1
|
Hu Y, Li Y, Cao Y, Shen Y, Zou X, Liu J, Zhao J. Advancements in enzymatic biotransformation and bioactivities of rare ginsenosides:A Review. J Biotechnol 2024; 392:S0168-1656(24)00177-9. [PMID: 38945483 DOI: 10.1016/j.jbiotec.2024.06.018] [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: 03/30/2024] [Revised: 06/24/2024] [Accepted: 06/24/2024] [Indexed: 07/02/2024]
Abstract
Ginsenoside, the principal active constituent of ginseng, exhibits enhanced bioavailability and medicinal efficacy in rare ginsenosides compared to major ginsenosides. Current research is focused on efficiently and selectively removing sugar groups attached to the major ginsenoside sugar chains to convert them into rare ginsenosides that meet the demands of medical industry and functional foods. The methods for preparing rare ginsenosides encompass chemical, microbial, and enzymatic approaches. Among these, the enzyme conversion method is highly favored by researchers due to its exceptional specificity and robust efficiency. This review summarizes the biological activities of different rare ginsenosides, explores the various glycosidases used in the biotransformation of different major ginsenosides as substrates, and elucidates their respective corresponding biotransformation pathways. These findings will provide valuable references for the development, utilization, and industrial production of ginsenosides.
Collapse
Affiliation(s)
- Yanbo Hu
- School of Food Sciences and Engineering, Changchun University, Changchun 130024, China
| | - Yiming Li
- School of Food Sciences and Engineering, Changchun University, Changchun 130024, China
| | - Yi Cao
- School of Food Sciences and Engineering, Changchun University, Changchun 130024, China
| | - Yuzhu Shen
- School of Food Sciences and Engineering, Changchun University, Changchun 130024, China
| | - Xianjun Zou
- School of Food Sciences and Engineering, Changchun University, Changchun 130024, China
| | - Jiaxin Liu
- Jilin Province Product Quality Supervision and Inspection Institute, Changchun, 130012, China
| | - Jun Zhao
- School of Food Sciences and Engineering, Changchun University, Changchun 130024, China.
| |
Collapse
|
2
|
de Assis MA, da Silva JJB, de Carvalho LM, Parreiras LS, Cairo JPLF, Marone MP, Gonçalves TA, Silva DS, Dantzger M, de Figueiredo FL, Carazzolle MF, Pereira GAG, Damasio A. A Multiomics Perspective on Plant Cell Wall-Degrading Enzyme Production: Insights from the Unexploited Fungus Trichoderma erinaceum. J Fungi (Basel) 2024; 10:407. [PMID: 38921393 PMCID: PMC11205114 DOI: 10.3390/jof10060407] [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: 04/08/2024] [Revised: 05/24/2024] [Accepted: 05/28/2024] [Indexed: 06/27/2024] Open
Abstract
Trichoderma erinaceum is a filamentous fungus that was isolated from decaying sugarcane straw at a Brazilian ethanol biorefinery. This fungus shows potential as a source of plant cell wall-degrading enzymes (PCWDEs). In this study, we conducted a comprehensive multiomics investigation of T. erinaceum to gain insights into its enzymatic capabilities and genetic makeup. Firstly, we performed genome sequencing and assembly, which resulted in the identification of 10,942 genes in the T. erinaceum genome. We then conducted transcriptomics and secretome analyses to map the gene expression patterns and identify the enzymes produced by T. erinaceum in the presence of different substrates such as glucose, microcrystalline cellulose, pretreated sugarcane straw, and pretreated energy cane bagasse. Our analyses revealed that T. erinaceum highly expresses genes directly related to lignocellulose degradation when grown on pretreated energy cane and sugarcane substrates. Furthermore, our secretome analysis identified 35 carbohydrate-active enzymes, primarily PCWDEs. To further explore the enzymatic capabilities of T. erinaceum, we selected a β-glucosidase from the secretome data for recombinant production in a fungal strain. The recombinant enzyme demonstrated superior performance in degrading cellobiose and laminaribiose compared to a well-known enzyme derived from Trichoderma reesei. Overall, this comprehensive study provides valuable insights into both the genetic patterns of T. erinaceum and its potential for lignocellulose degradation and enzyme production. The obtained genomic data can serve as an important resource for future genetic engineering efforts aimed at optimizing enzyme production from this fungus.
Collapse
Affiliation(s)
- Michelle A. de Assis
- Laboratory of Enzymology and Molecular Biology (LEBIMO), Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-862, São Paulo, Brazil; (M.A.d.A.); (J.P.L.F.C.); (T.A.G.); (F.L.d.F.)
| | - Jovanderson J. B. da Silva
- Genomics and BioEnergy Laboratory (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-862, São Paulo, Brazil; (J.J.B.d.S.); (L.M.d.C.); (L.S.P.); (M.D.); (M.F.C.); (G.A.G.P.)
| | - Lucas M. de Carvalho
- Genomics and BioEnergy Laboratory (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-862, São Paulo, Brazil; (J.J.B.d.S.); (L.M.d.C.); (L.S.P.); (M.D.); (M.F.C.); (G.A.G.P.)
| | - Lucas S. Parreiras
- Genomics and BioEnergy Laboratory (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-862, São Paulo, Brazil; (J.J.B.d.S.); (L.M.d.C.); (L.S.P.); (M.D.); (M.F.C.); (G.A.G.P.)
| | - João Paulo L. F. Cairo
- Laboratory of Enzymology and Molecular Biology (LEBIMO), Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-862, São Paulo, Brazil; (M.A.d.A.); (J.P.L.F.C.); (T.A.G.); (F.L.d.F.)
- York Structural Biology Laboratory (YSBL), Department of Chemistry, University of York, York YO10 5DD, UK
| | - Marina P. Marone
- Genomics and BioEnergy Laboratory (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-862, São Paulo, Brazil; (J.J.B.d.S.); (L.M.d.C.); (L.S.P.); (M.D.); (M.F.C.); (G.A.G.P.)
| | - Thiago A. Gonçalves
- Laboratory of Enzymology and Molecular Biology (LEBIMO), Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-862, São Paulo, Brazil; (M.A.d.A.); (J.P.L.F.C.); (T.A.G.); (F.L.d.F.)
| | - Desireé S. Silva
- SENAI Institute for Biomass Innovation, Três Lagoas 79640-250, Brazil;
| | - Miriam Dantzger
- Genomics and BioEnergy Laboratory (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-862, São Paulo, Brazil; (J.J.B.d.S.); (L.M.d.C.); (L.S.P.); (M.D.); (M.F.C.); (G.A.G.P.)
| | - Fernanda L. de Figueiredo
- Laboratory of Enzymology and Molecular Biology (LEBIMO), Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-862, São Paulo, Brazil; (M.A.d.A.); (J.P.L.F.C.); (T.A.G.); (F.L.d.F.)
| | - Marcelo F. Carazzolle
- Genomics and BioEnergy Laboratory (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-862, São Paulo, Brazil; (J.J.B.d.S.); (L.M.d.C.); (L.S.P.); (M.D.); (M.F.C.); (G.A.G.P.)
| | - Gonçalo A. G. Pereira
- Genomics and BioEnergy Laboratory (LGE), Department of Genetics, Evolution, Microbiology and Immunology, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-862, São Paulo, Brazil; (J.J.B.d.S.); (L.M.d.C.); (L.S.P.); (M.D.); (M.F.C.); (G.A.G.P.)
| | - André Damasio
- Laboratory of Enzymology and Molecular Biology (LEBIMO), Department of Biochemistry and Tissue Biology, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-862, São Paulo, Brazil; (M.A.d.A.); (J.P.L.F.C.); (T.A.G.); (F.L.d.F.)
| |
Collapse
|
3
|
Hu C, Wang Y, Wang W, Cui W, Jia X, Mayo KH, Zhou Y, Su J, Yuan Y. A trapped covalent intermediate as a key catalytic element in the hydrolysis of a GH3 β-glucosidase: An X-ray crystallographic and biochemical study. Int J Biol Macromol 2024; 265:131131. [PMID: 38527679 DOI: 10.1016/j.ijbiomac.2024.131131] [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: 01/10/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 03/27/2024]
Abstract
Glycoside hydrolases (GHs) are industrially important enzymes that hydrolyze glycosidic bonds in glycoconjugates. In this study, we found a GH3 β-glucosidase (CcBgl3B) from Cellulosimicrobium cellulans sp. 21 was able to selectively hydrolyze the β-1,6-glucosidic bond linked glucose of ginsenosides. X-ray crystallographic studies of the ligand complex ginsenoside-specific β-glucosidase provided a novel finding that support the catalytic mechanism of GH3. The substrate was clearly identified within the catalytic center of wild-type CcBgl3B, revealing that the C1 atom of the glucose was covalently bound to the Oδ1 group of the conserved catalytic nucleophile Asp264 as an enzyme-glycosyl intermediate. The glycosylated Asp264 could be identified by mass spectrometry. Through site-directed mutagenesis studies with Asp264, it was found that the covalent intermediate state formed by Asp264 and the substrate was critical for catalysis. In addition, Glu525 variants (E525A, E525Q and E525D) showed no or marginal activity against pNPβGlc; thus, this residue could supply a proton for the reaction. Overall, our study provides an insight into the catalytic mechanism of the GH3 enzyme CcBgl3B.
Collapse
Affiliation(s)
- Chenxing Hu
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Yibing Wang
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Weiyang Wang
- College of Life Science and Technology, Changchun University of Science & Technology, Changchun, Jilin 130022, China
| | - Wanli Cui
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Xinyue Jia
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Kevin H Mayo
- Department of Biochemistry, Molecular Biology & Biophysics, 6-155 Jackson Hall, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yifa Zhou
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China
| | - Jiyong Su
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China.
| | - Ye Yuan
- Engineering Research Center of Glycoconjugates Ministry of Education, Jilin Provincial Key Laboratory of Chemistry and Biology of Changbai Mountain Natural Drugs, School of Life Sciences, Northeast Normal University, Changchun 130024, China.
| |
Collapse
|
4
|
Erkanli ME, El-Halabi K, Kim JR. Exploring the diversity of β-glucosidase: Classification, catalytic mechanism, molecular characteristics, kinetic models, and applications. Enzyme Microb Technol 2024; 173:110363. [PMID: 38041879 DOI: 10.1016/j.enzmictec.2023.110363] [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: 09/25/2023] [Revised: 11/17/2023] [Accepted: 11/18/2023] [Indexed: 12/04/2023]
Abstract
High-value chemicals and energy-related products can be produced from biomass. Biorefinery technology offers a sustainable and cost-effective method for this high-value conversion. β-glucosidase is one of the key enzymes in biorefinery processes, catalyzing the production of glucose from aryl-glycosides and cello-oligosaccharides via the hydrolysis of β-glycosidic bonds. Although β-glucosidase plays a critical catalytic role in the utilization of cellulosic biomass, its efficacy is often limited by substrate or product inhibitions, low thermostability, and/or insufficient catalytic activity. To provide a detailed overview of β-glucosidases and their benefits in certain desired applications, we collected and summarized extensive information from literature and public databases, covering β-glucosidases in different glycosidase hydrolase families and biological kingdoms. These β-glucosidases show differences in amino acid sequence, which are translated into varying degrees of the molecular properties critical in enzymatic applications. This review describes studies on the diversity of β-glucosidases related to the classification, catalytic mechanisms, key molecular characteristics, kinetics models, and applications, and highlights several β-glucosidases displaying high stability, activity, and resistance to glucose inhibition suitable for desired biotechnological applications.
Collapse
Affiliation(s)
- Mehmet Emre Erkanli
- Department of Chemical and Biomolecular Engineering, New York University, 6 MetroTech Center, Brooklyn, NY 11201, United States
| | - Khalid El-Halabi
- Department of Chemical and Biomolecular Engineering, New York University, 6 MetroTech Center, Brooklyn, NY 11201, United States
| | - Jin Ryoun Kim
- Department of Chemical and Biomolecular Engineering, New York University, 6 MetroTech Center, Brooklyn, NY 11201, United States.
| |
Collapse
|
5
|
Lu X, Li X, Zhao J. Improving enzymatic efficiency of β-glucosidases in cellulase system by altering its binding behavior to the insoluble substrate during bioconversion of lignocellulose. BIORESOURCE TECHNOLOGY 2024; 391:129974. [PMID: 37939741 DOI: 10.1016/j.biortech.2023.129974] [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: 09/12/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/10/2023]
Abstract
The enzymatic efficiency of β-glucosidases is influenced by their binding behavior onto insoluble substrates (cellulose and lignin) during bioconversion of lignocellulose. This study suggested that the Bgl3 protein (Aspergillus fumigatus) showed strong adsorption affinity to lignin and the Bgl1 protein (Penicillium oxalicum) tended to adsorb to cellulose. It indicated that the various surface properties of the fibronectin type Ш-like domain (FnIII) led to different binding properties of β-glucosidases by investigating their binding mechanism. By engineering β-glucosidases' FnIII domain, Bgl3-1 and Bgl1-3 were constructed, which both showed lower binding capacities to insoluble substrates. As well as for Bgl1-3, its sensitivity to the phenolic component was also eased. Based on that, the reconstructed protein showed high catalytic efficiency during the enzymatic hydrolysis of corn stover by effectively transforming cellobiose to glucose. Thus, this study provided a new strategy to engineer β-glucosidases to enhance their performance in the cellulase system.
Collapse
Affiliation(s)
- Xianqin Lu
- State Key Laboratory of Microbial Technology, Shandong University, No.72, Binhai Road, Qingdao 266237, China
| | - Xuezhi Li
- State Key Laboratory of Microbial Technology, Shandong University, No.72, Binhai Road, Qingdao 266237, China
| | - Jian Zhao
- State Key Laboratory of Microbial Technology, Shandong University, No.72, Binhai Road, Qingdao 266237, China.
| |
Collapse
|
6
|
Chen B, Zhou Y, Duan L, Gong X, Liu X, Pan K, Zeng D, Ni X, Zeng Y. Complete genome analysis of Bacillus velezensis TS5 and its potential as a probiotic strain in mice. Front Microbiol 2023; 14:1322910. [PMID: 38125573 PMCID: PMC10731255 DOI: 10.3389/fmicb.2023.1322910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 11/13/2023] [Indexed: 12/23/2023] Open
Abstract
Introduction In recent years, a large number of studies have shown that Bacillus velezensis has the potential as an animal feed additive, and its potential probiotic properties have been gradually explored. Methods In this study, Illumina NovaSeq PE150 and Oxford Nanopore ONT sequencing platforms were used to sequence the genome of Bacillus velezensis TS5, a fiber-degrading strain isolated from Tibetan sheep. To further investigate the potential of B. velezensis TS5 as a probiotic strain, in vivo experiments were conducted using 40 five-week-old male specific pathogen-free C57BL/6J mice. The mice were randomly divided into four groups: high fiber diet control group (H group), high fiber diet probiotics group (HT group), low fiber diet control group (L group), and low fiber diet probiotics group (LT group). The H and HT groups were fed high-fiber diet (30%), while the L and LT groups were fed low-fiber diet (5%). The total bacteria amount in the vegetative forms of B. velezensis TS5 per mouse in the HT and LT groups was 1 × 109 CFU per day, mice in the H and L groups were given the same volume of sterile physiological saline daily by gavage, and the experiment period lasted for 8 weeks. Results The complete genome sequencing results of B. velezensis TS5 showed that it contained 3,929,788 nucleotides with a GC content of 46.50%. The strain encoded 3,873 genes that partially related to stress resistance, adhesion, and antioxidants, as well as the production of secondary metabolites, digestive enzymes, and other beneficial nutrients. The genes of this bacterium were mainly involved in carbohydrate metabolism, amino acid metabolism, vitamin and cofactor metabolism, biological process, and molecular function, as revealed by KEGG and GO databases. The results of mouse tests showed that B. velezensis TS5 could improve intestinal digestive enzyme activity, liver antioxidant capacity, small intestine morphology, and cecum microbiota structure in mice. Conclusion These findings confirmed the probiotic effects of B. velezensis TS5 isolated from Tibetan sheep feces and provided the theoretical basis for the clinical application and development of new feed additives.
Collapse
Affiliation(s)
- Benhao Chen
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
| | - Yi Zhou
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
| | - Lixiao Duan
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
| | - Xuemei Gong
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
| | - Xingmei Liu
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
| | - Kangcheng Pan
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
| | - Dong Zeng
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
| | - Xueqin Ni
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
| | - Yan Zeng
- Animal Microecology Institute, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
- Engineering Research Center of Southwest Animal Disease Prevention and Control Technology, Ministry of Education of the People’s Republic of China, Chengdu, China
| |
Collapse
|
7
|
Mou L, Pan R, Liu Y, Jiang W, Zhang W, Jiang Y, Xin F, Jiang M. Isolation of a newly Trichoderma asperellum LYS1 with abundant cellulase-hemicellulase enzyme cocktail for lignocellulosic biomass degradation. Enzyme Microb Technol 2023; 171:110318. [PMID: 37683573 DOI: 10.1016/j.enzmictec.2023.110318] [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: 03/27/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023]
Abstract
As the most abundant and renewable natural resource in the world, lignocellulose is a promising alternative to fossil energy to relieve environmental concerns and resource depletion. However, due to its recalcitrant structure, strains with efficient degradation capability still need exploring. In this study, a fungus was successfully isolated from decayed wood and named as Trichoderma asperellum LYS1 by phylogenetic and draft genomic analysis. The further investigations showed that strain LYS1 had an outstanding performance on lignocellulose degradation, especially for hemicellulose-rich biomass. After the analysis of encoded CAZymes, mainly on GH family, a large amount of genes coding β-glucosidase and xylanase may contribute to the high degradation of cellulose and hemicellulose. Collectively, the results generated in this study demonstrated that T. asperellum LYS1 is a potential cell factory for lignocellulose biorefinery.
Collapse
Affiliation(s)
- Lu Mou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Runze Pan
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Yansong Liu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Wankui Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; Jiangsu Academy of Chemical Inherent Safety, Nanjing 211800, PR China
| | - Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China.
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; Jiangsu Academy of Chemical Inherent Safety, Nanjing 211800, PR China.
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211800, PR China; Jiangsu Academy of Chemical Inherent Safety, Nanjing 211800, PR China
| |
Collapse
|
8
|
Kaenying W, Choengpanya K, Tagami T, Wattana-Amorn P, Lang W, Okuyama M, Li YK, Kimura A, Kongsaeree PT. Crystal structure and identification of amino acid residues for catalysis and binding of GH3 AnBX β-xylosidase from Aspergillus niger. Appl Microbiol Biotechnol 2023; 107:2335-2349. [PMID: 36877249 DOI: 10.1007/s00253-023-12445-z] [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: 12/06/2022] [Revised: 02/08/2023] [Accepted: 02/13/2023] [Indexed: 03/07/2023]
Abstract
β-Xylosidases catalyze the hydrolysis of xylooligosaccharides to xylose in the final step of hemicellulose degradation. AnBX, which is a GH3 β-xylosidase from Aspergillus niger, has a high catalytic efficiency toward xyloside substrates. In this study, we report the three-dimensional structure and the identification of catalytic and substrate binding residues of AnBX by performing site-directed mutagenesis, kinetic analysis, and NMR spectroscopy-associated analysis of the azide rescue reaction. The structure of the E88A mutant of AnBX, determined at 2.5-Å resolution, contains two molecules in the asymmetric unit, each of which is composed of three domains, namely an N-terminal (β/α)8 TIM-barrel-like domain, an (α/β)6 sandwich domain, and a C-terminal fibronectin type III domain. Asp288 and Glu500 of AnBX were experimentally confirmed to act as the catalytic nucleophile and acid/base catalyst, respectively. The crystal structure revealed that Trp86, Glu88 and Cys289, which formed a disulfide bond with Cys321, were located at subsite -1. Although the E88D and C289W mutations reduced catalytic efficiency toward all four substrates tested, the substitution of Trp86 with Ala, Asp and Ser increased the substrate preference for glucoside relative to xyloside substrates, indicating that Trp86 is responsible for the xyloside specificity of AnBX. The structural and biochemical information of AnBX obtained in this study provides invaluable insight into modulating the enzymatic properties for the hydrolysis of lignocellulosic biomass. KEY POINTS: • Asp288 and Glu500 of AnBX are the nucleophile and acid/base catalyst, respectively • Glu88 and the Cys289-Cys321 disulfide bond are crucial for the catalytic activity of AnBX • The W86A and W86S mutations in AnBX increased the preference for glucoside substrates.
Collapse
Affiliation(s)
- Wilaiwan Kaenying
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Khuanjarat Choengpanya
- Interdisciplinary Graduate Program in Genetic Engineering, Faculty of Graduate School, Kasetsart University, Bangkok, 10900, Thailand
- Program in Basic Science, Maejo University Phrae Campus, Phrae, 54140, Thailand
| | - Takayoshi Tagami
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Pakorn Wattana-Amorn
- Department of Chemistry, Special Research Unit for Advanced Magnetic Resonance and Center of Excellence for Innovation in Chemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Weeranuch Lang
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Masayuki Okuyama
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Yaw-Kuen Li
- Department of Applied Chemistry, College of Science, National Yang Ming Chiao Tung University, Hsinchu, 300, Taiwan
| | - Atsuo Kimura
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Prachumporn T Kongsaeree
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.
- Interdisciplinary Graduate Program in Genetic Engineering, Faculty of Graduate School, Kasetsart University, Bangkok, 10900, Thailand.
| |
Collapse
|
9
|
The evolutionary advantage of an aromatic clamp in plant family 3 glycoside exo-hydrolases. Nat Commun 2022; 13:5577. [PMID: 36151080 PMCID: PMC9508125 DOI: 10.1038/s41467-022-33180-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 09/03/2022] [Indexed: 11/08/2022] Open
Abstract
In the barley β-D-glucan glucohydrolase, a glycoside hydrolase family 3 (GH3) enzyme, the Trp286/Trp434 clamp ensures β-D-glucosides binding, which is fundamental for substrate hydrolysis during plant growth and development. We employ mutagenesis, high-resolution X-ray crystallography, and multi-scale molecular modelling methods to examine the binding and conformational behaviour of isomeric β-D-glucosides during substrate-product assisted processive catalysis that operates in GH3 hydrolases. Enzyme kinetics reveals that the W434H mutant retains broad specificity, while W434A behaves as a strict (1,3)-β-D-glucosidase. Investigations of reactant movements on the nanoscale reveal that processivity is sensitive to mutation-specific alterations of the tryptophan clamp. While wild-type and W434H utilise a lateral cavity for glucose displacement and sliding of (1,3)-linked hydrolytic products through the catalytic site without dissociation, consistent with their high hydrolytic rates, W434A does not adopt processive catalysis. Phylogenomic analyses of GH3 hydrolases disclose the evolutionary advantage of the tryptophan clamp that confers broad specificity, high catalytic efficiency, and processivity.
Collapse
|
10
|
Shang Z, Liu S, Duan Y, Bao C, Wang J, Dong B, Cao Y. Complete genome sequencing and investigation on the fiber-degrading potential of Bacillus amyloliquefaciens strain TL106 from the tibetan pig. BMC Microbiol 2022; 22:186. [PMID: 35906551 PMCID: PMC9336001 DOI: 10.1186/s12866-022-02599-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/19/2022] [Indexed: 12/05/2022] Open
Abstract
Background Cellulolytic microorganisms are considered a key player in the degradation of feed fiber. These microorganisms can be isolated from various resources, such as animal gut, plant surfaces, soil and oceans. A new strain of Bacillus amyloliquefaciens, TL106, was isolated from faeces of a healthy Tibetan pigs. This strain can produce cellulase and shows strong antimicrobial activity in mice. Thus, in this study, to better understand the strain of B. amyloliquefaciens TL106 on degradation of cellulose, the genome of the strain TL106 was completely sequenced and analyzed. In addition, we also explored the cellulose degradation ability of strain TL106 in vitro. Results TL106 was completely sequenced with the third generation high-throughput DNA sequencing. In vitro analysis with enzymatic hydrolysis identified the activity of cellulose degradation. TL106 consisted of one circular chromosome with 3,980,960 bp and one plasmid with 16,916 bp, the genome total length was 3.99 Mb and total of 4,130 genes were predicted. Several genes of cellulases and hemicellulase were blasted in Genbank, including β-glucosidase, endoglucanase, ß-glucanase and xylanase genes. Additionally, the activities of amylase (20.25 U/mL), cellulase (20.86 U/mL), xylanase (39.71 U/mL) and β-glucanase (36.13 U/mL) in the fermentation supernatant of strain TL106 were higher. In the study of degradation characteristics, we found that strain TL106 had a better degradation effect on crude fiber, neutral detergent fiber, acid detergent fiber, starch, arabinoxylan and β-glucan of wheat and highland barley . Conclusions The genome of B. amyloliquefaciens TL106 contained several genes of cellulases and hemicellulases, can produce carbohydrate-active enzymes, amylase, cellulase, xylanase and β-glucanase. The supernatant of fermented had activities of strain TL106. It could degrade the fiber fraction and non-starch polysaccharides (arabinoxylans and β-glucan) of wheat and highland barley. The present study demonstrated that the degradation activity of TL106 to crude fiber which can potentially be applied as a feed additive to potentiate the digestion of plant feed by monogastric animals. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02599-7.
Collapse
Affiliation(s)
- Zhenda Shang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, People's Republic of China.,College of Animal Science, Tibet Agricultural and Animal Husbandry University, 860000, Nyingchi, People's Republic of China
| | - Suozhu Liu
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, 860000, Nyingchi, People's Republic of China
| | - Yanzhen Duan
- College of Animal Science, Tibet Agricultural and Animal Husbandry University, 860000, Nyingchi, People's Republic of China
| | - Chengling Bao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, People's Republic of China
| | - Jian Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, People's Republic of China
| | - Bing Dong
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, People's Republic of China
| | - Yunhe Cao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, People's Republic of China.
| |
Collapse
|
11
|
Atanasova M, Nicholls RA, Joosten RP, Agirre J. Updated restraint dictionaries for carbohydrates in the pyranose form. Acta Crystallogr D Struct Biol 2022; 78:455-465. [PMID: 35362468 PMCID: PMC8972801 DOI: 10.1107/s2059798322001103] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 01/31/2022] [Indexed: 11/10/2022] Open
Abstract
Restraint dictionaries are used during macromolecular structure refinement to encapsulate intramolecular connectivity and geometric information. These dictionaries allow previously determined `ideal' values of features such as bond lengths, angles and torsions to be used as restraint targets. During refinement, restraints influence the model to adopt a conformation that agrees with prior observation. This is especially important when refining crystal structures of glycosylated proteins, as their resolutions tend to be worse than those of nonglycosylated proteins. Pyranosides, the overwhelming majority component in all forms of protein glycosylation, often display conformational errors in crystal structures. Whilst many of these flaws usually relate to model building, refinement issues may also have their root in suboptimal restraint dictionaries. In order to avoid subsequent misinterpretation and to improve the quality of all pyranose monosaccharide entries in the CCP4 Monomer Library, new dictionaries with improved ring torsion restraints, coordinates reflecting the lowest-energy ring pucker and updated geometry have been produced and evaluated. These new dictionaries are now part of the CCP4 Monomer Library and will be released with CCP4 version 8.0.
Collapse
Affiliation(s)
- Mihaela Atanasova
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Robert A. Nicholls
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Robbie P. Joosten
- Biochemistry Department, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, The Netherlands
| | - Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| |
Collapse
|
12
|
Xia W, Bai Y, Shi P. Improving the Substrate Affinity and Catalytic Efficiency of β-Glucosidase Bgl3A from Talaromyces leycettanus JCM12802 by Rational Design. Biomolecules 2021; 11:biom11121882. [PMID: 34944526 PMCID: PMC8699594 DOI: 10.3390/biom11121882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 12/31/2022] Open
Abstract
Improving the substrate affinity and catalytic efficiency of β-glucosidase is necessary for better performance in the enzymatic saccharification of cellulosic biomass because of its ability to prevent cellobiose inhibition on cellulases. Bgl3A from Talaromyces leycettanus JCM12802, identified in our previous work, was considered a suitable candidate enzyme for efficient cellulose saccharification with higher catalytic efficiency on the natural substrate cellobiose compared with other β-glucosidase but showed insufficient substrate affinity. In this work, hydrophobic stacking interaction and hydrogen-bonding networks in the active center of Bgl3A were analyzed and rationally designed to strengthen substrate binding. Three vital residues, Met36, Phe66, and Glu168, which were supposed to influence substrate binding by stabilizing adjacent binding site, were chosen for mutagenesis. The results indicated that strengthening the hydrophobic interaction between stacking aromatic residue and the substrate, and stabilizing the hydrogen-bonding networks in the binding pocket could contribute to the stabilized substrate combination. Four dominant mutants, M36E, M36N, F66Y, and E168Q with significantly lower Km values and 1.4–2.3-fold catalytic efficiencies, were obtained. These findings may provide a valuable reference for the design of other β-glucosidases and even glycoside hydrolases.
Collapse
Affiliation(s)
- Wei Xia
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Yingguo Bai
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence: (Y.B.); (P.S.)
| | - Pengjun Shi
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
- Correspondence: (Y.B.); (P.S.)
| |
Collapse
|
13
|
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.
Collapse
|
14
|
Kao MR, Yu SM, Ho THUD. Improvements of the productivity and saccharification efficiency of the cellulolytic β-glucosidase D2-BGL in Pichia pastoris via directed evolution. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:126. [PMID: 34059121 PMCID: PMC8166090 DOI: 10.1186/s13068-021-01973-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 05/17/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND β-Glucosidases are essential for cellulose hydrolysis by catalyzing the final cellulolytic degradation of cello-oligomers and cellobiose to glucose. D2-BGL is a fungal glycoside hydrolase family 3 (GH3) β-glucosidase isolated from Chaetomella raphigera with high substrate affinity, and is an efficient β-glucosidase supplement to Trichoderma reesei cellulase mixtures for the saccharification of lignocellulosic biomass. RESULTS We have carried out error-prone PCR to further increase catalytic efficiency of wild-type (WT) D2-BGL. Three mutants, each with substitution of two amino acids on D2-BGL, exhibited increased activity in a preliminary mutant screening in Saccharomyces cerevisiae. Effects of single amino acid replacements on catalysis efficiency and enzyme production have been investigated by subsequent expression in Pichia pastoris. Substitution F256M resulted in enhancing the tolerance to substrate inhibition and specific activity, and substitution D224G resulted in increasing the production of recombinant enzyme. The best D2-BGL mutant generated, Mut M, was constructed by combining beneficial mutations D224G, F256M and Y260D. Expression of Mut M in Pichia pastoris resulted in 2.7-fold higher production of recombinant protein, higher Vmax and greater substrate inhibition tolerance towards cellobiose relative to wild-type enzyme. Surprisingly, Mut M overexpression induced the ER unfolded protein response to a level lower than that with WT D2 overexpression in P. pastoris. When combined with the T. reesei cellulase preparation Celluclast 1.5L, Mut M hydrolyzed acid-pretreated sugarcane bagasse more efficiently than WT D2. CONCLUSIONS D2-BGL mutant Mut M was generated successfully by following directed evolution approach. Mut M carries three mutations that are not reported in other directed evolution studies of GH3 β-glucosidases, and this mutant exhibited greater tolerance to substrate inhibition and higher Vmax than wild-type enzyme. Besides the enhanced specific activity, Mut M also exhibited a higher protein titer than WT D2 when it was overexpressed in P. pastoris. Our study demonstrates that both catalytic efficiency and productivity of a cellulolytic enzyme can be enhanced via protein engineering.
Collapse
Affiliation(s)
- Mu-Rong Kao
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and National Defense Medical Center, Taipei, 115 Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, 115 Taiwan
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115 Taiwan
| | - Su-May Yu
- Institute of Molecular Biology, Academia Sinica, Taipei, 115 Taiwan
- Department of Plant Pathology, National Chung Hsing University, Taichung, 402 Taiwan
- Department of Life Sciences, National Chung Hsing University, Taichung, 402 Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung, 402 Taiwan
| | - Tuan-H ua David Ho
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115 Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung, 402 Taiwan
| |
Collapse
|
15
|
Lin MC, Kuo HW, Kao MR, Lin WD, Li CW, Hung KS, Yang SC, Yu SM, Ho THD. From simple and specific zymographic detections to the annotation of a fungus Daldinia caldariorum D263 that encodes a wide range of highly bioactive cellulolytic enzymes. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:120. [PMID: 34020690 PMCID: PMC8140500 DOI: 10.1186/s13068-021-01959-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 04/20/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Lignocellulolytic enzymes are essential for agricultural waste disposal and production of renewable bioenergy. Many commercialized cellulase mixtures have been developed, mostly from saprophytic or endophytic fungal species. The cost of complete cellulose digestion is considerable because a wide range of cellulolytic enzymes is needed. However, most fungi can only produce limited range of highly bioactive cellulolytic enzymes. We aimed to investigate a simple yet specific method for discovering unique enzymes so that fungal species producing a diverse group of cellulolytic enzymes can be identified. RESULTS The culture medium of an endophytic fungus, Daldinia caldariorum D263, contained a complete set of cellulolytic enzymes capable of effectively digesting cellulose residues into glucose. By taking advantage of the unique product inhibition property of β-glucosidases, we have established an improved zymography method that can easily distinguish β-glucosidase and exoglucanase activity. Our zymography method revealed that D263 can secrete a wide range of highly bioactive cellulases. Analyzing the assembled genome of D263, we found over 100 potential genes for cellulolytic enzymes that are distinct from those of the commercially used fungal species Trichoderma reesei and Aspergillus niger. We further identified several of these cellulolytic enzymes by mass spectrometry. CONCLUSIONS The genome of Daldinia caldariorum D263 has been sequenced and annotated taking advantage of a simple yet specific zymography method followed by mass spectrometry analysis, and it appears to encode and secrete a wide range of bioactive cellulolytic enzymes. The genome and cellulolytic enzyme secretion of this unique endophytic fungus should be of value for identifying active cellulolytic enzymes that can facilitate conversion of agricultural wastes to fermentable sugars for the industrial production of biofuels.
Collapse
Affiliation(s)
- Meng-Chun Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - Hsion-Wen Kuo
- Department of Environmental Science and Engineering, Tunghai University, Taichung, Taiwan, ROC
| | - Mu-Rong Kao
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - Wen-Dar Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - Chen-Wei Li
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - Kuo-Sheng Hung
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - Sheng-Chih Yang
- Institute of Tropical Plant Science, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Su-May Yu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC
- Biotechnology Research Center, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Tuan-Hua David Ho
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC.
- Biotechnology Research Center, National Chung Hsing University, Taichung, Taiwan, ROC.
| |
Collapse
|
16
|
Dadwal A, Singh V, Sharma S, Satyanarayana T. Structural aspects of β-glucosidase of Myceliophthora thermophila (MtBgl3c) by homology modelling and molecular docking. J Biomol Struct Dyn 2021; 40:5211-5228. [PMID: 33413029 DOI: 10.1080/07391102.2020.1869095] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Cellulases are the enzymes with diverse range of industrial applications. Cellulases degrade cellulose into monomeric glucose units by hydrolysing β-1,4-glycosidic bonds. There are three components of cellulases: a) endoglucanase, b) exoglucanase and c) β-glucosidase which act synergistically in cellulose bioconversion. The cellulases are the third largest industrial enzymes with a great potential in bioethanol production. In this investigation, a β-glucosidase of a thermophilic fungus Myceliophthora thermophila (MtBgl3c) was analysed for its structural characterization using in silico approaches. The protein structure of MtBgl3c is unknown, therefore an attempt has been made to model 3D structure using Modeller 9.23 software. The MtBgl3c protein model generated was validated from Verify 3D and ERRAT scores of 89.37% and 71.25%, respectively derived from SAVES. Using RAMPAGE the Ramachandran plot was generated, which predicted the accuracy of the 3D model with 91.5% amino acid residues in the favored region. The ion binding and N-glycosylation sites were also predicted. The generated model was docked with cellobiose to predict the most favorable binding sites of MtBgl3c. The key amino acid residues involved in cellobiose bonding are Val88, Asp106, Asp287, Tyr255, Arg170, Glu514. The catalytic conserved amino residues of MtBgl3c were identified. The dock score of cellobiose with MtBgl3c is much lower (-6.46 kcal/mol) than that of glucose (-5.61 kcal/mol), suggesting its high affinity for cellobiose. The docking data of MtBgl3c with glucose illustrate its tolerance to glucose. The present study provides insight into structural characteristics of the MtBgl3c which can be further validated by experimental data. Highlights3D structure of β-glucosidase (MtBgl3c) of Myceliophthora thermophila is being proposed based on computational analysesThe amino acid residues Asp106, Asp287, Tyr255, Arg170 and Glu514 have been identified to play catalytically important role in substrate bindingDocking and interaction of MtBgl3c with cellobiose and glucose has been confirmedDocking analysis of MtBgl3c with glucose suggested its glucose toleranceThe data would be useful in engineering enzymes for attaining higher catalytic efficiencyCommunicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Anica Dadwal
- Department of Biological Sciences and Engineering, Netaji Subhas Institute of Technology (University of Delhi), New Delhi, India
| | - Vishal Singh
- Department of Applied Sciences, Indian Institute of Information Technology Allahabad, Allahabad, Uttar Pradesh, India
| | - Shilpa Sharma
- Department of Biological Sciences and Engineering, Netaji Subhas Institute of Technology (University of Delhi), New Delhi, India
| | - Tulasi Satyanarayana
- Department of Biological Sciences and Engineering, Netaji Subhas Institute of Technology (University of Delhi), New Delhi, India
| |
Collapse
|
17
|
Deepa P, Thirumeignanam D. Rising trend on the halogen and non-halogen derivatives (Br, Cl, CF 3, F, CH 3 and NH 2) in ruminal β-d-Xylopyranose - a quantum chemical perspective. J Biomol Struct Dyn 2020; 40:449-467. [PMID: 32880211 DOI: 10.1080/07391102.2020.1815577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The utmost aim of the current study is to find significance of the binding affinity in the halogen and non-halogen derivatives: Br, Cl, CF3, F, CH3 and NH2 of β-d-Xylopyranose with the hinge region amino acids of ruminant-β-glycosidase. The interaction energy analysis was carried out in detail through various density functional studies as M062X/def2-QZVP, M062X/LANL2DZ, B3LYP/LANL2DZ and M06HF/LANL2DZ level of theories. The total interaction energy of halogen derivatives: Br, Cl, F and CF3 are -618.21, -599.00, -720.45 and -553.08 kcal/mol respectively, and non-halogen derivative: amine group (NH2) is -87.96 kcal/mol at M062X/def2-QZVP level of theory, which exist with strong binding affinity. Ligand properties: dipole moment, polarizability, volume, molecular mass, electrostatic potential map was evaluated to understand its electrostatic and structural behavior. The nature of the bonds was inferred from the electrostatic potential map for all the halogen and non-halogen derivatives ligand. The stabilization energy from NBO analysis reveals the stability of single hydrogen and halogen bonds (N-H…Br, C-Br…O, N-H…Cl, C-Cl…O, O-H…F, C-H…F, N-H…F, C-F…O, N-H…O, O-H…O, N-H…N, O-H…N) in β-d-Xylopyranose and its derivatives. Overall, this study paves way for scientist and medicinal chemist in modelling new drugs. Further, it suggests mutations that increase the binding and may enhance the catalytic action and strengthen the complex diet in animals and hence recommended for experimental synthesis.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Palanisamy Deepa
- Department of Physics, Manonmaniam Sundaranar University, Tirunelveli, India
| | - Duraisamy Thirumeignanam
- Department of Animal Nutrition, Veterinary College and Research Institute, TamilNadu Veterinary and Animal Sciences University, Tirunelveli, India
| |
Collapse
|
18
|
Identification of an intracellular β-glucosidase in Aspergillus niger with transglycosylation activity. Appl Microbiol Biotechnol 2020; 104:8367-8380. [DOI: 10.1007/s00253-020-10840-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 07/29/2020] [Accepted: 08/14/2020] [Indexed: 10/23/2022]
|
19
|
Prawisut A, Choknud S, Ketudat Cairns JR. Expression of rice β-exoglucanase II (OsExoII) in Escherichia coli, purification, and characterization. Protein Expr Purif 2020; 175:105708. [PMID: 32738438 DOI: 10.1016/j.pep.2020.105708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/10/2020] [Accepted: 07/10/2020] [Indexed: 11/15/2022]
Abstract
Enzymes involved in β-glucan breakdown in plants include endoglucanases, exoglucanases and β-glucosidases. Glycoside hydrolase family 3 (GH3) exoglucanases from barley and maize and a few plant GH3 β-glucosidases have been characterized, but none from rice. A few of these enzymes have been expressed in recombinant yeast and plant systems, but bacterial expression of plant GH3 enzymes has not been successful. We expressed the rice GH3 exoglucanase OsExo2 in Escherichia coli as a thioredoxin fusion protein, while other active plant GH3 enzymes could not be produced in this system. The protein was purified over 2000-fold in three chromatographic steps. The enzyme hydrolyzed β-1,3- and β-1,4-linked oligosaccharides and polysaccharides, consistent with a role in cell wall remodeling. Of the oligosaccharides tested, it had highest catalytic efficiency toward laminaritriose, (apparent kcat/Km = 37.7 mM-1s-1). Among polysaccharides, OsExoII hydrolyzed barley mixed β-glucan and laminarin with similar efficiencies (apparent kcat/Km = 3.7 and 3.4 mL mg-1 s-1, respectively), but achieved its highest apparent kcat with lichenan (2.9 s-1). OsExoII was found to be stimulated by ethylene glycol, which increased the apparent kcat and decreased the Km and was transglycosylated. These results imply that E. coli expression may be successful for certain plant GH3 enzymes and OsExoII may be a useful enzyme for application to glycoside production.
Collapse
Affiliation(s)
- Akkarawit Prawisut
- School of Chemistry, Institute of Science and Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, 111 University Avenue, Muang District, Nakhon Ratchasima, 30000, Thailand
| | - Sunaree Choknud
- School of Chemistry, Institute of Science and Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, 111 University Avenue, Muang District, Nakhon Ratchasima, 30000, Thailand
| | - James R Ketudat Cairns
- School of Chemistry, Institute of Science and Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, 111 University Avenue, Muang District, Nakhon Ratchasima, 30000, Thailand.
| |
Collapse
|
20
|
Sidar A, Albuquerque ED, Voshol GP, Ram AFJ, Vijgenboom E, Punt PJ. Carbohydrate Binding Modules: Diversity of Domain Architecture in Amylases and Cellulases From Filamentous Microorganisms. Front Bioeng Biotechnol 2020; 8:871. [PMID: 32850729 PMCID: PMC7410926 DOI: 10.3389/fbioe.2020.00871] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/07/2020] [Indexed: 12/11/2022] Open
Abstract
Enzymatic degradation of abundant renewable polysaccharides such as cellulose and starch is a field that has the attention of both the industrial and scientific community. Most of the polysaccharide degrading enzymes are classified into several glycoside hydrolase families. They are often organized in a modular manner which includes a catalytic domain connected to one or more carbohydrate-binding modules. The carbohydrate-binding modules (CBM) have been shown to increase the proximity of the enzyme to its substrate, especially for insoluble substrates. Therefore, these modules are considered to enhance enzymatic hydrolysis. These properties have played an important role in many biotechnological applications with the aim to improve the efficiency of polysaccharide degradation. The domain organization of glycoside hydrolases (GHs) equipped with one or more CBM does vary within organisms. This review comprehensively highlights the presence of CBM as ancillary modules and explores the diversity of GHs carrying one or more of these modules that actively act either on cellulose or starch. Special emphasis is given to the cellulase and amylase distribution within the filamentous microorganisms from the genera of Streptomyces and Aspergillus that are well known to have a great capacity for secreting a wide range of these polysaccharide degrading enzyme. The potential of the CBM and other ancillary domains for the design of improved polysaccharide decomposing enzymes is discussed.
Collapse
Affiliation(s)
- Andika Sidar
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands.,Department of Food Science and Agricultural Product Technology, Faculty of Agricultural Technology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Erica D Albuquerque
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands.,Sun Pharmaceutical Industries Europe BV., Hoofddorp, Netherlands
| | - Gerben P Voshol
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands.,Dutch DNA Biotech B.V., Utrecht, Netherlands
| | - Arthur F J Ram
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands
| | - Erik Vijgenboom
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands
| | - Peter J Punt
- Department of Microbial Biotechnology, Institute of Biology Leiden, Leiden, Netherlands.,Dutch DNA Biotech B.V., Utrecht, Netherlands
| |
Collapse
|
21
|
Keller MB, Sørensen TH, Krogh KBRM, Wogulis M, Borch K, Westh P. Activity of fungal β-glucosidases on cellulose. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:121. [PMID: 32670408 PMCID: PMC7350674 DOI: 10.1186/s13068-020-01762-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 07/04/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Fungal beta-glucosidases (BGs) from glucoside hydrolase family 3 (GH3) are industrially important enzymes, which convert cellooligosaccharides into glucose; the end product of the cellulolytic process. They are highly active against the β-1,4 glycosidic bond in soluble substrates but typically reported to be inactive against insoluble cellulose. RESULTS We studied the activity of four fungal GH3 BGs on cellulose and found significant activity. At low temperatures (10 ℃), we derived the approximate kinetic parameters k cat = 0.3 ± 0.1 s-1 and K M = 80 ± 30 g/l for a BG from Aspergillus fumigatus (AfBG) acting on Avicel. Interestingly, this maximal turnover is higher than reported values for typical cellobiohydrolases (CBH) at this temperature and comparable to those of endoglucanases (EG). The specificity constant of AfGB on Avicel was only moderately lowered compared to values for EGs and CBHs. CONCLUSIONS Overall these observations suggest a significant promiscuous side activity of the investigated GH3 BGs on insoluble cellulose. This challenges the traditional definition of a BG and supports suggestions that functional classes of cellulolytic enzymes may represent a continuum of overlapping modes of action.
Collapse
Affiliation(s)
- Malene B. Keller
- Department of Geosciences and Natural Resource Management, University of Copenhagen, 23 Rolighedsvej, 1958 Frederiksberg, Denmark
- Department of Science and Environment, Roskilde University, 1 Universitetsvej, 4000 Roskilde, Denmark
| | - Trine H. Sørensen
- Department of Science and Environment, Roskilde University, 1 Universitetsvej, 4000 Roskilde, Denmark
- Novozymes A/S, 2 Biologiens Vej, 2800 Kgs. Lyngby, Denmark
| | | | - Mark Wogulis
- Novozymes Ltd, 1445 Drew Ave, Davis, CA 95618 USA
| | - Kim Borch
- Novozymes A/S, 2 Biologiens Vej, 2800 Kgs. Lyngby, Denmark
| | - Peter Westh
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 221 Søltofts Plads, 2800 Kgs. Lyngby, Denmark
| |
Collapse
|
22
|
Monteiro LMO, Vici AC, Pinheiro MP, Heinen PR, de Oliveira AHC, Ward RJ, Prade RA, Buckeridge MS, Polizeli MDLTDM. A Highly Glucose Tolerant ß-Glucosidase from Malbranchea pulchella (MpBg3) Enables Cellulose Saccharification. Sci Rep 2020; 10:6998. [PMID: 32332833 PMCID: PMC7181827 DOI: 10.1038/s41598-020-63972-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 03/13/2020] [Indexed: 02/07/2023] Open
Abstract
β-glucosidases catalyze the hydrolysis β-1,4, β-1,3 and β-1,6 glucosidic linkages from non-reducing end of short chain oligosaccharides, alkyl and aryl β-D-glucosides and disaccharides. They catalyze the rate-limiting reaction in the conversion of cellobiose to glucose in the saccharification of cellulose for second-generation ethanol production, and due to this important role the search for glucose tolerant enzymes is of biochemical and biotechnological importance. In this study we characterize a family 3 glycosyl hydrolase (GH3) β-glucosidase (Bgl) produced by Malbranchea pulchella (MpBgl3) grown on cellobiose as the sole carbon source. Kinetic characterization revealed that the MpBgl3 was highly tolerant to glucose, which is in contrast to many Bgls that are completely inhibited by glucose. A 3D model of MpBgl3 was generated by molecular modeling and used for the evaluation of structural differences with a Bgl3 that is inhibited by glucose. Taken together, our results provide new clues to understand the glucose tolerance in GH3 β-glucosidases.
Collapse
Affiliation(s)
- Lummy Maria Oliveira Monteiro
- Faculdade de Medicina de Ribeirão Preto. Universidade de São Paulo. Bandeirantes Av., 3.900, 14049-900, Ribeirão Preto, SP, Brazil
| | - Ana Claudia Vici
- Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto. Universidade de São Paulo. Bandeirantes Av., 3.900, 14040-901, Ribeirão Preto, SP, Brazil
| | - Matheus Pinto Pinheiro
- Laboratório Nacional de Biociência (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP, Brazil
| | - Paulo Ricardo Heinen
- Faculdade de Medicina de Ribeirão Preto. Universidade de São Paulo. Bandeirantes Av., 3.900, 14049-900, Ribeirão Preto, SP, Brazil
| | | | - Richard John Ward
- Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto. Universidade de São Paulo. Bandeirantes Av., 3.900, 14040-901, Ribeirão Preto, SP, Brazil
| | - Rolf Alexander Prade
- Department of Microbiology and Molecular Genetics. Oklahoma State University, Stillwater, USA
| | - Marcos S Buckeridge
- Instituto de Biociências, Universidade de São Paulo. Matão Street, 277, 05508-090, São Paulo, SP, Brazil
| | - Maria de Lourdes Teixeira de Moraes Polizeli
- Faculdade de Medicina de Ribeirão Preto. Universidade de São Paulo. Bandeirantes Av., 3.900, 14049-900, Ribeirão Preto, SP, Brazil. .,Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto. Universidade de São Paulo. Bandeirantes Av., 3.900, 14040-901, Ribeirão Preto, SP, Brazil.
| |
Collapse
|
23
|
Characterization and diversity of the complete set of GH family 3 enzymes from Rhodothermus marinus DSM 4253. Sci Rep 2020; 10:1329. [PMID: 31992772 PMCID: PMC6987092 DOI: 10.1038/s41598-020-58015-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 01/07/2020] [Indexed: 11/08/2022] Open
Abstract
The genome of Rhodothermus marinus DSM 4253 encodes six glycoside hydrolases (GH) classified under GH family 3 (GH3): RmBgl3A, RmBgl3B, RmBgl3C, RmXyl3A, RmXyl3B and RmNag3. The biochemical function, modelled 3D-structure, gene cluster and evolutionary relationships of each of these enzymes were studied. The six enzymes were clustered into three major evolutionary lineages of GH3: β-N-acetyl-glucosaminidases, β-1,4-glucosidases/β-xylosidases and macrolide β-glucosidases. The RmNag3 with additional β-lactamase domain clustered with the deepest rooted GH3-lineage of β-N-acetyl-glucosaminidases and was active on acetyl-chitooligosaccharides. RmBgl3B displayed β-1,4-glucosidase activity and was the only representative of the lineage clustered with macrolide β-glucosidases from Actinomycetes. The β-xylosidases, RmXyl3A and RmXyl3B, and the β-glucosidases RmBgl3A and RmBgl3C clustered within the major β-glucosidases/β-xylosidases evolutionary lineage. RmXyl3A and RmXyl3B showed β-xylosidase activity with different specificities for para-nitrophenyl (pNP)-linked substrates and xylooligosaccharides. RmBgl3A displayed β-1,4-glucosidase/β-xylosidase activity while RmBgl3C was active on pNP-β-Glc and β-1,3-1,4-linked glucosyl disaccharides. Putative polysaccharide utilization gene clusters were also investigated for both R. marinus DSM 4253 and DSM 4252T (homolog strain). The analysis showed that in the homolog strain DSM 4252TRmar_1080 (RmXyl3A) and Rmar_1081 (RmXyl3B) are parts of a putative polysaccharide utilization locus (PUL) for xylan utilization.
Collapse
|
24
|
Structures of β-glycosidase LXYL-P1-2 reveals the product binding state of GH3 family and a specific pocket for Taxol recognition. Commun Biol 2020; 3:22. [PMID: 31925310 PMCID: PMC6954215 DOI: 10.1038/s42003-019-0744-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 12/16/2019] [Indexed: 11/08/2022] Open
Abstract
LXYL-P1-2 is one of the few xylosidases that efficiently catalyze the reaction from 7-β-xylosyl-10-deacetyltaxol (XDT) to 10-deacetyltaxol (DT), and is a potential enzyme used in Taxol industrial production. Here we report the crystal structure of LXYL-P1-2 and its XDT binding complex. These structures reveal an enzyme/product complex with the sugar conformation different from the enzyme/substrate complex reported previously in GH3 enzymes, even in the whole glycohydrolases family. In addition, the DT binding pocket is identified as the structural basis for the substrate specificity. Further structure analysis reveals common features in LXYL-P1-2 and Taxol binding protein tubulin, which might provide useful information for designing new Taxol carrier proteins for drug delivery.
Collapse
|
25
|
Crystal Structure of a GH3 β-Glucosidase from the Thermophilic Fungus Chaetomium thermophilum. Int J Mol Sci 2019; 20:ijms20235962. [PMID: 31783503 PMCID: PMC6929035 DOI: 10.3390/ijms20235962] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/20/2019] [Accepted: 11/25/2019] [Indexed: 11/17/2022] Open
Abstract
Beta-glucosidases (β-glucosidases) have attracted considerable attention in recent years for use in various biotechnological applications. They are also essential enzymes for lignocellulose degradation in biofuel production. However, cost-effective biomass conversion requires the use of highly efficient enzymes. Thus, the search for new enzymes as better alternatives of the currently available enzyme preparations is highly important. Thermophilic fungi are nowadays considered as a promising source of enzymes with improved stability. Here, the crystal structure of a family GH3 β-glucosidase from the thermophilic fungus Chaetomium thermophilum (CtBGL) was determined at a resolution of 2.99 Å. The structure showed the three-domain architecture found in other β-glucosidases with variations in loops and linker regions. The active site catalytic residues in CtBGL were identified as Asp287 (nucleophile) and Glu517 (acid/base). Structural comparison of CtBGL with Protein Data Bank (PDB)-deposited structures revealed variations among glycosylated Asn residues. The enzyme displayed moderate glycosylation compared to other GH3 family β-glucosidases with similar structure. A new glycosylation site at position Asn504 was identified in CtBGL. Moreover, comparison with respect to several thermostability parameters suggested that glycosylation and charged residues involved in electrostatic interactions may contribute to the stability of the enzyme at elevated temperatures. The reported CtBGL structure provides additional insights into the family GH3 enzymes and could offer new ideas for further improvements in β-glucosidases for more efficient use in biotechnological applications regarding cellulose degradation.
Collapse
|
26
|
Weiz G, Mazzaferro LS, Kotik M, Neher BD, Halada P, Křen V, Breccia JD. The flavonoid degrading fungus Acremonium sp. DSM 24697 produces two diglycosidases with different specificities. Appl Microbiol Biotechnol 2019; 103:9493-9504. [PMID: 31705182 DOI: 10.1007/s00253-019-10180-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 09/30/2019] [Accepted: 10/09/2019] [Indexed: 01/01/2023]
Abstract
AbstractDiglycosidases hydrolyze the heterosidic linkage of diglycoconjugates, releasing the disaccharide and the aglycone. Usually, these enzymes do not hydrolyze or present only low activities towards monoglycosylated compounds. The flavonoid degrading fungus Acremonium sp. DSM 24697 produced two diglycosidases, which were termed 6-O-α-rhamnosyl-β-glucosidase I and II (αRβG I and II) because of their function of releasing the disaccharide rutinose (6-O-α-L-rhamnosyl-β-D-glucose) from the diglycoconjugates hesperidin or rutin. In this work, the genome of Acremonium sp. DSM 24697 was sequenced and assembled with a size of ~ 27 Mb. The genes encoding αRβG I and II were expressed in Pichia pastoris KM71 and the protein products were purified with apparent molecular masses of 42 and 82 kDa, respectively. A phylogenetic analysis showed that αRβG I grouped in glycoside hydrolase family 5, subfamily 23 (GH5), together with other fungal diglycosidases whose substrate specificities had been reported to be different from αRβG I. On the other hand, αRβG II grouped in glycoside hydrolase family 3 (GH3) and thus is the first GH3 member that hydrolyzes the heterosidic linkage of rutinosylated compounds. The substrate scopes of the enzymes were different: αRβG I showed exclusive specificity toward 7-O-β-rutinosyl flavonoids, whereas αRβG II hydrolyzed both 7-O-β-rutinosyl- and 3-O-β-rutinosyl- flavonoids. None of the enzymes displayed activity toward 7-O-β-neohesperidosyl- flavonoids. The recombinant enzymes also exhibited transglycosylation activities, transferring rutinose from hesperidin or rutin onto various alcoholic acceptors. The different substrate scopes of αRβG I and II may be part of an optimized strategy of the original microorganism to utilize different carbon sources.
Collapse
Affiliation(s)
- Gisela Weiz
- Facultad de Ciencias Exactas y Naturales, Instituto de Ciencias de la Tierra y Ambientales de La Pampa (INCITAP), Universidad Nacional de La Pampa - Consejo Nacional de Investigaciones Científicas y Técnicas (UNLPam-CONICET), Av. Uruguay 151, 6300, Santa Rosa, La Pampa, Argentina
| | - Laura S Mazzaferro
- Facultad de Ciencias Exactas y Naturales, Instituto de Ciencias de la Tierra y Ambientales de La Pampa (INCITAP), Universidad Nacional de La Pampa - Consejo Nacional de Investigaciones Científicas y Técnicas (UNLPam-CONICET), Av. Uruguay 151, 6300, Santa Rosa, La Pampa, Argentina
| | - Michael Kotik
- Laboratory of Biotransformation, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czech Republic
| | - Bárbara D Neher
- Facultad de Ciencias Exactas y Naturales, Instituto de Ciencias de la Tierra y Ambientales de La Pampa (INCITAP), Universidad Nacional de La Pampa - Consejo Nacional de Investigaciones Científicas y Técnicas (UNLPam-CONICET), Av. Uruguay 151, 6300, Santa Rosa, La Pampa, Argentina
| | - Petr Halada
- Laboratory of Molecular Structure Characterization, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czech Republic
| | - Vladimír Křen
- Laboratory of Biotransformation, Institute of Microbiology, Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czech Republic
| | - Javier D Breccia
- Facultad de Ciencias Exactas y Naturales, Instituto de Ciencias de la Tierra y Ambientales de La Pampa (INCITAP), Universidad Nacional de La Pampa - Consejo Nacional de Investigaciones Científicas y Técnicas (UNLPam-CONICET), Av. Uruguay 151, 6300, Santa Rosa, La Pampa, Argentina.
| |
Collapse
|
27
|
β-Xylosidases: Structural Diversity, Catalytic Mechanism, and Inhibition by Monosaccharides. Int J Mol Sci 2019; 20:ijms20225524. [PMID: 31698702 PMCID: PMC6887791 DOI: 10.3390/ijms20225524] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/02/2019] [Accepted: 11/04/2019] [Indexed: 12/20/2022] Open
Abstract
Xylan, a prominent component of cellulosic biomass, has a high potential for degradation into reducing sugars, and subsequent conversion into bioethanol. This process requires a range of xylanolytic enzymes. Among them, β-xylosidases are crucial, because they hydrolyze more glycosidic bonds than any of the other xylanolytic enzymes. They also enhance the efficiency of the process by degrading xylooligosaccharides, which are potent inhibitors of other hemicellulose-/xylan-converting enzymes. On the other hand, the β-xylosidase itself is also inhibited by monosaccharides that may be generated in high concentrations during the saccharification process. Structurally, β-xylosidases are diverse enzymes with different substrate specificities and enzyme mechanisms. Here, we review the structural diversity and catalytic mechanisms of β-xylosidases, and discuss their inhibition by monosaccharides.
Collapse
|
28
|
Rudakiya DM, Patel SH, Narra M. Structural insight into the fungal β-glucosidases and their interactions with organics. Int J Biol Macromol 2019; 138:1019-1028. [PMID: 31356936 DOI: 10.1016/j.ijbiomac.2019.07.177] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/20/2019] [Accepted: 07/25/2019] [Indexed: 11/30/2022]
Abstract
Fungal β-glucosidases (BGLs) have unceasingly utilized for industrial applications and recently, they possess a crucial role in bioethanol production. To engineer the BGLs, understanding their structures, intermolecular interactions and molecular docking is requisite, which is carried out in this work based on the glycosyl hydrolase (GH) family. Among 12 BGLs, protein sequence, structure, and conserved sites of GH1 BGLs are evidently diverged to GH3 BGLs. Even biophysical and chemical features of GH1 BGLs are utterly varied from GH3 BGLs, wherein pI, instability index, aliphatic index, surface & buried area, thermostability and thermodynamics are included. On the contrary, aromatic, charged, polar, and hydrophobic residues are significantly higher in GH1 BGLs as compared to that of GH3 BGLs. Moreover, molecular docking of BGLs with 12 substrates and 5 inhibitors revealed that the GH3 BGLs efficiently bound with laminaribose, gentibiose, aryl- and cello-substrates than GH1 BGLs; however, GH3 BGLs are noticeably inhibited by glucose, glucono-δ-lactone, methanetriamine. So, structural insight of BGLs provides an explicit knowledge regarding the catalytic residues, biophysical chemistry and notable binding ligands, which are most important factors for enzyme engineering.
Collapse
Affiliation(s)
- Darshan M Rudakiya
- Bioconversion Technology Division, Sardar Patel Renewable Energy Research Institute, Vallabh Vidyanagar, Anand, Gujarat, India.
| | - Shriram H Patel
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Madhuri Narra
- Bioconversion Technology Division, Sardar Patel Renewable Energy Research Institute, Vallabh Vidyanagar, Anand, Gujarat, India.
| |
Collapse
|
29
|
Molecular Dynamics Gives New Insights into the Glucose Tolerance and Inhibition Mechanisms on β-Glucosidases. Molecules 2019; 24:molecules24183215. [PMID: 31487855 PMCID: PMC6766793 DOI: 10.3390/molecules24183215] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/15/2019] [Accepted: 08/23/2019] [Indexed: 12/23/2022] Open
Abstract
β-Glucosidases are enzymes with high importance for many industrial processes, catalyzing the last and limiting step of the conversion of lignocellulosic material into fermentable sugars for biofuel production. However, β-glucosidases are inhibited by high concentrations of the product (glucose), which limits the biofuel production on an industrial scale. For this reason, the structural mechanisms of tolerance to product inhibition have been the target of several studies. In this study, we performed in silico experiments, such as molecular dynamics (MD) simulations, free energy landscape (FEL) estimate, Poisson-Boltzmann surface area (PBSA), and grid inhomogeneous solvation theory (GIST) seeking a better understanding of the glucose tolerance and inhibition mechanisms of a representative GH1 β-glucosidase and a GH3 one. Our results suggest that the hydrophobic residues Y180, W350, and F349, as well the polar one D238 act in a mechanism for glucose releasing, herein called "slingshot mechanism", dependent also on an allosteric channel (AC). In addition, water activity modulation and the protein loop motions suggest that GH1 β-Glucosidases present an active site more adapted to glucose withdrawal than GH3, in consonance with the GH1s lower product inhibition. The results presented here provide directions on the understanding of the molecular mechanisms governing inhibition and tolerance to the product in β-glucosidases and can be useful for the rational design of optimized enzymes for industrial interests.
Collapse
|
30
|
Song X, Li Y, Wu Y, Cai M, Liu Q, Gao K, Zhang X, Bai Y, Xu H, Qiao M. Metabolic engineering strategies for improvement of ethanol production in cellulolytic Saccharomyces cerevisiae. FEMS Yeast Res 2019; 18:5071949. [PMID: 30107496 DOI: 10.1093/femsyr/foy090] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/09/2018] [Indexed: 01/31/2023] Open
Abstract
As a traditional ethanol-producing microorganism, Saccharomyces cerevisiae is an ideal host for consolidated bioprocessing. However, expression of heterologous cellulase increases the metabolic burden in yeast, which results in low cellulase activity and poor cellulose degradation efficiency. In this study, cellulase-expressing yeast strains that could efficiently degrade different cellulosic substrates were created by optimizing cellulase ratios through a POT1-mediated δ-integration strategy. Metabolic engineering strategies, including optimization of codon usage, promoter and signal peptide, were also included in this system. We also confirmed that heterologous cellulase expression in cellulosic yeast induced the unfolded protein response. To enhance protein folding capacity, the endoplasmic reticulum chaperone protein BiP and the disulfide isomerase Pdi1p were overexpressed, and the Golgi membrane protein Ca2+/Mn2+ ATPase Pmr1p was disrupted to decrease the glycosylation of cellulase. The resultant strain, SK18-3, could produce 5.4 g L-1 ethanol with carboxymethyl-cellulose. Strain SK12-50 achieved 4.7 g L-1 ethanol production with phosphoric acid swollen cellulose hydrolysis. When Avicel was used as the substrate, 3.8 g L-1 ethanol (75% of the theoretical maximum yield) was produced in SK13-34. This work will significantly increase our knowledge of how to engineer optimal yeast strains for biofuel production from cellulosic biomass.
Collapse
Affiliation(s)
- Xiaofei Song
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, China
| | - Yuanzi Li
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, China
| | - Yuzhen Wu
- Department of Microbiology, College of Life Sciences, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, China
| | - Miao Cai
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, China
| | - Quanli Liu
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, China
| | - Kai Gao
- Tianjin Academy of Environmental Sciences, No. 17 Fukang Road, Nankai District, Tianjin 300071, China
| | - Xiuming Zhang
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, China
| | - Yanling Bai
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, China
| | - Haijin Xu
- Department of Microbiology, College of Life Sciences, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, China
| | - Mingqiang Qiao
- The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, No. 94 Weijin Road, Nankai District, Tianjin 300071, China
| |
Collapse
|
31
|
Discovery of processive catalysis by an exo-hydrolase with a pocket-shaped active site. Nat Commun 2019; 10:2222. [PMID: 31110237 PMCID: PMC6527550 DOI: 10.1038/s41467-019-09691-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 03/22/2019] [Indexed: 11/08/2022] Open
Abstract
Substrates associate and products dissociate from enzyme catalytic sites rapidly, which hampers investigations of their trajectories. The high-resolution structure of the native Hordeum exo-hydrolase HvExoI isolated from seedlings reveals that non-covalently trapped glucose forms a stable enzyme-product complex. Here, we report that the alkyl β-d-glucoside and methyl 6-thio-β-gentiobioside substrate analogues perfused in crystalline HvExoI bind across the catalytic site after they displace glucose, while methyl 2-thio-β-sophoroside attaches nearby. Structural analyses and multi-scale molecular modelling of nanoscale reactant movements in HvExoI reveal that upon productive binding of incoming substrates, the glucose product modifies its binding patterns and evokes the formation of a transient lateral cavity, which serves as a conduit for glucose departure to allow for the next catalytic round. This path enables substrate-product assisted processive catalysis through multiple hydrolytic events without HvExoI losing contact with oligo- or polymeric substrates. We anticipate that such enzyme plasticity could be prevalent among exo-hydrolases. Enzyme substrates and products often diffuse too rapidly to assess the catalytic implications of these movements. Here, the authors characterise the structural basis of product and substrate diffusion for an exo-hydrolase and discover a substrate-product assisted processive catalytic mechanism.
Collapse
|
32
|
Andrades DD, Graebin NG, Ayub MA, Fernandez-Lafuente R, Rodrigues RC. Physico-chemical properties, kinetic parameters, and glucose inhibition of several beta-glucosidases for industrial applications. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.01.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
33
|
Geronimo I, Ntarima P, Piens K, Gudmundsson M, Hansson H, Sandgren M, Payne CM. Kinetic and molecular dynamics study of inhibition and transglycosylation in Hypocrea jecorina family 3 β-glucosidases. J Biol Chem 2019; 294:3169-3180. [PMID: 30602567 DOI: 10.1074/jbc.ra118.007027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Indexed: 01/09/2023] Open
Abstract
β-Glucosidases enhance enzymatic biomass conversion by relieving cellobiose inhibition of endoglucanases and cellobiohydrolases. However, the susceptibility of these enzymes to inhibition and transglycosylation at high glucose or cellobiose concentrations severely limits their activity and, consequently, the overall efficiency of enzyme mixtures. We determined the impact of these two processes on the hydrolytic activity of the industrially relevant family 3 β-glucosidases from Hypocrea jecorina, HjCel3A and HjCel3B, and investigated the underlying molecular mechanisms through kinetic studies, binding free energy calculations, and molecular dynamics (MD) simulations. HjCel3B had a 7-fold higher specificity for cellobiose than HjCel3A but greater tendency for glucose inhibition. Energy decomposition analysis indicated that cellobiose has relatively weak electrostatic interactions with binding site residues, allowing it to be easily displaced by glucose and free to inhibit other hydrolytic enzymes. HjCel3A is, thus, preferable as an industrial β-glucosidase despite its lower activity caused by transglycosylation. This competing pathway to hydrolysis arises from binding of glucose or cellobiose at the product site after formation of the glycosyl-enzyme intermediate. MD simulations revealed that binding is facilitated by hydrophobic interactions with Trp-37, Phe-260, and Tyr-443. Targeting these aromatic residues for mutation to reduce substrate affinity at the product site would therefore potentially mitigate transglycosidic activity. Engineering improved variants of HjCel3A and other structurally similar β-glucosidases would have a significant economic effect on enzymatic biomass conversion in terms of yield and production cost as the process can be consequently conducted at higher substrate loadings.
Collapse
Affiliation(s)
- Inacrist Geronimo
- From the Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506-0046
| | - Patricia Ntarima
- the Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium, and
| | - Kathleen Piens
- the Department of Biochemistry and Microbiology, Ghent University, Ghent 9000, Belgium, and
| | - Mikael Gudmundsson
- the Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, 750 07 Uppsala, Sweden
| | - Henrik Hansson
- the Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, 750 07 Uppsala, Sweden
| | - Mats Sandgren
- the Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, 750 07 Uppsala, Sweden
| | - Christina M Payne
- From the Department of Chemical and Materials Engineering, University of Kentucky, Lexington, Kentucky 40506-0046, .,the Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, 750 07 Uppsala, Sweden
| |
Collapse
|
34
|
Kao MR, Kuo HW, Lee CC, Huang KY, Huang TY, Li CW, Chen CW, Wang AHJ, Yu SM, Ho THD. Chaetomella raphigera β-glucosidase D2-BGL has intriguing structural features and a high substrate affinity that renders it an efficient cellulase supplement for lignocellulosic biomass hydrolysis. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:258. [PMID: 31700541 PMCID: PMC6825360 DOI: 10.1186/s13068-019-1599-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 10/22/2019] [Indexed: 05/17/2023]
Abstract
BACKGROUND To produce second-generation biofuels, enzymatic catalysis is required to convert cellulose from lignocellulosic biomass into fermentable sugars. β-Glucosidases finalize the process by hydrolyzing cellobiose into glucose, so the efficiency of cellulose hydrolysis largely depends on the quantity and quality of these enzymes used during saccharification. Accordingly, to reduce biofuel production costs, new microbial strains are needed that can produce highly efficient enzymes on a large scale. RESULTS We heterologously expressed the fungal β-glucosidase D2-BGL from a Taiwanese indigenous fungus Chaetomella raphigera in Pichia pastoris for constitutive production by fermentation. Recombinant D2-BGL presented significantly higher substrate affinity than the commercial β-glucosidase Novozyme 188 (N188; K m = 0.2 vs 2.14 mM for p-nitrophenyl β-d-glucopyranoside and 0.96 vs 2.38 mM for cellobiose). When combined with RUT-C30 cellulases, it hydrolyzed acid-pretreated lignocellulosic biomasses more efficiently than the commercial cellulase mixture CTec3. The extent of conversion from cellulose to glucose was 83% for sugarcane bagasse and 63% for rice straws. Compared to N188, use of D2-BGL halved the time necessary to produce maximal levels of ethanol by a semi-simultaneous saccharification and fermentation process. We upscaled production of recombinant D2-BGL to 33.6 U/mL within 15 days using a 1-ton bioreactor. Crystal structure analysis revealed that D2-BGL belongs to glycoside hydrolase (GH) family 3. Removing the N-glycosylation N68 or O-glycosylation T431 residues by site-directed mutagenesis negatively affected enzyme production in P. pastoris. The F256 substrate-binding residue in D2-BGL is located in a shorter loop surrounding the active site pocket relative to that of Aspergillus β-glucosidases, and this short loop is responsible for its high substrate affinity toward cellobiose. CONCLUSIONS D2-BGL is an efficient supplement for lignocellulosic biomass saccharification, and we upscaled production of this enzyme using a 1-ton bioreactor. Enzyme production could be further improved using optimized fermentation, which could reduce biofuel production costs. Our structure analysis of D2-BGL offers new insights into GH3 β-glucosidases, which will be useful for strain improvements via a structure-based mutagenesis approach.
Collapse
Affiliation(s)
- Mu-Rong Kao
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and National Defense Medical Center, Taipei, Taiwan, ROC
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - Hsion-Wen Kuo
- Department of Environmental Science and Engineering, Tunghai University, Taichung, Taiwan, ROC
| | - Cheng-Chung Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan, ROC
| | - Kuan-Ying Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - Ting-Yen Huang
- Department of Bioengineering, Tatung University, Taipei, Taiwan, ROC
| | - Chen-Wei Li
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - C. Will Chen
- Department of Bioengineering, Tatung University, Taipei, Taiwan, ROC
| | | | - Su-May Yu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC
- Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Tuan-Hua David Ho
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, ROC
- Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC
| |
Collapse
|
35
|
Karkehabadi S, Hansson H, Mikkelsen NE, Kim S, Kaper T, Sandgren M, Gudmundsson M. Structural studies of a glycoside hydrolase family 3 β-glucosidase from the model fungus Neurospora crassa. Acta Crystallogr F Struct Biol Commun 2018; 74:787-796. [PMID: 30511673 PMCID: PMC6277957 DOI: 10.1107/s2053230x18015662] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 11/05/2018] [Indexed: 11/29/2022] Open
Abstract
The glycoside hydrolase family 3 (GH3) β-glucosidases are a structurally diverse family of enzymes. Cel3A from Neurospora crassa (NcCel3A) belongs to a subfamily of key enzymes that are crucial for industrial biomass degradation. β-Glucosidases hydrolyse the β-1,4 bond at the nonreducing end of cellodextrins. The hydrolysis of cellobiose is of special importance as its accumulation inhibits other cellulases acting on crystalline cellulose. Here, the crystal structure of the biologically relevant dimeric form of NcCel3A is reported. The structure has been refined to 2.25 Å resolution, with an Rcryst and Rfree of 0.18 and 0.22, respectively. NcCel3A is an extensively N-glycosylated glycoprotein that shares 46% sequence identity with Hypocrea jecorina Cel3A, the structure of which has recently been published, and 61% sequence identity with the thermophilic β-glucosidase from Rasamsonia emersonii. NcCel3A is a three-domain protein with a number of extended loops that deepen the active-site cleft of the enzyme. These structures characterize this subfamily of GH3 β-glucosidases and account for the high cellobiose specificity of this subfamily.
Collapse
Affiliation(s)
- Saeid Karkehabadi
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
| | - Henrik Hansson
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
| | - Nils Egil Mikkelsen
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
| | - Steve Kim
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, CA 94304, USA
| | - Thijs Kaper
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, CA 94304, USA
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
| | - Mikael Gudmundsson
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07 Uppsala, Sweden
| |
Collapse
|
36
|
Alves LDF, Meleiro LP, Silva RN, Westmann CA, Guazzaroni ME. Novel Ethanol- and 5-Hydroxymethyl Furfural-Stimulated β-Glucosidase Retrieved From a Brazilian Secondary Atlantic Forest Soil Metagenome. Front Microbiol 2018; 9:2556. [PMID: 30420843 PMCID: PMC6215845 DOI: 10.3389/fmicb.2018.02556] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 10/08/2018] [Indexed: 11/13/2022] Open
Abstract
Beta-glucosidases are key enzymes involved in lignocellulosic biomass degradation for bioethanol production, which complete the final step during cellulose hydrolysis by converting cellobiose into glucose. Currently, industry requires enzymes with improved catalytic performance or tolerance to process-specific parameters. In this sense, metagenomics has become a powerful tool for accessing and exploring the biochemical biodiversity present in different natural environments. Here, we report the identification of a novel β-glucosidase from metagenomic DNA isolated from soil samples enriched with decaying plant matter from a Secondary Atlantic Forest region. For this, we employed a functional screening approach using an optimized and synthetic broad host-range vector for library production. The novel β-glucosidase – named Lfa2 – displays three GH3-family conserved domains and conserved catalytic amino acids D283 and E487. The purified enzyme was most active in pH 5.5 and at 50°C, and showed hydrolytic activity toward several pNP synthetic substrates containing β-glucose, β-galactose, β-xylose, β-fucose, and α-arabinopyranose, as well as toward cellobiose. Lfa2 showed considerable glucose tolerance, exhibiting an IC50 of 300 mM glucose and 30% of remaining activity in 600 mM glucose. In addition, Lfa2 retained full or slightly enhanced activity in the presence of several metal ions. Further, β-glucosidase activity was increased by 1.7-fold in the presence of 10% (v/v) ethanol, a concentration that can be reached in conventional fermentation processes. Similarly, Lfa2 showed 1.7-fold enhanced activity at high concentrations of 5-hydroxymethyl furfural, one of the most important cellulase inhibitors in pretreated sugarcane bagasse hydrolysates. Moreover, the synergistic effect of Lfa2 on Bacillus subtilis GH5-CBM3 endoglucanase activity was demonstrated by the increased production of glucose (1.6-fold). Together, these results indicate that β-glucosidase Lfa2 is a promissory enzyme candidate for utilization in diverse industrial applications, such as cellulosic biomass degradation or flavor enhancement in winemaking and grape processing.
Collapse
Affiliation(s)
- Luana de Fátima Alves
- Department of Biochemistry and Immunology, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Luana Parras Meleiro
- Department of Chemistry, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Roberto N Silva
- Department of Biochemistry and Immunology, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - Cauã Antunes Westmann
- Department of Cellular and Molecular Biology, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| | - María-Eugenia Guazzaroni
- Department of Biology, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
| |
Collapse
|
37
|
Torabizadeh H, Mikani M. Nano-magnetic cross-linked enzyme aggregates of naringinase an efficient nanobiocatalyst for naringin hydrolysis. Int J Biol Macromol 2018; 117:134-143. [DOI: 10.1016/j.ijbiomac.2018.05.162] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 05/15/2018] [Accepted: 05/22/2018] [Indexed: 12/18/2022]
|
38
|
An acid-stable β-glucosidase from Aspergillus aculeatus: Gene expression, biochemical characterization and molecular dynamics simulation. Int J Biol Macromol 2018; 119:462-469. [PMID: 30063929 DOI: 10.1016/j.ijbiomac.2018.07.165] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 07/17/2018] [Accepted: 07/26/2018] [Indexed: 11/23/2022]
Abstract
β-Glucosidases hydrolyze terminal, non-reducing β-d-glucosyl residues and thereby release β-d-glucose. They have applications in the production of biofuels, beverages and pharmaceuticals. In this study, a β-glucosidase derived from Aspergillus aculeatus (BGLA) was expressed, characterized, and the molecular mechanism of its acid denaturation was comprehensively probed. BGLA exhibited maximal activity at pH 5.0-6.0. Its optimal temperature was 70 °C. Its enzyme activity was enhanced by Mg2+, Ca2+ and Ba2+, while Cu2+, Mn2+, Zn2+, Fe2+ and Fe3+ had a negative effect. BGLA showed activity on a broad range of substrates including salicin, cellobiose, arbutin, geniposide and polydatin. Finally, the acid-denaturation mechanism of BGLA was probed using molecular dynamics (MD) simulations. The results of simulation at pH 2.0 imply that the contact number, solvent accessible surface area and number of hydrogen bonds in BGLA decreased greatly. Moreover, the distance between the residues Asp280 and Glu509 that are part of the active site increased, which eventually destroyed the enzyme's catalytic activity. These MD results explain the molecular mechanism of acid denaturation of BGLA, which will greatly benefit the rational design of more acid-stable β-glucosidase variants in the future.
Collapse
|
39
|
Structural and biochemical characterization of a GH3 β-glucosidase from the probiotic bacteria Bifidobacterium adolescentis. Biochimie 2018; 148:107-115. [DOI: 10.1016/j.biochi.2018.03.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 03/13/2018] [Indexed: 11/20/2022]
|
40
|
Liu JY, Chang MC, Meng JL, Feng CP, Zhao H, Zhang ML. Comparative Proteome Reveals Metabolic Changes during the Fruiting Process in Flammulina velutipes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:5091-5100. [PMID: 28570075 DOI: 10.1021/acs.jafc.7b01120] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Understanding the molecular mechanisms regulating the fruiting process in macro-fungi, especially industrially cultivated mushrooms, has long been a goal in mycological research. To gain insights into the events accompanying the transformation of mycelia into fruit-bodies in Flammulina velutipes, proteins expressed characteristically and abundantly at primordium and fruit-body stages were investigated by using the iTRAQ labeling technique. Among the 171 differentially expressed proteins, a total of 68 displayed up-regulated expression levels that were associated with 84 specific KEGG pathways. Some up-regulated proteins, such as pyruvate carboxylase, aldehyde dehydrogenase, fatty acid synthase, aspartate aminotransferase, 2-cysteine peroxiredoxin, FDS protein, translation elongation factor 1-alpha, mitogen-activated protein kinases (MAPKs), and heat-shock protein 70 that are involved in carbohydrate metabolism, carotenoid formation, the TCA cycle, MAPK signaling pathway, and the biosynthesis of fatty acids and branched-chain amino acids, could serve as potential stage-specific biomarkers to study the fruiting process in F. velutipes. Knowledge of the proteins might provide valuable evidence to better understand the molecular mechanisms of fruit-body initiation and development in basidiomycete fungi. Furthermore, this study also offers valuable evidence for yield improvement and quality control of super golden-needle mushroom in practice.
Collapse
Affiliation(s)
- Jing-Yu Liu
- College of Food Science and Engineering, Shanxi Agricultural University , Taigu 030801, China
- Shanxi Engineering Research Center of Edible Fungi , Taigu 030801, China
| | - Ming-Chang Chang
- College of Food Science and Engineering, Shanxi Agricultural University , Taigu 030801, China
- Shanxi Engineering Research Center of Edible Fungi , Taigu 030801, China
| | - Jun-Long Meng
- College of Food Science and Engineering, Shanxi Agricultural University , Taigu 030801, China
- Shanxi Engineering Research Center of Edible Fungi , Taigu 030801, China
| | - Cui-Ping Feng
- College of Food Science and Engineering, Shanxi Agricultural University , Taigu 030801, China
- Shanxi Engineering Research Center of Edible Fungi , Taigu 030801, China
| | - Hui Zhao
- College of Food Science and Engineering, Shanxi Agricultural University , Taigu 030801, China
| | - Ming-Liang Zhang
- College of Food Science and Engineering, Shanxi Agricultural University , Taigu 030801, China
| |
Collapse
|
41
|
Agirre J. Strategies for carbohydrate model building, refinement and validation. Acta Crystallogr D Struct Biol 2017; 73:171-186. [PMID: 28177313 PMCID: PMC5297920 DOI: 10.1107/s2059798316016910] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/21/2016] [Indexed: 12/19/2022] Open
Abstract
Sugars are the most stereochemically intricate family of biomolecules and present substantial challenges to anyone trying to understand their nomenclature, reactions or branched structures. Current crystallographic programs provide an abstraction layer allowing inexpert structural biologists to build complete protein or nucleic acid model components automatically either from scratch or with little manual intervention. This is, however, still not generally true for sugars. The need for carbohydrate-specific building and validation tools has been highlighted a number of times in the past, concomitantly with the introduction of a new generation of experimental methods that have been ramping up the production of protein-sugar complexes and glycoproteins for the past decade. While some incipient advances have been made to address these demands, correctly modelling and refining carbohydrates remains a challenge. This article will address many of the typical difficulties that a structural biologist may face when dealing with carbohydrates, with an emphasis on problem solving in the resolution range where X-ray crystallography and cryo-electron microscopy are expected to overlap in the next decade.
Collapse
Affiliation(s)
- Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, England
| |
Collapse
|
42
|
Méndez-Líter JA, Gil-Muñoz J, Nieto-Domínguez M, Barriuso J, de Eugenio LI, Martínez MJ. A novel, highly efficient β-glucosidase with a cellulose-binding domain: characterization and properties of native and recombinant proteins. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:256. [PMID: 29142591 PMCID: PMC5674860 DOI: 10.1186/s13068-017-0946-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 10/26/2017] [Indexed: 05/07/2023]
Abstract
BACKGROUND Cellulose, the most abundant biopolymer on earth, is an alternative for fossil fuels as a renewable feedstock for the production of second-generation biofuels and other chemicals. The discovery of novel, highly efficient β-glucosidases remains as one of the major bottlenecks for cellulose degradation. In this context, the ascomycete Talaromyces amestolkiae, isolated from cereal samples, has been studied as a promising source for these enzymes. RESULTS BGL-2 is the major β-glucosidase secreted by this fungus in the presence of cellulosic inductors. This enzyme possesses a CBD (Cellulose Binding Domain), an unusual feature among this type of proteins. Besides, when growing on cellulose, the fungus produced two different bgl-2 mRNAs that were cloned and expressed in Pichia pastoris. A complete recombinant protein (BGL-2*) and its truncated form, lacking CBD (BGL-2T*), have been purified, characterized and compared with the native enzyme (BGL-2). The three BGL-2 forms studied are highly stable in a wide pH range, but BGL-2T* showed an improved thermal stability at 50 °C after 72 h. Using p-nitrophenyl-β-d-glucopyranoside as a substrate, the steady-state kinetic characterization of the three proteins showed a similar Km and kcat for BGL-2 and BGL-2*, while the truncated protein displayed a threefold higher value for kcat . All tested BGL-2 enzymes were as well highly efficient using cellobiose and other short oligosaccharides as a substrate. In view of biotechnological applications, the recombinant T. amestolkiae enzymes in saccharification of brewers' spent grain were studied, being comparable to commercial β-glucosidase cocktails. CONCLUSION A new β-glucosidase from T. amestolkiae has been studied. The enzyme, containing a functional CBD, has been expressed in P. pastoris. The comparative analyses of the native protein and its recombinant forms, with and without CBD, suggest that they could be suitable tools for valorization of lignocellulosic biomass.
Collapse
Affiliation(s)
- J. A. Méndez-Líter
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - J. Gil-Muñoz
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - M. Nieto-Domínguez
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - J. Barriuso
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - L. I. de Eugenio
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - M. J. Martínez
- Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| |
Collapse
|
43
|
Ramírez-Escudero M, Del Pozo MV, Marín-Navarro J, González B, Golyshin PN, Polaina J, Ferrer M, Sanz-Aparicio J. Structural and Functional Characterization of a Ruminal β-Glycosidase Defines a Novel Subfamily of Glycoside Hydrolase Family 3 with Permuted Domain Topology. J Biol Chem 2016; 291:24200-24214. [PMID: 27679487 PMCID: PMC5104943 DOI: 10.1074/jbc.m116.747527] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/16/2016] [Indexed: 01/01/2023] Open
Abstract
Metagenomics has opened up a vast pool of genes for putative, yet uncharacterized, enzymes. It widens our knowledge on the enzyme diversity world and discloses new families for which a clear classification is still needed, as is exemplified by glycoside hydrolase family-3 (GH3) proteins. Herein, we describe a GH3 enzyme (GlyA1) from resident microbial communities in strained ruminal fluid. The enzyme is a β-glucosidase/β-xylosidase that also shows β-galactosidase, β-fucosidase, α-arabinofuranosidase, and α-arabinopyranosidase activities. Short cello- and xylo-oligosaccharides, sophorose and gentibiose, are among the preferred substrates, with the large polysaccharide lichenan also being hydrolyzed by GlyA1. The determination of the crystal structure of the enzyme in combination with deletion and site-directed mutagenesis allowed identification of its unusual domain composition and the active site architecture. Complexes of GlyA1 with glucose, galactose, and xylose allowed picturing the catalytic pocket and illustrated the molecular basis of the substrate specificity. A hydrophobic platform defined by residues Trp-711 and Trp-106, located in a highly mobile loop, appears able to allocate differently β-linked bioses. GlyA1 includes an additional C-terminal domain previously unobserved in GH3 members, but crystallization of the full-length enzyme was unsuccessful. Therefore, small angle x-ray experiments have been performed to investigate the molecular flexibility and overall putative shape. This study provided evidence that GlyA1 defines a new subfamily of GH3 proteins with a novel permuted domain topology. Phylogenetic analysis indicates that this topology is associated with microbes inhabiting the digestive tracts of ruminants and other animals, feeding on chemically diverse plant polymeric materials.
Collapse
Affiliation(s)
- Mercedes Ramírez-Escudero
- From the Department of Crystallography and Structural Biology, Institute of Physical-Chemistry "Rocasolano," Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| | - Mercedes V Del Pozo
- the Institute of Catalysis and Petrochemistry, Consejo Superior de Investigaciones Científicas, Marie Curie 2, Cantoblanco, 28049 Madrid, Spain
| | - Julia Marín-Navarro
- the Institute of Agrochemistry and Food Technology, Consejo Superior de Investigaciones Científicas, Carrer Catedràtic Agustín Escardino Benlloch 7, 46980 Paterna, Valencia, Spain
| | - Beatriz González
- From the Department of Crystallography and Structural Biology, Institute of Physical-Chemistry "Rocasolano," Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain
| | - Peter N Golyshin
- the School of Biological Sciences, Bangor University, LL57 2UW Gwynedd, United Kingdom, and.,the Immanuel Kant Baltic Federal University, 236040 Kaliningrad, Russia
| | - Julio Polaina
- the Institute of Agrochemistry and Food Technology, Consejo Superior de Investigaciones Científicas, Carrer Catedràtic Agustín Escardino Benlloch 7, 46980 Paterna, Valencia, Spain
| | - Manuel Ferrer
- the Institute of Catalysis and Petrochemistry, Consejo Superior de Investigaciones Científicas, Marie Curie 2, Cantoblanco, 28049 Madrid, Spain,
| | - Julia Sanz-Aparicio
- From the Department of Crystallography and Structural Biology, Institute of Physical-Chemistry "Rocasolano," Consejo Superior de Investigaciones Científicas, Serrano 119, 28006 Madrid, Spain,
| |
Collapse
|
44
|
Baba Y, Sumitani JI, Tanaka K, Tani S, Kawaguchi T. Site-saturation mutagenesis for β-glucosidase 1 from Aspergillus aculeatus to accelerate the saccharification of alkaline-pretreated bagasse. Appl Microbiol Biotechnol 2016; 100:10495-10507. [DOI: 10.1007/s00253-016-7726-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 06/30/2016] [Accepted: 07/04/2016] [Indexed: 01/05/2023]
|
45
|
Gudmundsson M, Hansson H, Karkehabadi S, Larsson A, Stals I, Kim S, Sunux S, Fujdala M, Larenas E, Kaper T, Sandgren M. Structural and functional studies of the glycoside hydrolase family 3 β-glucosidase Cel3A from the moderately thermophilic fungus Rasamsonia emersonii. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:860-70. [PMID: 27377383 PMCID: PMC4932919 DOI: 10.1107/s2059798316008482] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 05/25/2016] [Indexed: 12/16/2022]
Abstract
Cel3A from the thermophilic fungus R. emersonii has proven to be more efficient in the hydrolysis of β-glycosidic linkages than Cel3A from H. jecorina. The filamentous fungus Hypocrea jecorina produces a number of cellulases and hemicellulases that act in a concerted fashion on biomass and degrade it into monomeric or oligomeric sugars. β-Glucosidases are involved in the last step of the degradation of cellulosic biomass and hydrolyse the β-glycosidic linkage between two adjacent molecules in dimers and oligomers of glucose. In this study, it is shown that substituting the β-glucosidase from H. jecorina (HjCel3A) with the β-glucosidase Cel3A from the thermophilic fungus Rasamsonia emersonii (ReCel3A) in enzyme mixtures results in increased efficiency in the saccharification of lignocellulosic materials. Biochemical characterization of ReCel3A, heterologously produced in H. jecorina, reveals a preference for disaccharide substrates over longer gluco-oligosaccharides. Crystallographic studies of ReCel3A revealed a highly N-glycosylated three-domain dimeric protein, as has been observed previously for glycoside hydrolase family 3 β-glucosidases. The increased thermal stability and saccharification yield and the superior biochemical characteristics of ReCel3A compared with HjCel3A and mixtures containing HjCel3A make ReCel3A an excellent candidate for addition to enzyme mixtures designed to operate at higher temperatures.
Collapse
Affiliation(s)
- Mikael Gudmundsson
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Box 7015, 750 07 Uppsala, Sweden
| | - Henrik Hansson
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Box 7015, 750 07 Uppsala, Sweden
| | - Saeid Karkehabadi
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Box 7015, 750 07 Uppsala, Sweden
| | - Anna Larsson
- Department of Cell and Molecular Biology, Uppsala University, Box 596, 751 24 Uppsala, Sweden
| | - Ingeborg Stals
- Laboratory for Protein Biochemistry and Biomolecular Engineering, Ghent University, Ledeganckstraat 35, B-9000 Ghent, Belgium
| | - Steve Kim
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, CA 94304, USA
| | - Sergio Sunux
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, CA 94304, USA
| | - Meredith Fujdala
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, CA 94304, USA
| | - Edmund Larenas
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, CA 94304, USA
| | - Thijs Kaper
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, CA 94304, USA
| | - Mats Sandgren
- Department of Chemistry and Biotechnology, Swedish University of Agricultural Sciences, Box 7015, 750 07 Uppsala, Sweden
| |
Collapse
|
46
|
Xia W, Bai Y, Cui Y, Xu X, Qian L, Shi P, Zhang W, Luo H, Zhan X, Yao B. Functional diversity of family 3 β-glucosidases from thermophilic cellulolytic fungus Humicola insolens Y1. Sci Rep 2016; 6:27062. [PMID: 27271847 PMCID: PMC4897640 DOI: 10.1038/srep27062] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 05/09/2016] [Indexed: 11/09/2022] Open
Abstract
The fungus Humicola insolens is one of the most powerful decomposers of crystalline cellulose. However, studies on the β-glucosidases from this fungus remain insufficient, especially on glycosyl hydrolase family 3 enzymes. In the present study, we analyzed the functional diversity of three distant family 3 β-glucosidases from Humicola insolens strain Y1, which belonged to different evolutionary clades, by heterogeneous expression in Pichia pastoris strain GS115. The recombinant enzymes shared similar enzymatic properties including thermophilic and neutral optima (50-60 °C and pH 5.5-6.0) and high glucose tolerance, but differed in substrate specificities and kinetics. HiBgl3B was solely active towards aryl β-glucosides while HiBgl3A and HiBgl3C showed broad substrate specificities including both disaccharides and aryl β-glucosides. Of the three enzymes, HiBgl3C exhibited the highest specific activity (158.8 U/mg on pNPG and 56.4 U/mg on cellobiose) and catalytic efficiency and had the capacity to promote cellulose degradation. Substitutions of three key residues Ile48, Ile278 and Thr484 of HiBgl3B to the corresponding residues of HiBgl3A conferred the enzyme activity towards sophorose, and vice versa. This study reveals the functional diversity of GH3 β-glucosidases as well as the key residues in recognizing +1 subsite of different substrates.
Collapse
Affiliation(s)
- Wei Xia
- College of Animal Science, Zhejiang University, Hangzhou 310058, People's Republic of China.,Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, 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 100081, People's Republic of China
| | - Ying Cui
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China
| | - Xinxin Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China
| | - Lichun Qian
- College of Animal Science, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Pengjun Shi
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China
| | - Huiying Luo
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, People's Republic of China
| | - Xiuan Zhan
- College of Animal Science, Zhejiang University, Hangzhou 310058, 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 100081, People's Republic of China
| |
Collapse
|
47
|
Pei X, Zhao J, Cai P, Sun W, Ren J, Wu Q, Zhang S, Tian C. Heterologous expression of a GH3 β-glucosidase from Neurospora crassa in Pichia pastoris with high purity and its application in the hydrolysis of soybean isoflavone glycosides. Protein Expr Purif 2016; 119:75-84. [PMID: 26596358 DOI: 10.1016/j.pep.2015.11.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 09/30/2015] [Accepted: 11/10/2015] [Indexed: 01/30/2023]
Abstract
Previous studies have shown isoflavone aglycones to have more biological effects than their counterparts, isoflavone glycones. Some β-glucosidases can hydrolyze isoflavone glucosides to release aglycones, and discovery of these has attracted great interest. A glycoside hydrolase (GH) family 3 β-glucosidase (bgl2) gene from Neurospora crassa was heterologously expressed in Pichia pastoris with high purity. The recombinant BGL2 enzyme displayed its highest activity at pH 5.0 and 60 °C, and had its maximum activity against p-nitrophenyl-β-d-glucopyranoside (pNPG) (143.27 ± 4.79 U/mg), followed by cellobiose (74.99 ± 0.78 U/mg), gentiobiose (47.55 ± 0.15 U/mg), p-nitrophenyl-β-d-cellobioside (pNPC) (40.07 ± 0.87 U/mg), cellotriose (12.31 ± 0.36 U/mg) and cellotetraose (9.04 ± 0.14 U/mg). The kinetic parameters of Km and Vmax were 0.21 ± 0.01 mM and 147.93 ± 2.77 μM/mg/min for pNPG. The purified enzyme showed a heightened ability to convert the major soybean isoflavone glycosides (daidzin, genistin and glycitin) into their corresponding aglycone forms (daidzien, genistein and glycitein). With this activity against soybean isoflavone glycosides, BGL2 shows great potential for applications in the food, animal feed, and pharmaceutical industries.
Collapse
Affiliation(s)
- Xue Pei
- College of Plant Sciences, Jilin University, Changchun 130062, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Junqi Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Pengli Cai
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Wenliang Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Jie Ren
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Qiaqing Wu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Shihong Zhang
- College of Plant Sciences, Jilin University, Changchun 130062, China
| | - Chaoguang Tian
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
| |
Collapse
|
48
|
Nakajima M, Yoshida R, Miyanaga A, Abe K, Takahashi Y, Sugimoto N, Toyoizumi H, Nakai H, Kitaoka M, Taguchi H. Functional and Structural Analysis of a β-Glucosidase Involved in β-1,2-Glucan Metabolism in Listeria innocua. PLoS One 2016; 11:e0148870. [PMID: 26886583 PMCID: PMC4757417 DOI: 10.1371/journal.pone.0148870] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 01/25/2016] [Indexed: 11/18/2022] Open
Abstract
Despite the presence of β-1,2-glucan in nature, few β-1,2-glucan degrading enzymes have been reported to date. Recently, the Lin1839 protein from Listeria innocua was identified as a 1,2-β-oligoglucan phosphorylase. Since the adjacent lin1840 gene in the gene cluster encodes a putative glycoside hydrolase family 3 β-glucosidase, we hypothesized that Lin1840 is also involved in β-1,2-glucan dissimilation. Here we report the functional and structural analysis of Lin1840. A recombinant Lin1840 protein (Lin1840r) showed the highest hydrolytic activity toward sophorose (Glc-β-1,2-Glc) among β-1,2-glucooligosaccharides, suggesting that Lin1840 is a β-glucosidase involved in sophorose degradation. The enzyme also rapidly hydrolyzed laminaribiose (β-1,3), but not cellobiose (β-1,4) or gentiobiose (β-1,6) among β-linked gluco-disaccharides. We determined the crystal structures of Lin1840r in complexes with sophorose and laminaribiose as productive binding forms. In these structures, Arg572 forms many hydrogen bonds with sophorose and laminaribiose at subsite +1, which seems to be a key factor for substrate selectivity. The opposite side of subsite +1 from Arg572 is connected to a large empty space appearing to be subsite +2 for the binding of sophorotriose (Glc-β-1,2-Glc-β-1,2-Glc) in spite of the higher Km value for sophorotriose than that for sophorose. The conformations of sophorose and laminaribiose are almost the same on the Arg572 side but differ on the subsite +2 side that provides no interaction with a substrate. Therefore, Lin1840r is unable to distinguish between sophorose and laminaribiose as substrates. These results provide the first mechanistic insights into β-1,2-glucooligosaccharide recognition by β-glucosidase.
Collapse
Affiliation(s)
- Masahiro Nakajima
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
- * E-mail:
| | - Ryuta Yoshida
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
| | - Akimasa Miyanaga
- Department of Chemistry, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan
| | - Koichi Abe
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
| | - Yuta Takahashi
- Graduate School of Science & Technology, Niigata University, Nishi-ku, Niigata, Japan
| | - Naohisa Sugimoto
- Graduate School of Science & Technology, Niigata University, Nishi-ku, Niigata, Japan
| | - Hiroyuki Toyoizumi
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
| | - Hiroyuki Nakai
- Graduate School of Science & Technology, Niigata University, Nishi-ku, Niigata, Japan
| | - Motomitsu Kitaoka
- National Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Hayao Taguchi
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda, Chiba, Japan
| |
Collapse
|
49
|
Agirre J, Ariza A, Offen WA, Turkenburg JP, Roberts SM, McNicholas S, Harris PV, McBrayer B, Dohnalek J, Cowtan KD, Davies GJ, Wilson KS. Three-dimensional structures of two heavily N-glycosylated Aspergillus sp. family GH3 β-D-glucosidases. Acta Crystallogr D Struct Biol 2016; 72:254-65. [PMID: 26894673 PMCID: PMC4756609 DOI: 10.1107/s2059798315024237] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 12/16/2015] [Indexed: 01/25/2023] Open
Abstract
The industrial conversion of cellulosic plant biomass into useful products such as biofuels is a major societal goal. These technologies harness diverse plant degrading enzymes, classical exo- and endo-acting cellulases and, increasingly, cellulose-active lytic polysaccharide monooxygenases, to deconstruct the recalcitrant β-D-linked polysaccharide. A major drawback with this process is that the exo-acting cellobiohydrolases suffer from severe inhibition from their cellobiose product. β-D-Glucosidases are therefore important for liberating glucose from cellobiose and thereby relieving limiting product inhibition. Here, the three-dimensional structures of two industrially important family GH3 β-D-glucosidases from Aspergillus fumigatus and A. oryzae, solved by molecular replacement and refined at 1.95 Å resolution, are reported. Both enzymes, which share 78% sequence identity, display a three-domain structure with the catalytic domain at the interface, as originally shown for barley β-D-glucan exohydrolase, the first three-dimensional structure solved from glycoside hydrolase family GH3. Both enzymes show extensive N-glycosylation, with only a few external sites being truncated to a single GlcNAc molecule. Those glycans N-linked to the core of the structure are identified purely as high-mannose trees, and establish multiple hydrogen bonds between their sugar components and adjacent protein side chains. The extensive glycans pose special problems for crystallographic refinement, and new techniques and protocols were developed especially for this work. These protocols ensured that all of the D-pyranosides in the glycosylation trees were modelled in the preferred minimum-energy (4)C1 chair conformation and should be of general application to refinements of other crystal structures containing O- or N-glycosylation. The Aspergillus GH3 structures, in light of other recent three-dimensional structures, provide insight into fungal β-D-glucosidases and provide a platform on which to inform and inspire new generations of variant enzymes for industrial application.
Collapse
Affiliation(s)
- Jon Agirre
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Antonio Ariza
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Wendy A. Offen
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Johan P. Turkenburg
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Shirley M. Roberts
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Stuart McNicholas
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | | | | | - Jan Dohnalek
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Kevin D. Cowtan
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Gideon J. Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| | - Keith S. Wilson
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, England
| |
Collapse
|
50
|
Larue K, Melgar M, Martin VJJ. Directed evolution of a fungal β-glucosidase in Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:52. [PMID: 26949413 PMCID: PMC4778352 DOI: 10.1186/s13068-016-0470-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 02/22/2016] [Indexed: 05/13/2023]
Abstract
BACKGROUND β-glucosidases (BGLs) catalyze the hydrolysis of soluble cellodextrins to glucose and are a critical component of cellulase systems. In order to engineer Saccharomyces cerevisiae for the production of ethanol from cellulosic biomass, a BGL tailored to industrial bioconversions is needed. RESULTS We applied a directed evolution strategy to a glycosyl hydrolase family 3 (GH3) BGL from Aspergillus niger (BGL1) by expressing a library of mutated bgl1 genes in S. cerevisiae and used a two-step functional screen to identify improved enzymes. Twelve BGL variants that supported growth of S. cerevisiae on cellobiose and showed increased activity on the synthetic substrate p-nitrophenyl-β-D-glucopyranoside were identified and characterized. By performing kinetic experiments, we found that a Tyr → Cys substitution at position 305 of BGL1 dramatically reduced transglycosidation activity that causes inhibition of the hydrolytic reaction at high substrate concentrations. Targeted mutagenesis demonstrated that the position 305 residue is critical in GH3 BGLs and likely determines the extent to which transglycosidation reactions occur. We also found that a substitution at Gln(140) reduced the inhibitory effect of glucose and could be combined with the Y305C substitution to produce a BGL with decreased sensitivity to both the product and substrate. Using the crystal structure of a GH3 BGL from A. aculeatus, we mapped a group of beneficial mutations to the β/α domain of the molecule and postulate that this region modulates activity through subunit interactions. Six BGL variants were identified with substitutions in the MFα pre-sequence that was used to mediate secretion of the protein. Substitutions at Pro(21) or Val(22) of the MFα pre-sequence could produce up to a twofold increase in supernatant hydrolase activity and provides evidence that expression and/or secretion was an additional factor limiting hydrolytic activity. CONCLUSIONS Using directed evolution on BGL1, we identified a key residue that controls hydrolytic and transglycosidation reactions in GH3 BGLs. We also found that several beneficial mutations could be combined and increased the hydrolytic activity for both synthetic and natural substrates.
Collapse
Affiliation(s)
- Kane Larue
- Department of Biology, Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke West, Montreal, QC H4B 1R6 Canada
| | - Mindy Melgar
- Department of Biology, Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke West, Montreal, QC H4B 1R6 Canada
| | - Vincent J. J. Martin
- Department of Biology, Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke West, Montreal, QC H4B 1R6 Canada
| |
Collapse
|