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Dong CD, Patel AK, Madhavan A, Chen CW, Singhania RR. Significance of glycans in cellulolytic enzymes for lignocellulosic biorefinery - A review. BIORESOURCE TECHNOLOGY 2023; 379:128992. [PMID: 37011847 DOI: 10.1016/j.biortech.2023.128992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/28/2023] [Accepted: 03/29/2023] [Indexed: 05/03/2023]
Abstract
Lignocellulosic (LC) biomass is the most abundant renewable resource for mankind gravitating society towards sustainable solution for energy that can reduce the carbon footprint. The economic feasibility of 'biomass biorefinery' depends upon the efficiency cellulolytic enzymes which is the main crux. Its high production cost and low efficiencies are the major limitations, that need to be resolved. As the complexity of the genome increases, so does the complexity of the proteome, further facilitated by protein post-translational modifications (PTMs). Glycosylation is regarded the major PTMs and hardly any recent work is focused on importance of glycosylation in cellulase. By modifying protein side chains and glycans, superior cellulases with improved stability and efficiency can be obtained. Functional proteomics relies heavily on PTMs because they regulate activity, localization, and interactions with protein, lipid, nucleic acid, and cofactor molecules. O- and N- glycosylation in cellulases influences its characteristics adding positive attributes to the enzymes.
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Affiliation(s)
- Cheng-Di Dong
- Institute of Aquatic Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan; Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung 81157, Taiwan; Sustainable Environment Research Center, National Kaohsiung University of Science and Technology, Kaohsiung City 81157, Taiwan
| | - Anil Kumar Patel
- Institute of Aquatic Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan; Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung 81157, Taiwan; Centre for Energy and Environmental Sustainability, Lucknow 226 029, India
| | - Aravind Madhavan
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kollam, Kerala 690 525, India
| | - Chiu-Wen Chen
- Institute of Aquatic Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan; Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung 81157, Taiwan; Sustainable Environment Research Center, National Kaohsiung University of Science and Technology, Kaohsiung City 81157, Taiwan
| | - Reeta Rani Singhania
- Institute of Aquatic Science and Technology, National Kaohsiung University of Science and Technology, Kaohsiung City, Taiwan; Department of Marine Environmental Engineering, National Kaohsiung University of Science and Technology, Kaohsiung 81157, Taiwan; Centre for Energy and Environmental Sustainability, Lucknow 226 029, India.
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2017-2018. MASS SPECTROMETRY REVIEWS 2023; 42:227-431. [PMID: 34719822 DOI: 10.1002/mas.21721] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2018. Also included are papers that describe methods appropriate to glycan and glycoprotein analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, new methods, matrices, derivatization, MALDI imaging, fragmentation and the use of arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Most of the applications are presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and highlights the impact that MALDI imaging is having across a range of diciplines. MALDI is still an ideal technique for carbohydrate analysis and advancements in the technique and the range of applications continue steady progress.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
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Zhao J, Wang Q, Ni X, Shen S, Nan C, Li X, Chen X, Yang F. Dissecting the essential role of N-glycosylation in catalytic performance of xanthan lyase. BIORESOUR BIOPROCESS 2022; 9:129. [PMID: 38647758 PMCID: PMC10992191 DOI: 10.1186/s40643-022-00620-5] [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: 08/11/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
Modified xanthan produced by xanthan lyase has broad application prospects in the food industry. However, the catalytic performance of xanthan lyase still needs to be improved through rational design. To address this problem, in this work, the glycosylation and its influences on the catalytic performance of a xanthan lyase (EcXly), which was heterologously expressed in Escherichia coli, were reported. Liquid chromatography coupled to tandem mass spectrometry analysis revealed that the N599 site of EcXly was modified by a single N-glycan chain. Based on sequence alignment and three-dimensional structure prediction, it could be deduced that the N599 site was located in the catalytic domain of EcXly and in close proximity to the catalytic residues. After site-directed mutagenesis of N599 with alanine, aspartic acid and glycine, respectively, the EcXly and its mutants were characterized and compared. The results demonstrated that elimination of the N-glycosylation had diminished the specific activity, pH stability, and substrate affinity of EcXly. Fluorescence spectra further revealed that the glycosylation could significantly affect the overall tertiary structure of EcXly. Therefore, in prokaryotic hosts, the N-glycosylation could influence the catalytic performance of the enzyme by changing its structure. To the best of our knowledge, this is the first report about the post-translational modification of xanthan lyase in prokaryotes. Overall, our work enriched research on the role of glycan chains in the functional performance of proteins expressed in prokaryotes and should be valuable for the rational design of xanthan lyase to produce modified xanthan for industrial application.
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Affiliation(s)
- Jingjing Zhao
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, 116034, Dalian, People's Republic of China
| | - Qian Wang
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, 116034, Dalian, People's Republic of China
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, People's Republic of China
| | - Xin Ni
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, 116034, Dalian, People's Republic of China
| | - Shaonian Shen
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, 116034, Dalian, People's Republic of China
| | - Chenchen Nan
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, 116034, Dalian, People's Republic of China
| | - Xianzhen Li
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, 116034, Dalian, People's Republic of China
| | - Xiaoyi Chen
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, 116034, Dalian, People's Republic of China.
| | - Fan Yang
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, 116034, Dalian, People's Republic of China.
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Fungal cellulases: protein engineering and post-translational modifications. Appl Microbiol Biotechnol 2021; 106:1-24. [PMID: 34889986 DOI: 10.1007/s00253-021-11723-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 11/28/2021] [Accepted: 11/30/2021] [Indexed: 12/18/2022]
Abstract
Enzymatic degradation of lignocelluloses into fermentable sugars to produce biofuels and other biomaterials is critical for environmentally sustainable development and energy resource supply. However, there are problems in enzymatic cellulose hydrolysis, such as the complex cellulase composition, low degradation efficiency, high production cost, and post-translational modifications (PTMs), all of which are closely related to specific characteristics of cellulases that remain unclear. These problems hinder the practical application of cellulases. Due to the rapid development of computer technology in recent years, computer-aided protein engineering is being widely used, which also brings new opportunities for the development of cellulases. Especially in recent years, a large number of studies have reported on the application of computer-aided protein engineering in the development of cellulases; however, these articles have not been systematically reviewed. This article focused on the aspect of protein engineering and PTMs of fungal cellulases. In this manuscript, the latest literatures and the distribution of potential sites of cellulases for engineering have been systematically summarized, which provide reference for further improvement of cellulase properties. KEY POINTS: •Rational design based on virtual mutagenesis can improve cellulase properties. •Modifying protein side chains and glycans helps obtain superior cellulases. •N-terminal glutamine-pyroglutamate conversion stabilizes fungal cellulases.
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Sinitsyn AP, Sinitsyna OA. Bioconversion of Renewable Plant Biomass. Second-Generation Biofuels: Raw Materials, Biomass Pretreatment, Enzymes, Processes, and Cost Analysis. BIOCHEMISTRY (MOSCOW) 2021; 86:S166-S195. [PMID: 33827407 DOI: 10.1134/s0006297921140121] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The review discusses various aspects of renewable plant biomass conversion and production of the second-generation biofuels, including the types of plant biomass, its composition and reaction ability in the enzymatic hydrolysis, and various pretreatment methods for increasing the biomass reactivity. Conversion of plant biomass into sugars requires the use of a complex of enzymes, the composition of which should be adapted to the biomass type and the pretreatment method. The efficiency of enzymatic hydrolysis can be increased by optimizing the composition of the enzymatic complex and by increasing the catalytic activity and operational stability of its constituent enzymes. The availability of active enzyme producers also plays an important role. Examples of practical implementation and scaling of processes for the production of second-generation biofuels are presented together with the cost analysis of bioethanol production.
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Affiliation(s)
- Arkadij P Sinitsyn
- Bakh Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 119071, Russia. .,Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Olga A Sinitsyna
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
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Stabilization of Glycosylated β-Glucosidase by Intramolecular Crosslinking Between Oxidized Glycosidic Chains and Lysine Residues. Appl Biochem Biotechnol 2020; 192:325-337. [DOI: 10.1007/s12010-020-03321-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/23/2020] [Indexed: 02/06/2023]
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Han C, Wang Q, Sun Y, Yang R, Liu M, Wang S, Liu Y, Zhou L, Li D. Improvement of the catalytic activity and thermostability of a hyperthermostable endoglucanase by optimizing N-glycosylation sites. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:30. [PMID: 32127917 PMCID: PMC7045587 DOI: 10.1186/s13068-020-1668-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 01/26/2020] [Indexed: 05/23/2023]
Abstract
BACKGROUND Endoglucanase has been extensively employed in industrial processes as a key biocatalyst for lignocellulosic biomass degradation. Thermostable endoglucanases with high catalytic activity at elevated temperatures are preferred in industrial use. To improve the activity and thermostability, site-directed mutagenesis was conducted to modify the N-glycosylation sites of the thermostable β-1,4-endoglucanase CTendo45 from Chaetomium thermophilum. RESULTS In this study, structure-based rational design was performed based on the modification of N-glycosylation sites in CTendo45. Eight single mutants and one double mutant were constructed and successfully expressed in Pichia pastoris. When the unique N-glycosylation site of N88 was eliminated, a T90A variant was active, and its specific activity towards CMC-Na and β-d-glucan was increased 1.85- and 1.64-fold, respectively. The mutant R67S with an additional N-glycosylation site of N65 showed a distinct enhancement in catalytic efficiency. Moreover, T90A and R67S were endowed with extraordinary heat endurance after 200 min of incubation at different temperatures ranging from 30 to 90 °C. Likewise, the half-lives (t 1/2) indicated that T90A and R67S exhibited improved enzyme thermostability at 80 °C and 90 °C. Notably, the double-mutant T90A/R67S possessed better hydrolysis activity and thermal stability than its single-mutant counterparts and the wild type. CONCLUSIONS This study provides initial insight into the biochemical function of N-glycosylation in thermostable endoglucanases. Moreover, the design approach to the optimization of N-glycosylation sites presents an effective and feasible strategy to improve enzymatic activity and thermostability.
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Affiliation(s)
- Chao Han
- Shandong Key Laboratory for Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai’an, 271018 Shandong China
| | - Qunqing Wang
- Shandong Key Laboratory for Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai’an, 271018 Shandong China
| | - Yanxu Sun
- Shandong Key Laboratory for Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai’an, 271018 Shandong China
| | - Ruirui Yang
- Shandong Key Laboratory for Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai’an, 271018 Shandong China
| | - Mengyu Liu
- Shandong Key Laboratory for Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai’an, 271018 Shandong China
| | - Siqi Wang
- Shandong Key Laboratory for Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai’an, 271018 Shandong China
| | - Yifan Liu
- Shandong Key Laboratory for Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai’an, 271018 Shandong China
| | - Lifan Zhou
- Shandong Key Laboratory for Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai’an, 271018 Shandong China
| | - Duochuan Li
- Shandong Key Laboratory for Agricultural Microbiology, College of Plant Protection, Shandong Agricultural University, Tai’an, 271018 Shandong China
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Semenova MV, Gusakov AV, Telitsin VD, Rozhkova AM, Kondratyeva EG, Sinitsyn AP. Purification and characterization of two forms of the homologously expressed lytic polysaccharide monooxygenase (PvLPMO9A) from Penicillium verruculosum. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140297. [DOI: 10.1016/j.bbapap.2019.140297] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/17/2019] [Accepted: 10/04/2019] [Indexed: 10/25/2022]
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Gu Y, Zheng F, Wang Y, Su X, Bai Y, Yao B, Huang H, Luo H. Characterization of two thermophilic cellulases from Talaromyces leycettanus JCM12802 and their synergistic action on cellulose hydrolysis. PLoS One 2019; 14:e0224803. [PMID: 31730665 PMCID: PMC6857856 DOI: 10.1371/journal.pone.0224803] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/22/2019] [Indexed: 11/29/2022] Open
Abstract
Talaromyces leycettanus JCM12802 is a great producer of thermophilic glycoside hydrolases (GHs). In this study, two cellulases (TlCel5A and TlCel6A) belonging to GH5 and GH6 respectively were expressed in Pichia pastoris and functionally characterized. The enzymes had acidic and thermophilic properties, showing optimal activities at pH 3.5–4.5 and 75–80°C, and retained stable at temperatures up to 60°C and over a broad pH range of 2.0−8.0. TlCel5A and TlCel6A acted against several cellulose substrates with varied activities (3,101.1 vs. 92.9 U/mg to barley β-glucan, 3,905.6 U/mg vs. 109.0 U/mg to lichenan, and 840.3 and 0.09 U/mg to CMC-Na). When using Avicel, phosphoric acid swollen cellulose (PASC) or steam-exploded corn straw (SECS) as the substrate, combination of TlCel5A and TlCel6A showed significant synergistic action, releasing more reduced sugars (1.08–2.87 mM) than the individual enzymes. These two cellulases may represent potential enzyme additives for the efficient biomass conversion and bioethanol production.
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Affiliation(s)
- Yuan Gu
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Fei Zheng
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, People’s Republic of China
| | - Yuan Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Xiaoyun Su
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Yingguo Bai
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Bin Yao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
| | - Huoqing Huang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
- * E-mail: (HL); (HH)
| | - Huiying Luo
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, People’s Republic of China
- * E-mail: (HL); (HH)
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Rubio MV, Terrasan CRF, Contesini FJ, Zubieta MP, Gerhardt JA, Oliveira LC, de Souza Schmidt Gonçalves AE, Almeida F, Smith BJ, de Souza GHMF, Dias AHS, Skaf M, Damasio A. Redesigning N-glycosylation sites in a GH3 β-xylosidase improves the enzymatic efficiency. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:269. [PMID: 31754374 PMCID: PMC6854716 DOI: 10.1186/s13068-019-1609-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 11/04/2019] [Indexed: 05/27/2023]
Abstract
BACKGROUND β-Xylosidases are glycoside hydrolases (GHs) that cleave xylooligosaccharides and/or xylobiose into shorter oligosaccharides and xylose. Aspergillus nidulans is an established genetic model and good source of carbohydrate-active enzymes (CAZymes). Most fungal enzymes are N-glycosylated, which influences their secretion, stability, activity, signalization, and protease protection. A greater understanding of the N-glycosylation process would contribute to better address the current bottlenecks in obtaining high secretion yields of fungal proteins for industrial applications. RESULTS In this study, BxlB-a highly secreted GH3 β-xylosidase from A. nidulans, presenting high activity and several N-glycosylation sites-was selected for N-glycosylation engineering. Several glycomutants were designed to investigate the influence of N-glycans on BxlB secretion and function. The non-glycosylated mutant (BxlBnon-glyc) showed similar levels of enzyme secretion and activity compared to the wild-type (BxlBwt), while a partially glycosylated mutant (BxlBN1;5;7) exhibited increased activity. Additionally, there was no enzyme secretion in the mutant in which the N-glycosylation context was changed by the introduction of four new N-glycosylation sites (BxlBCC), despite the high transcript levels. BxlBwt, BxlBnon-glyc, and BxlBN1;5;7 formed similar secondary structures, though the mutants had lower melting temperatures compared to the wild type. Six additional glycomutants were designed based on BxlBN1;5;7, to better understand its increased activity. Among them, the two glycomutants which maintained only two N-glycosylation sites each (BxlBN1;5 and BxlBN5;7) showed improved catalytic efficiency, whereas the other four mutants' catalytic efficiencies were reduced. The N-glycosylation site N5 is important for improved BxlB catalytic efficiency, but needs to be complemented by N1 and/or N7. Molecular dynamics simulations of BxlBnon-glyc and BxlBN1;5 reveals that the mobility pattern of structural elements in the vicinity of the catalytic pocket changes upon N1 and N5 N-glycosylation sites, enhancing substrate binding properties which may underlie the observed differences in catalytic efficiency between BxlBnon-glyc and BxlBN1;5. CONCLUSIONS This study demonstrates the influence of N-glycosylation on A. nidulans BxlB production and function, reinforcing that protein glycoengineering is a promising tool for enhancing thermal stability, secretion, and enzymatic activity. Our report may also support biotechnological applications for N-glycosylation modification of other CAZymes.
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Affiliation(s)
- Marcelo Ventura Rubio
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz, Campinas, SP 13083-862 Brazil
| | - César Rafael Fanchini Terrasan
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz, Campinas, SP 13083-862 Brazil
| | - Fabiano Jares Contesini
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz, Campinas, SP 13083-862 Brazil
| | - Mariane Paludetti Zubieta
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz, Campinas, SP 13083-862 Brazil
| | - Jaqueline Aline Gerhardt
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz, Campinas, SP 13083-862 Brazil
| | - Leandro Cristante Oliveira
- Department of Physics, Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (UNESP), São José do Rio Preto, SP 15054-000 Brazil
| | | | - Fausto Almeida
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, SP 14049-900 Brazil
| | - Bradley Joseph Smith
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz, Campinas, SP 13083-862 Brazil
| | - Gustavo Henrique Martins Ferreira de Souza
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz, Campinas, SP 13083-862 Brazil
| | - Artur Hermano Sampaio Dias
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas (UNICAMP), Campinas, SP 13084-862 Brazil
| | - Munir Skaf
- Institute of Chemistry and Center for Computing in Engineering and Sciences, University of Campinas (UNICAMP), Campinas, SP 13084-862 Brazil
| | - André Damasio
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Rua Monteiro Lobato, 255, Cidade Universitária Zeferino Vaz, Campinas, SP 13083-862 Brazil
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Ma J, Li Q, Tan H, Jiang H, Li K, Zhang L, Shi Q, Yin H. Unique N-glycosylation of a recombinant exo-inulinase from Kluyveromyces cicerisporus and its effect on enzymatic activity and thermostability. J Biol Eng 2019; 13:81. [PMID: 31737090 PMCID: PMC6844067 DOI: 10.1186/s13036-019-0215-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/16/2019] [Indexed: 01/05/2023] Open
Abstract
Background Inulinase can hydrolyze polyfructan into high-fructose syrups and fructoligosaccharides, which are widely used in food, the medical industry and the biorefinery of Jerusalem artichoke. In the present study, a recombinant exo-inulinase (rKcINU1), derived from Kluyveromyces cicerisporus CBS4857, was proven as an N-linked glycoprotein, and the removal of N-linked glycan chains led to reduced activity. Results Five N-glycosylation sites with variable high mannose-type oligosaccharides (Man3–9GlcNAc2) were confirmed in the rKcINU1. The structural modeling showed that all five glycosylation sites (Asn-362, Asn-370, Asn-399, Asn-467 and Asn-526) were located at the C-terminus β-sandwich domain, which has been proven to be more conducive to the occurrence of glycosylation modification than the N-terminus domain. Single-site N-glycosylation mutants with Asn substituted by Gln were obtained, and the Mut with all five N-glycosylation sites removed was constructed, which resulted in the loss of all enzyme activity. Interestingly, the N362Q led to an 18% increase in the specific activity against inulin, while a significant decrease in thermostability (2.91 °C decrease in Tm) occurred, and other single mutations resulted in the decrease in the specific activity to various extents, among which N467Q demonstrated the lowest enzyme activity. Conclusion The increased enzyme activity in N362Q, combined with thermostability testing, 3D modeling, kinetics data and secondary structure analysis, implied that the N-linked glycan chains at the Asn-362 position functioned negatively, mainly as a type of steric hindrance toward its adjacent N-glycans to bring rigidity. Meanwhile, the N-glycosylation at the other four sites positively regulated enzyme activity caused by altered substrate affinity by means of fine-tuning the β-sandwich domain configuration. This may have facilitated the capture and transfer of substrates to the enzyme active cavity, in a manner quite similar to that of carbohydrate binding modules (CBMs), i.e. the chains endowed the β-sandwich domain with the functions of CBM. This study discovered a unique C-terminal sequence which is more favorable to glycosylation, thereby casting a novel view for glycoengineering of enzymes from fungi via redesigning the amino acid sequence at the C-terminal domain, so as to optimize the enzymatic properties.
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Affiliation(s)
- Junyan Ma
- 1Natural Products and Glyco-Biotechnology Research Group, Liaoning Province Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023 China.,2Liaoning Province Key Laboratory of Bio-Organic Chemistry, Dalian University, Dalian, 116622 China
| | - Qian Li
- 2Liaoning Province Key Laboratory of Bio-Organic Chemistry, Dalian University, Dalian, 116622 China
| | - Haidong Tan
- 1Natural Products and Glyco-Biotechnology Research Group, Liaoning Province Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023 China
| | - Hao Jiang
- 3Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023 China
| | - Kuikui Li
- 1Natural Products and Glyco-Biotechnology Research Group, Liaoning Province Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023 China
| | - Lihua Zhang
- 3Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023 China
| | - Quan Shi
- 3Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023 China
| | - Heng Yin
- 1Natural Products and Glyco-Biotechnology Research Group, Liaoning Province Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023 China
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Wang Z, Zhang T, Long L, Ding S. Altering the linker in processive GH5 endoglucanase 1 modulates lignin binding and catalytic properties. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:332. [PMID: 30568732 PMCID: PMC6297974 DOI: 10.1186/s13068-018-1333-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 12/07/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND The non-productive adsorption of cellulases onto lignin in biomass is a key issue for the biofuel process economy. It would be helpful to reduce the inhibitory effect of lignin on enzymatic hydrolysis by engineering weak lignin-binding cellulases. Cellulase linkers are highly divergent in their lengths, compositions, and glycosylations. Numerous studies have revealed that linkers can facilitate optimal interactions between structured domains. Recently, efforts have focused on the contributions and mechanisms of carbohydrate-binding modules and catalytic domains that affect lignin affinity and processivity of cellulases, but our understanding of the effects of the linker regions on lignin adsorption and processivity of GH5 processive endoglucanases is still limited. RESULTS Eight GH5 endoglucanase 1 variants of varying length, flexibility, and sequence in the linker region were constructed. Their characteristics were then compared to the wild-type enzyme (EG1). Remarkably, significant differences in the lignin adsorption profiles and processivities were observed for EG1 and other variants. Our studies suggest that either the length or the specific amino acid composition of the linker has a prominent influence on the lignin-binding affinity of the enzymes. Comparatively, the processivity may depend primarily on the length of the linker and less so on the specific amino acid composition. EG1-ApCel5A, a variant with better performance in enzymatic hydrolysis in the presence of lignin, was obtained by replacing a longer, flexible linker. In total, up to between 28.2 and 30.1% more reducing sugars were generated from filter paper by EG1-ApCel5A in the presence of lignin compared to EG1. CONCLUSIONS Our results highlight the relevance of the linker region in the lignin adsorption and processivity of a processive endoglucanase. Our findings suggest that the linker region may be used as a target for the design of more active and weaker lignin-binding cellulases.
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Affiliation(s)
- Zhen Wang
- The Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Key Lab for the Chemistry & Utilization of Agricultural and Forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
| | - Tianrui Zhang
- The Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Key Lab for the Chemistry & Utilization of Agricultural and Forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
| | - Liangkun Long
- The Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Key Lab for the Chemistry & Utilization of Agricultural and Forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
| | - Shaojun Ding
- The Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Jiangsu Key Lab for the Chemistry & Utilization of Agricultural and Forest Biomass, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
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Dotsenko A, Gusakov A, Rozhkova A, Sinitsyna O, Shashkov I, Sinitsyn A. Enzymatic hydrolysis of cellulosic materials using synthetic mixtures of purified cellulases bioengineered at N-glycosylation sites. 3 Biotech 2018; 8:396. [PMID: 30221109 DOI: 10.1007/s13205-018-1419-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 09/01/2018] [Indexed: 01/18/2023] Open
Abstract
Mutant forms of recombinant endoglucanase II (EG II, N194A), cellobiohydrolase I (CBH I, N45A) and cellobiohydrolase II (CBH II, N219A) from Penicillium verruculosum with enhanced cellulase activities, achieved by engineering of enzyme N-glycosylation sites in our previous studies, were used as components of the binary and ternary mixtures of cellulases in hydrolysis of Avicel and milled aspen wood. Using the engineered forms of the enzymes at a dosage of 10 mg/g substrate resulted in significant boosting of the glucose release from cellulose in the presence of excess β-glucosidase relative to the performance of the corresponding wild-type mixtures at the same loading. The boosting effects reached 11-40% depending on the reaction time and substrate type. In hydrolysis of both cellulosic substrates by the binary mixtures of cellulases, all the enzyme pairs exhibited synergism. The magnitude of the synergistic effects (Ks) did not depend notably upon the induced mutations in the enzymes, and they were in the range of 1.3-1.8 for the combinations of EG II with CBH I (or CBH II), and 2.3-2.9 for the CBH I-CBH II pair. The results of this study should provide a basis for the development of a more effective fungal strain capable of producing cellulase cocktails with enhanced hydrolytic performance against lignocellulosic materials.
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Affiliation(s)
- Anna Dotsenko
- 1Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Leninsky Pr. 33/2, Moscow, 119071 Russia
| | - Alexander Gusakov
- 1Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Leninsky Pr. 33/2, Moscow, 119071 Russia
- 2Department of Chemistry, M.V. Lomonosov Moscow State University, Vorobyovy Gory 1/11, Moscow, 119991 Russia
| | - Aleksandra Rozhkova
- 1Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Leninsky Pr. 33/2, Moscow, 119071 Russia
- 2Department of Chemistry, M.V. Lomonosov Moscow State University, Vorobyovy Gory 1/11, Moscow, 119991 Russia
| | - Olga Sinitsyna
- 1Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Leninsky Pr. 33/2, Moscow, 119071 Russia
- 2Department of Chemistry, M.V. Lomonosov Moscow State University, Vorobyovy Gory 1/11, Moscow, 119991 Russia
| | - Igor Shashkov
- 1Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Leninsky Pr. 33/2, Moscow, 119071 Russia
| | - Arkady Sinitsyn
- 1Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Leninsky Pr. 33/2, Moscow, 119071 Russia
- 2Department of Chemistry, M.V. Lomonosov Moscow State University, Vorobyovy Gory 1/11, Moscow, 119991 Russia
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Rabinovich ML, Melnik MS, Herner ML, Voznyi YV, Vasilchenko LG. Predominant Nonproductive Substrate Binding by Fungal Cellobiohydrolase I and Implications for Activity Improvement. Biotechnol J 2018; 14:e1700712. [PMID: 29781240 DOI: 10.1002/biot.201700712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 05/08/2018] [Indexed: 12/20/2022]
Abstract
Enzymatic conversion of the most abundant renewable source of organic compounds, cellulose to fermentable sugars is attractive for production of green fuels and chemicals. The major component of industrial enzyme systems, cellobiohydrolase I from Hypocrea jecorina (Trichoderma reesei) (HjCel7A) processively splits disaccharide units from the reducing ends of tightly packed cellulose chains. HjCel7A consists of a catalytic domain (CD) and a carbohydrate-binding module (CBM) separated by a linker peptide. A tunnel-shaped substrate-binding site in the CD includes nine subsites for β-d-glucose units, seven of which (-7 to -1) precede the catalytic center. Low catalytic activity of Cel7A is the bottleneck and the primary target for improvement. Here it is shown for the first time that, in spite of much lower apparent kcat of HjCel7A at the hydrolysis of β-1,4-glucosidic linkages in the fluorogenic cellotetra- and -pentaose compared to the structurally related endoglucanase I (HjCel7B), the specificity constants (catalytic efficiency) kcat /Km for both enzymes are almost equal in these reactions. The observed activity difference appears from strong nonproductive substrate binding by HjCel7A, particularly significant for MU-β-cellotetraose (MUG4 ). Interaction of substrates with the subsites -6 and -5 proximal to the nonconserved Gln101 residue in HjCel7A decreases Km,ap by >1500 times. HjCel7A can be nonproductively bound onto cellulose surface with Kd ≈2-9 nM via CBM and CD that captures six terminal glucose units of cellulose chain. Decomposition of this nonproductive complex can determine the rate of cellulose conversion. MUG4 is a promising substrate to select active cellobiohydrolase I variants with reduced nonproductive substrate binding.
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Affiliation(s)
- Mikhail L Rabinovich
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow 119071, Russia
| | - Maria S Melnik
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow 119071, Russia
| | - Mikhail L Herner
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow 119071, Russia
| | - Yakov V Voznyi
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russia
| | - Lilia G Vasilchenko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow 119071, Russia
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Meier KK, Jones SM, Kaper T, Hansson H, Koetsier MJ, Karkehabadi S, Solomon EI, Sandgren M, Kelemen B. Oxygen Activation by Cu LPMOs in Recalcitrant Carbohydrate Polysaccharide Conversion to Monomer Sugars. Chem Rev 2018; 118:2593-2635. [PMID: 29155571 PMCID: PMC5982588 DOI: 10.1021/acs.chemrev.7b00421] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Natural carbohydrate polymers such as starch, cellulose, and chitin provide renewable alternatives to fossil fuels as a source for fuels and materials. As such, there is considerable interest in their conversion for industrial purposes, which is evidenced by the established and emerging markets for products derived from these natural polymers. In many cases, this is achieved via industrial processes that use enzymes to break down carbohydrates to monomer sugars. One of the major challenges facing large-scale industrial applications utilizing natural carbohydrate polymers is rooted in the fact that naturally occurring forms of starch, cellulose, and chitin can have tightly packed organizations of polymer chains with low hydration levels, giving rise to crystalline structures that are highly recalcitrant to enzymatic degradation. The topic of this review is oxidative cleavage of carbohydrate polymers by lytic polysaccharide mono-oxygenases (LPMOs). LPMOs are copper-dependent enzymes (EC 1.14.99.53-56) that, with glycoside hydrolases, participate in the degradation of recalcitrant carbohydrate polymers. Their activity and structural underpinnings provide insights into biological mechanisms of polysaccharide degradation.
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Affiliation(s)
- Katlyn K. Meier
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Stephen M. Jones
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Thijs Kaper
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, California 94304, United States
| | - Henrik Hansson
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden
| | - Martijn J. Koetsier
- DuPont Industrial Biosciences, Netherlands, Nieuwe Kanaal 7-S, 6709 PA Wageningen, The Netherlands
| | - Saeid Karkehabadi
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, P.O. Box 7015, SE-750 07 Uppsala, Sweden
| | - Bradley Kelemen
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, California 94304, United States
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