while Xyn11B and Xyn11C presented higher activities against beechwood xylan. Xyn11A catalyzed the hydrolysis of beechwood xylan with a Km of 4.25 ± 0.29 mg·mL-1 and kcat/Km of 30.34 ± 0.65 mL·s-1·mg-1, while the hydrolysis of corncob xylan had Km and kcat/Km values of 14.73 ± 1.43 mg·mL-1and 26.48 ± 0.11 mL·s-1·mg-1, respectively. Xyn11B and Xyn11C hydrolyzed beechwood xylan with Km of 9.8 ± 0.69 mg·mL-1, and 4.89 ± 0.38 mg·mL-1and kcat/Km values of 45.07 ± 1.66 mL-1·mg-1, and 26.95 ± 0.67 mL·s-1·mg-1, respectively. Beechwood xylan hydrolysates catalyzed by these three xylanases contained xylobiose, xylotriose and xylooligosaccharides (XOS). The clarification of orange juice was improved when treated with these three xylanases. Conclusively, the desirable pH stability and substrate specificity make Xyn11A, Xyn11B and Xyn11C have high potential for application in fiber biobleaching, wine and fruit juice clarification, as well as probiotic XOS production.
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46
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Cai L, Zhang M, Shao T, He Y, Li J, Ren B, Zhou C. Effect of introducing disulfide bridges in C-terminal structure on the thermostability of xylanase XynZF-2 from Aspergillus niger. J GEN APPL MICROBIOL 2019; 65:240-245. [PMID: 30905899 DOI: 10.2323/jgam.2018.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In this study, a mutant xylanase of high thermostability was obtained by site-directed mutagenesis. The homologous 3D structure of xylanase was successfully modeled and the mutation sites were predicted using bioinformatics software. Two amino acids of XynZF-2 were respectively substituted by cysteines (T205C and A52C) and a disulfide bridge was introduced into the C-terminal of XynZF-2. The mutant gene xynZFTA was cloned into pPIC9K and expressed in P. pastoris. The optimum temperature of the variant XynZFTA was improved from 45°C to 60°C, and XynZFTA retained greater than 90.0% activity (XynZF-2 retained only 50.0% activity) after treatment at 50°C for 5 min. The optimum pH of mutant xylanase was similar to XynZF-2 (pH = 5.0). The pH stability span (5.0~7.0) of the mutant xylanase was increased to 3.0~9.0. Overall, the results implied that the introduction of a disulfide bridge in the C-terminal structure improved the thermostability and pH stability of XynZF-2.
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Affiliation(s)
- Liutengzi Cai
- School of Life Science and Technology, Xinxiang Medical University.,Synthetic Biology Engineering Lab of Henan Province
| | - Mishuai Zhang
- School of Life Science and Technology, Xinxiang Medical University.,Synthetic Biology Engineering Lab of Henan Province
| | - Tianci Shao
- School of Life Science and Technology, Xinxiang Medical University.,Synthetic Biology Engineering Lab of Henan Province
| | - You He
- School of Life Science and Technology, Xinxiang Medical University.,Synthetic Biology Engineering Lab of Henan Province
| | - Jingyi Li
- School of Life Science and Technology, Xinxiang Medical University.,Synthetic Biology Engineering Lab of Henan Province
| | - Bingjie Ren
- School of Life Science and Technology, Xinxiang Medical University.,Synthetic Biology Engineering Lab of Henan Province
| | - Chenyan Zhou
- School of Life Science and Technology, Xinxiang Medical University.,Synthetic Biology Engineering Lab of Henan Province
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47
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Malgas S, Mafa MS, Mkabayi L, Pletschke BI. A mini review of xylanolytic enzymes with regards to their synergistic interactions during hetero-xylan degradation. World J Microbiol Biotechnol 2019; 35:187. [PMID: 31728656 DOI: 10.1007/s11274-019-2765-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 11/06/2019] [Indexed: 10/25/2022]
Abstract
This review examines the recent models describing the mode of action of various xylanolytic enzymes and how these enzymes can be applied (sequentially or simultaneously) with their distinctive roles in mind to achieve efficient xylan degradation. With respect to homeosynergy, synergism appears to be as a result of β-xylanase and/or oligosaccharide reducing-end β-xylanase liberating xylo-oligomers (XOS) that are preferred substrates of the processive β-xylosidase. With regards to hetero-synergism, two cross relationships appear to exist and seem to be the reason for synergism between the enzymes during xylan degradation. These cross relations are the debranching enzymes such as α-glucuronidase or side-chain cleaving enzymes such as carbohydrate esterases (CE) removing decorations that would have hindered back-bone-cleaving enzymes, while backbone-cleaving-enzymes liberate XOS that are preferred substrates of the debranching and side-chain-cleaving enzymes. This interaction is demonstrated by high yields in co-production of xylan substituents such as arabinose, glucuronic acid and ferulic acid, and XOS. Finally, lytic polysaccharide monooxygenases (LPMO) have also been implicated in boosting whole lignocellulosic biomass or insoluble xylan degradation by glycoside hydrolases (GH) by possibly disrupting entangled xylan residues. Since it has been observed that the same enzyme (same Enzyme Commission, EC, classification) from different GH or CE and/or AA families can display different synergistic interactions with other enzymes due to different substrate specificities and properties, in this review, we propose an approach of enzyme selection (and mode of application thereof) during xylan degradation, as this can improve the economic viability of the degradation of xylan for producing precursors of value added products.
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Affiliation(s)
- Samkelo Malgas
- Enzyme Science Programme (ESP), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, Eastern Cape, 6140, South Africa
| | - Mpho S Mafa
- Enzyme Science Programme (ESP), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, Eastern Cape, 6140, South Africa.,Protein Structure-Function Research Unit (PSFRU), School of Molecular and Cell Biology, Wits University, Johannesburg, Gauteng, 2000, South Africa
| | - Lithalethu Mkabayi
- Enzyme Science Programme (ESP), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, Eastern Cape, 6140, South Africa
| | - Brett I Pletschke
- Enzyme Science Programme (ESP), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, Eastern Cape, 6140, South Africa.
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48
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Hamedi J, Vaez Fakhri A, Mahdavi S. Biobleaching of mechanical paper pulp usingStreptomyces rutgersensisUTMC 2445 isolated from a lignocellulose‐rich soil. J Appl Microbiol 2019; 128:161-170. [DOI: 10.1111/jam.14489] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 07/06/2018] [Accepted: 07/18/2018] [Indexed: 12/22/2022]
Affiliation(s)
- J. Hamedi
- Department of Microbial Biotechnology School of Biology and Center of Excellence in Phylogeny of Living Organisms College of Science University of Tehran Tehran Iran
- Microbial Technology and products Research Center University of Tehran Tehran Iran
| | - A. Vaez Fakhri
- Department of Microbial Biotechnology School of Biology and Center of Excellence in Phylogeny of Living Organisms College of Science University of Tehran Tehran Iran
- Microbial Technology and products Research Center University of Tehran Tehran Iran
| | - S. Mahdavi
- Wood and Forest Products Division Research Institute of Forest and Rangelands Agricultural Research Education and Extension Organization (AREEO) Tehran Iran
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49
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Alokika, Singh B. Production, characteristics, and biotechnological applications of microbial xylanases. Appl Microbiol Biotechnol 2019; 103:8763-8784. [PMID: 31641815 DOI: 10.1007/s00253-019-10108-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/09/2019] [Accepted: 08/28/2019] [Indexed: 01/29/2023]
Abstract
Microbial xylanases have gathered great attention due to their biotechnological potential at industrial scale for many processes. A variety of lignocellulosic materials, such as sugarcane bagasse, rice straw, rice bran, wheat straw, wheat bran, corn cob, and ragi bran, are used for xylanase production which also solved the great issue of solid waste management. Both solid-state and submerged fermentation have been used for xylanase production controlled by various physical and nutritional parameters. Majority of xylanases have optimum pH in the range of 4.0-9.0 with optimum temperature at 30-60 °C. For biochemical, molecular studies and also for successful application in industries, purification and characterization of xylanase have been carried out using various appropriate techniques. Cloning and genetic engineering are used for commercial-level production of xylanase, to meet specific economic viability and industrial needs. Microbial xylanases are used in various biotechnological applications like biofuel production, pulp and paper industry, baking and brewing industry, food and feed industry, and deinking of waste paper. This review describes production, characteristics, and biotechnological applications of microbial xylanases.
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Affiliation(s)
- Alokika
- Laboratory of Bioprocess Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India
| | - Bijender Singh
- Laboratory of Bioprocess Technology, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana, 124001, India. .,Department of Biotechnology, School of Interdisciplinary and Applied Life Sciences, Central University of Haryana, Jant-Pali, Mahendergarh, Haryana, 123031, India.
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Shukla P. Synthetic Biology Perspectives of Microbial Enzymes and Their Innovative Applications. Indian J Microbiol 2019; 59:401-409. [PMID: 31762501 DOI: 10.1007/s12088-019-00819-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 08/19/2019] [Indexed: 11/29/2022] Open
Abstract
Microbial enzymes are high in demand and there is focus on their efficient, cost effective and eco-friendly production. The relevant microbial enzymes for respective industries needs to be identified but the conventional technologies don't have much edge over it. So, there is more attention towards high throughput methods for production of efficient enzymes. The enzymes produced by microbes need to be modified to bear the extreme conditions of the industries in order to get prolific outcomes and here the synthetic biology tools may be augmented to modify such microbes and enzymes. These tools are applied to synthesize novel and efficient enzymes. Use of computational tools for enzyme modification has provided new avenues for faster and specific modification of enzymes in a shorter time period. This review focuses on few important enzymes and their modification through synthetic biology tools including genetic modification, nanotechnology, post translational modification.
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Affiliation(s)
- Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana 124001 India
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