1
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Nguyen TA, Hoang T, Nguyen TT, Jeong C, Tran TV, Choi MG, Lee C. Substitution of acidic residues near the catalytic Glu131 leads to human HYAL1 activity at neutral pH via charge-charge interactions. PLoS One 2024; 19:e0308370. [PMID: 39121049 PMCID: PMC11315327 DOI: 10.1371/journal.pone.0308370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 07/23/2024] [Indexed: 08/11/2024] Open
Abstract
Human hyaluronidase 1 (HYAL1) and PH20 play vital roles in degrading hyaluronic acids through the substrate-assisted double displacement mechanism. While HYAL1, a lysosomal enzyme, functions optimally under acidic conditions, PH20, a sperm surface hyaluronidase, displays a broader pH range, from acidic to neutral. Our objective was to extend HYAL1's pH range towards neutral pH by introducing repulsive charge-charge interactions involving the catalytic Glu131, increasing its pKa as the proton donor. Substituting individual acidic residues in the β3-loop (S77D), β3'-β3″ hairpin (T86D and P87E), and at Ala132 (A132D and A132E) enabled HYAL1 to demonstrate enzyme activity at pH 7, with the mutants S77D, P87E, and A132E showing the highest activity in the substrate gel assay. However, double and triple substitutions, including S77D/T86D/A132E as found in the PH20 configuration, did not result in enhanced activity compared to single substitutions. Conversely, PH20 mutants with non-acidic substitutions, such as D94S in the β3-loop and D103T in the β3'-β3″ hairpin, significantly reduced activity within the pH range of 4 to 7. However, the PH20 mutant E149A, reciprocally substituted compared to A132E in HYAL1, exhibited activity similar to PH20 wild-type (WT) at pH 7. In a turbidimetric assay, HYAL1 mutants with single acidic substitutions exhibited activity similar to that of PH20 WT at pH 7. These results suggest that substituting acidic residues near Glu131 results in HYAL1 activity at neutral pH through electrostatic repulsion. This study highlights the significance of charge-charge interactions in both HYAL1 and PH20 in regulating the pH-dependent activity of hyaluronidases.
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Affiliation(s)
- Tu Anh Nguyen
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| | - Trang Hoang
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| | - Thu-Thuy Nguyen
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| | - ChanSu Jeong
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| | - Trang Van Tran
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
| | | | - ChangWoo Lee
- Department of Biomedical Science and Center for Bio-Nanomaterials, Daegu University, Gyeongsan, South Korea
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2
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Rao D, Zhu L, Liu W, Guo Z. Molecular Mechanism of Double-Displacement Retaining β-Kdo Glycosyltransferase WbbB. J Phys Chem B 2024. [PMID: 39051443 DOI: 10.1021/acs.jpcb.4c02073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Glycosyltransferases (GTs) are pivotal enzymes involved in glycosidic bond synthesis, which can lead to either retention or inversion of the glycosyl moiety's anomeric configuration. However, the catalytic mechanism for retaining GTs remains a subject of controversy. In this study, we employ MD and QM/MM metadynamics to investigate the double-displacement catalytic mechanism of the retaining β-Kdo transferase WbbB. Our findings demonstrate that the nucleophile Asp232 initiates the reaction by attacking the sugar ring containing a carboxylate at the anomeric position, forming a covalent adduct. Subsequently, the adduct undergoes a rotational rearrangement, ensuring proper orientation of the anomeric carbon for the acceptor substrate. In the second step, Glu158 acts as the catalytic base to abstract the proton of the acceptor substrate to complete the transglycosylation reaction. Notably, His265 does not function as the anticipated catalytic acid; instead, it stabilizes the phosphate group through H-bonding interactions. Our simulations support the double-displacement mechanism implicated from the crystallographic studies of WbbB. This mechanism deviates from the common SNi-type and retaining glycoside hydrolase mechanisms, thereby expanding our understanding of GT catalytic mechanisms.
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Affiliation(s)
- Deming Rao
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, People's Republic of China
| | - Lin Zhu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, People's Republic of China
| | - Weiqiong Liu
- State Key Laboratory of Food Science and Resources, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, People's Republic of China
| | - Zhiyong Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, People's Republic of China
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3
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Li Y, Jiao H, Zhang H, Wang X, Fu Y, Wang Q, Liu H, Yong YC, Guo J, Liu J. Biosafety consideration of nanocellulose in biomedical applications: A review. Int J Biol Macromol 2024; 265:130900. [PMID: 38499126 DOI: 10.1016/j.ijbiomac.2024.130900] [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: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 03/20/2024]
Abstract
Nanocellulose-based biomaterials have gained significant attention in various fields, especially in medical and pharmaceutical areas, due to their unique properties, including non-toxicity, high specific surface area, biodegradability, biocompatibility, and abundant feasible and sophisticated strategies for functional modification. The biosafety of nanocellulose itself is a prerequisite to ensure the safe and effective application of biomaterials as they interact with living cells, tissues, and organs at the nanoscale. Potential residual endogenous impurities and exogenous contaminants could lead to the failure of the intended functionalities or even serious health complications if they are not adequately removed and assessed before use. This review summarizes the sources of impurities in nanocellulose that may pose potential hazards to their biosafety, including endogenous impurities that co-exist in the cellulosic raw materials themselves and exogenous contaminants caused by external exposure. Strategies to reduce or completely remove these impurities are outlined and classified as chemical, physical, biological, and combined methods. Additionally, key points that require careful consideration in the interpretation of the biosafety evaluation outcomes were discussed to ensure the safety and effectiveness of the nanocellulose-based biomaterials in medical applications.
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Affiliation(s)
- Yan Li
- Biofuels Institute, School of Environment and Safety Engineering, c/o School of Emergency Management, Jiangsu University, Zhenjiang 212013, China
| | - Haixin Jiao
- Biofuels Institute, School of Environment and Safety Engineering, c/o School of Emergency Management, Jiangsu University, Zhenjiang 212013, China
| | - Hongxing Zhang
- Biofuels Institute, School of Environment and Safety Engineering, c/o School of Emergency Management, Jiangsu University, Zhenjiang 212013, China
| | - Xiangyu Wang
- Biofuels Institute, School of Environment and Safety Engineering, c/o School of Emergency Management, Jiangsu University, Zhenjiang 212013, China
| | - Yinyi Fu
- Biofuels Institute, School of Environment and Safety Engineering, c/o School of Emergency Management, Jiangsu University, Zhenjiang 212013, China
| | - Qianqian Wang
- Biofuels Institute, School of Environment and Safety Engineering, c/o School of Emergency Management, Jiangsu University, Zhenjiang 212013, China
| | - Huan Liu
- Biofuels Institute, School of Environment and Safety Engineering, c/o School of Emergency Management, Jiangsu University, Zhenjiang 212013, China
| | - Yang-Chun Yong
- Biofuels Institute, School of Environment and Safety Engineering, c/o School of Emergency Management, Jiangsu University, Zhenjiang 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China
| | - Jiaqi Guo
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources and International Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing 210037, China
| | - Jun Liu
- Biofuels Institute, School of Environment and Safety Engineering, c/o School of Emergency Management, Jiangsu University, Zhenjiang 212013, China; Jiangsu Collaborative Innovation Center of Technology and Material of Water Treatment, Suzhou University of Science and Technology, Suzhou 215009, China.
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4
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Munzone A, Eijsink VGH, Berrin JG, Bissaro B. Expanding the catalytic landscape of metalloenzymes with lytic polysaccharide monooxygenases. Nat Rev Chem 2024; 8:106-119. [PMID: 38200220 DOI: 10.1038/s41570-023-00565-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2023] [Indexed: 01/12/2024]
Abstract
Lytic polysaccharide monooxygenases (LPMOs) have an essential role in global carbon cycle, industrial biomass processing and microbial pathogenicity by catalysing the oxidative cleavage of recalcitrant polysaccharides. Despite initially being considered monooxygenases, experimental and theoretical studies show that LPMOs are essentially peroxygenases, using a single copper ion and H2O2 for C-H bond oxygenation. Here, we examine LPMO catalysis, emphasizing key studies that have shaped our comprehension of their function, and address side and competing reactions that have partially obscured our understanding. Then, we compare this novel copper-peroxygenase reaction with reactions catalysed by haem iron enzymes, highlighting the different chemistries at play. We conclude by addressing some open questions surrounding LPMO catalysis, including the importance of peroxygenase and monooxygenase reactions in biological contexts, how LPMOs modulate copper site reactivity and potential protective mechanisms against oxidative damage.
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Affiliation(s)
- Alessia Munzone
- UMR1163 Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille University, Marseille, France
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology, and Food Science, The Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Jean-Guy Berrin
- UMR1163 Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille University, Marseille, France
| | - Bastien Bissaro
- UMR1163 Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille University, Marseille, France.
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5
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Song WS, Jo SH, Lee JS, Kwon JE, Park JH, Kim YR, Baek JH, Kim MG, Kwon SY, Kim YG. Multiomics analysis reveals the biological effects of live Roseburia intestinalis as a high-butyrate-producing bacterium in human intestinal epithelial cells. Biotechnol J 2023; 18:e2300180. [PMID: 37596881 DOI: 10.1002/biot.202300180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/29/2023] [Accepted: 08/14/2023] [Indexed: 08/20/2023]
Abstract
Butyrate-producing bacteria play a key role in human health, and recent studies have triggered interest in their development as next-generation probiotics. However, there remains limited knowledge not only on the identification of high-butyrate-producing bacteria in the human gut but also in the metabolic capacities for prebiotic carbohydrates and their interaction with the host. Herein, it was discovered that Roseburia intestinalis produces higher levels of butyrate and digests a wider variety of prebiotic polysaccharide structures compared with other human major butyrate-producing bacteria (Eubacterium rectale, Faecalibacterium prausnitzii, and Roseburia hominis). Moreover, R. intestinalis extracts upregulated the mRNA expression of tight junction proteins (TJP1, OCLN, and CLDN3) in human intestinal epithelial cells more than other butyrate-producing bacteria. R. intestinalis was cultured with human intestinal epithelial cells in the mimetic intestinal host-microbe interaction coculture system to explore the health-promoting effects using multiomics approaches. Consequently, it was discovered that live R. intestinalis only enhances purine metabolism and the oxidative pathway, increasing adenosine triphosphate levels in human intestinal epithelial cells, but that heat-killed bacteria had no effect. Therefore, this study proposes that R. intestinalis has potentially high value as a next-generation probiotic to promote host intestinal health.
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Affiliation(s)
- Won-Suk Song
- Department of Chemical Engineering, Soongsil University, Seoul, Republic of Korea
| | - Sung-Hyun Jo
- Department of Chemical Engineering, Soongsil University, Seoul, Republic of Korea
| | - Jae-Seung Lee
- Department of Chemical Engineering, Soongsil University, Seoul, Republic of Korea
| | - Ji-Eun Kwon
- Department of Chemical Engineering, Soongsil University, Seoul, Republic of Korea
| | - Ji-Hyeon Park
- Department of Chemical Engineering, Soongsil University, Seoul, Republic of Korea
| | - Ye-Rim Kim
- Department of Chemical Engineering, Soongsil University, Seoul, Republic of Korea
| | - Ji-Hyun Baek
- Department of Chemical Engineering, Soongsil University, Seoul, Republic of Korea
| | - Min-Gyu Kim
- Department of Chemical Engineering, Soongsil University, Seoul, Republic of Korea
| | - Seo-Young Kwon
- Department of Chemical Engineering, Soongsil University, Seoul, Republic of Korea
| | - Yun-Gon Kim
- Department of Chemical Engineering, Soongsil University, Seoul, Republic of Korea
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6
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Li Z, Qing Y, Cui G, Li M, Liu T, Zeng Y, Zhou C, Hu X, Jiang J, Wang D, Gao Y, Zhang J, Cai C, Wang T, Wan C. Shotgun metagenomics reveals abnormal short-chain fatty acid-producing bacteria and glucose and lipid metabolism of the gut microbiota in patients with schizophrenia. Schizophr Res 2023; 255:59-66. [PMID: 36965360 DOI: 10.1016/j.schres.2023.03.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 01/11/2023] [Accepted: 03/03/2023] [Indexed: 03/27/2023]
Abstract
Evidence has shown that the gut microbiota is closely related to the pathogenesis of schizophrenia, but temporal changes in the gut microbiota of patients with schizophrenia (SZ) during treatment remain unclear. Here, to evaluate temporal changes in the gut microbiota in schizophrenia, we performed whole-genome shotgun metagenomics on fecal samples from 36 healthy controls (HCs) and 19 baseline-period patients, and followed up with patients upon treatment. Compared to that in HCs, beta diversity in SZ was significantly distinct. The genera Bacteroides, Prevotella and Clostridium were the top 3 altered genera between SZ and HCs, and the Bacteroides-Prevotella ratio was significantly increased in SZ. Thirty-three percent of differentially abundant species were short-chain fatty acid (SCFA)-producing bacteria. Functional analysis showed that glucose and lipid metabolism of the gut microbiota was decreased in SZ compared with those in HCs. The abundances of two rate-limiting enzymes in glucose and lipid metabolism, phosphofructokinase (PFK) and acetyl-CoA carboxylase (ACC), were significantly decreased in SZ, and differentially abundant metabolism-related enzymes were significantly associated with SCFA-producing bacteria. Next, we found that the abundance of SCFA-producing bacteria also changed after treatment and that Clostridium was significantly negatively correlated with the total positive and negative syndrome scale (PANSS) score in patients. Functional analysis showed that glycoside hydrolase family 30 incrementally increased in abundance during treatment and were significantly associated with SCFA-producing bacteria. Our findings help to provide evidence for the role of gut microbiota in the occurrence and development of schizophrenia.
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Affiliation(s)
- Zhuyun Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Ying Qing
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Gaoping Cui
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Minghui Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Tiantian Liu
- Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University, Shanghai, China; SJTU-Yale Joint Center for Biostatistics and Data Science, Shanghai Jiao Tong University, Shanghai, China
| | - Yanyan Zeng
- Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University, Shanghai, China; SJTU-Yale Joint Center for Biostatistics and Data Science, Shanghai Jiao Tong University, Shanghai, China
| | - Chao Zhou
- Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University, Shanghai, China; SJTU-Yale Joint Center for Biostatistics and Data Science, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaowen Hu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Jiang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Dandan Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Gao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Juan Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Changqun Cai
- The Fourth People's Hospital of Wuhu, Wuhu, China
| | - Tao Wang
- Department of Bioinformatics and Biostatistics, Shanghai Jiao Tong University, Shanghai, China; SJTU-Yale Joint Center for Biostatistics and Data Science, Shanghai Jiao Tong University, Shanghai, China.
| | - Chunling Wan
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China.
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7
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Li SF, Cheng F, Wang YJ, Zheng YG. Strategies for tailoring pH performances of glycoside hydrolases. Crit Rev Biotechnol 2023; 43:121-141. [PMID: 34865578 DOI: 10.1080/07388551.2021.2004084] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Glycoside hydrolases (GHs) exhibit high activity and stability under harsh conditions, such as high temperatures and extreme pHs, given their wide use in industrial biotechnology. However, strategies for improving the acidophilic and alkalophilic adaptations of GHs are poorly summarized due to the complexity of the mechanisms of these adaptations. This review not only highlights the adaptation mechanisms of acidophilic and alkalophilic GHs under extreme pH conditions, but also summarizes the recent advances in engineering the pH performances of GHs with a focus on four strategies of protein engineering, enzyme immobilization, chemical modification, and medium engineering (additives). The examples described here summarize the methods used in modulating the pH performances of GHs and indicate that methods integrated in different protein engineering techniques or methods are efficient to generate industrial biocatalysts with the desired pH performance and other adapted enzyme properties.
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Affiliation(s)
- Shu-Fang Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Feng Cheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Ya-Jun Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, P. R. China.,Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang, P. R. China.,The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou, P. R. China
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8
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Pabbathi NPP, Velidandi A, Tavarna T, Gupta S, Raj RS, Gandam PK, Baadhe RR. Role of metagenomics in prospecting novel endoglucanases, accentuating functional metagenomics approach in second-generation biofuel production: a review. BIOMASS CONVERSION AND BIOREFINERY 2023; 13:1371-1398. [PMID: 33437563 PMCID: PMC7790359 DOI: 10.1007/s13399-020-01186-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/30/2020] [Accepted: 12/01/2020] [Indexed: 05/02/2023]
Abstract
As the fossil fuel reserves are depleting rapidly, there is a need for alternate fuels to meet the day to day mounting energy demands. As fossil fuel started depleting, a quest for alternate forms of fuel was initiated and biofuel is one of its promising outcomes. First-generation biofuels are made from edible sources like vegetable oils, starch, and sugars. Second-generation biofuels (SGB) are derived from lignocellulosic crops and the third-generation involves algae for biofuel production. Technical challenges in the production of SGB are hampering its commercialization. Advanced molecular technologies like metagenomics can help in the discovery of novel lignocellulosic biomass-degrading enzymes for commercialization and industrial production of SGB. This review discusses the metagenomic outcomes to enlighten the importance of unexplored habitats for novel cellulolytic gene mining. It also emphasizes the potential of different metagenomic approaches to explore the uncultivable cellulose-degrading microbiome as well as cellulolytic enzymes associated with them. This review also includes effective pre-treatment technology and consolidated bioprocessing for efficient biofuel production.
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Affiliation(s)
- Ninian Prem Prashanth Pabbathi
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Aditya Velidandi
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Tanvi Tavarna
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Shreyash Gupta
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Ram Sarvesh Raj
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Pradeep Kumar Gandam
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
| | - Rama Raju Baadhe
- Integrated Biorefinery Research Lab, Department of Biotechnology, National Institute of Technology, Warangal, Telangana 506004 India
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9
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Li H, Xu X, Zhang M, Zhang Y, Zhao Y, Jiang X, Xin X, Zhang Z, Zhang R, Gui Z. Accelerated degradation of cellulose in silkworm excrement by the interaction of housefly larvae and cellulose-degrading bacteria. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 323:116295. [PMID: 36150354 DOI: 10.1016/j.jenvman.2022.116295] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/11/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
The environmental pollution caused by silkworm (Bombyx mori) excrement is prominent, and rich in refractory cellulose is the bottleneck restricting the efficient recycling of silkworm excrement. This study was performed to investigate the effects of housefly larvae vermicomposting on the biodegradation of cellulose in silkworm excrement. After six days, a 58.90% reduction of cellulose content in treatment groups was observed, which was significantly higher than 11.5% of the control groups without housefly larvae. Three cellulose-degrading bacterial strains were isolated from silkworm excrement, which were identified as Bacillus licheniformis, Bacillus amyloliquefaciens, and Bacillus subtilis based on 16S rRNA gene sequence analysis. These three bacterial stains had a high cellulose degradation index (HC value ranged to between 1.86 and 5.97 and FPase ranged from 5.07 U/mL to 7.31 U/mL). It was found that housefly larvae increased the abundance of cellulose-degrading bacterial genus (Bacillus and Pseudomonas) by regulating the external environmental conditions (temperature and pH). Carbohydrate metabolism was the bacterial communities' primary function during vermicomposting based on the PICRUSt. The results of Tax4Fun indicated that the abundance of endo-β-1,4-glucanase and exo-β-1,4-glucanase increased rapidly and maintained at a higher level in silkworm excrement due to the addition of housefly larvae, which contributed to the accelerated degradation of cellulose in silkworm excrement. The finding of this investigation showed that housefly larvae can significantly accelerate the degradation of cellulose in silkworm excrement by increasing the abundance of cellulose-degrading bacterial genera and cellulase.
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Affiliation(s)
- Hao Li
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, Jiangsu, China; Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, 212100, Jiangsu, China
| | - Xueming Xu
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, Jiangsu, China
| | - Minqi Zhang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, Jiangsu, China
| | - Yuanhao Zhang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, Jiangsu, China
| | - Ying Zhao
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, Jiangsu, China
| | - Xueping Jiang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, Jiangsu, China
| | - Xiangdong Xin
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, Jiangsu, China
| | - Zhendong Zhang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, Jiangsu, China; Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, 212100, Jiangsu, China
| | - Ran Zhang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, Jiangsu, China; Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, 212100, Jiangsu, China
| | - Zhongzheng Gui
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212100, Jiangsu, China; Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, 212100, Jiangsu, China.
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10
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Ramakrishnan R, Singh AK, Singh S, Chakravortty D, Das D. Enzymatic Dispersion of Biofilms: An Emerging Biocatalytic Avenue to Combat Biofilm-Mediated Microbial Infections. J Biol Chem 2022; 298:102352. [PMID: 35940306 PMCID: PMC9478923 DOI: 10.1016/j.jbc.2022.102352] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 08/02/2022] [Accepted: 08/03/2022] [Indexed: 01/01/2023] Open
Abstract
Drug resistance by pathogenic microbes has emerged as a matter of great concern to mankind. Microorganisms such as bacteria and fungi employ multiple defense mechanisms against drugs and the host immune system. A major line of microbial defense is the biofilm, which comprises extracellular polymeric substances that are produced by the population of microorganisms. Around 80% of chronic bacterial infections are associated with biofilms. The presence of biofilms can increase the necessity of doses of certain antibiotics up to 1000-fold to combat infection. Thus, there is an urgent need for strategies to eradicate biofilms. Although a few physicochemical methods have been developed to prevent and treat biofilms, these methods have poor efficacy and biocompatibility. In this review, we discuss the existing strategies to combat biofilms and their challenges. Subsequently, we spotlight the potential of enzymes, in particular, polysaccharide degrading enzymes, for biofilm dispersion, which might lead to facile antimicrobial treatment of biofilm-associated infections.
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Affiliation(s)
- Reshma Ramakrishnan
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, Karnataka, India
| | - Ashish Kumar Singh
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka, India
| | - Simran Singh
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, Karnataka, India
| | - Dipshikha Chakravortty
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka, India
| | - Debasis Das
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, Karnataka, India.
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11
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Shi X, Wu D, Xu Y, Yu X. Engineering the optimum pH of β-galactosidase from Aspergillus oryzae for efficient hydrolysis of lactose. J Dairy Sci 2022; 105:4772-4782. [PMID: 35450720 DOI: 10.3168/jds.2021-21760] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 02/19/2022] [Indexed: 11/19/2022]
Abstract
β-Galactosidase (lacA) from Aspergillus oryzae is widely used in the dairy industry. Its acidic pH optimum and severe product inhibition limit its application for lactose hydrolysis in milk. In the present study, structure-based sequence alignment was conducted to determine the candidate mutations to shift the pH optimum of lacA to the neutral range. The Y138F and Y364F mutants shifted the pH optimum of lacA from 4.5 to 5.5 and 6.0, respectively. The acid dissociation constant (pKa) values of catalytic acid/base residues with upwards shift were consistent with the increased pH optimum. All variants in the present study also alleviated galactose inhibition to various extents. Molecular dynamics demonstrated that the less rigid tertiary structures and lower galactose-binding free energy of Y138F and Y364F might facilitate the release of the end product. Both Y138F and Y364F mutants exhibited better hydrolytic ability than lacA in milk lactose hydrolysis. The higher pH optimum and lower galactose inhibition of Y138F and Y364F may explain their superiority over lacA. The Y138F and Y364F mutants in the present study showed potential in producing low-lactose milk, and our studies provide a novel strategy for engineering the pH optimum of glycoside hydrolase.
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Affiliation(s)
- Xin Shi
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Dan Wu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Yan Xu
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Xiaowei Yu
- Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, People's Republic of China.
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12
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Xia W, Liu G, Wang D, Chen H, Zhu L, Li D. Functional convergence of Yunnan snub-nosed monkey and bamboo-eating panda gut microbiomes revealing the driving by dietary flexibility on mammal gut microbiome. Comput Struct Biotechnol J 2022; 20:685-699. [PMID: 35140888 PMCID: PMC8814018 DOI: 10.1016/j.csbj.2022.01.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 12/15/2021] [Accepted: 01/13/2022] [Indexed: 12/28/2022] Open
Abstract
The gut microbiomes of non-human primates have received a great deal of attention due to their close relationship to humans. In recent years, these studies have mainly focused on the gut microbiome of wild primates, which will be helpful to understanding the evolution of primates and their gut microbiomes (e.g., gut microbiome plasticity and diet flexibility). However, there is still a lack of basic information on the gut microbiomes from wild populations. Here, we investigated the gut microbial composition (16S rRNA gene) and function (metagenome and metagenome-assembled genomes (MAGs)) of Yunnan snub-nosed monkey populations in Weixi County, Yunnan Province, China, that had diets either completely based on wild-foraging or were regularly supplemented with human provisioned food. We found a significant difference in the gut microbiome between these two populations: the gut microbiome of the wild-foraging (no food provision) population was enriched genes involved in the detoxification of bamboo cyanide (high proportion of bamboo shoot intake) and chitin (from insect diet) digestion, while the gut microbiome of the food provisioned (e.g., fruits) wild populations were enriched genes involved in carbohydrate metabolism. Moreover, the gut microbiome of the wild-foraging population shared a putatively functional convergence with the gut microbiome of wild bamboo-eating pandas: such as microbes and genes involved in the cyanide detoxification. Therefore, the gut microbiome of the Yunnan snub-nosed monkey displayed the potential plasticity in response to diet flexibility. Long-term food-provisioning of the wild population has led to dramatic changes in gut microbial composition, function, and even antibiotic resistance. The antibiotic resistance profile for the wild Yunnan snub-nosed monkey population could be considered the baseline and an important piece of information for conservation.
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Affiliation(s)
- Wancai Xia
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, Sichuan, China
- Institute of Rare Animals and Plants, China West Normal University, Nanchong, Sichuan, China
| | - Guoqi Liu
- Mingke Biotechnology, Hangzhou, China
| | - Dali Wang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, Sichuan, China
- Institute of Rare Animals and Plants, China West Normal University, Nanchong, Sichuan, China
| | - Hua Chen
- Mingke Biotechnology, Hangzhou, China
| | - Lifeng Zhu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
- Corresponding authors at: College of Life Science, Nanjing Normal University, Nanjing, China (L. Zhu); Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), Nanchong, China West Normal University, China (D. Li).
| | - Dayong Li
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, Sichuan, China
- Institute of Rare Animals and Plants, China West Normal University, Nanchong, Sichuan, China
- Corresponding authors at: College of Life Science, Nanjing Normal University, Nanjing, China (L. Zhu); Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), Nanchong, China West Normal University, China (D. Li).
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13
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Xu J, Cui Z, Zhang W, Lu J, Lu X, Yu W. Characterizing of a new α-agarase AgaE from Thalassomonas sp. LD5 and probing its catalytically essential residues. Int J Biol Macromol 2022; 194:50-57. [PMID: 34863832 DOI: 10.1016/j.ijbiomac.2021.11.194] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 11/15/2021] [Accepted: 11/28/2021] [Indexed: 11/26/2022]
Abstract
A new α-agarase AgaE belonging to glycoside hydrolase (GH) family 96 was identified and cloned from marine bacterium Thalassomonas sp. LD5. AgaE consists of 926 amino acids with a theoretical molecular mass of 97 kDa. The optimum temperature and pH for recombinant AgaE were 35 °C and 7.0, respectively. In contrast to known α-agarases, the activity of AgaE does not depend on Ca2+, but on Na+. Thin-layer chromatography and 13C NMR analysis revealed that AgaE endohydrolytic of agarose to produce agarotetraose and agarohexaose as the final main products. Extensive site-directed mutagenesis studies on the conserved carboxylic amino acids of GH96 revealed two essential amino acids for AgaE, D779 and D781. Replacing D779 with G779 leads to complete inactivation of the enzyme, while D781G results in 70% loss of activity. Later studies showed that site D781 involved in the binding of Na+, and its mutation raised the optimal concentration of Na+ 4 times higher than that of the wild type. However, attempts to rescue the mutant's activities with sodium azide were failed. Kinetic parameters comparison of AgaE, AgaD, another α-agarase from LD5, and their mutants revealed that the former aspartic acid plays critical role in the catalysis.
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Affiliation(s)
- Jingnan Xu
- School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Key Laboratory of Glycoscience & Glycotechnology of Shandong Province, Key Laboratory of Marine Drugs, Chinese Ministry of Education, China
| | - Zibo Cui
- School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Key Laboratory of Glycoscience & Glycotechnology of Shandong Province, Key Laboratory of Marine Drugs, Chinese Ministry of Education, China
| | - Weibin Zhang
- School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Key Laboratory of Glycoscience & Glycotechnology of Shandong Province, Key Laboratory of Marine Drugs, Chinese Ministry of Education, China
| | - Jingxuan Lu
- School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Key Laboratory of Glycoscience & Glycotechnology of Shandong Province, Key Laboratory of Marine Drugs, Chinese Ministry of Education, China
| | - Xinzhi Lu
- School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Key Laboratory of Glycoscience & Glycotechnology of Shandong Province, Key Laboratory of Marine Drugs, Chinese Ministry of Education, China.
| | - Wengong Yu
- School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Key Laboratory of Glycoscience & Glycotechnology of Shandong Province, Key Laboratory of Marine Drugs, Chinese Ministry of Education, China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, China.
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14
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Cha JH, Hong M, Cha CJ. Fungal β-Glycosidase Belonging to Subfamily 4 of Glycoside Hydrolase Family 30 with Transglycosylation Activity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:15261-15267. [PMID: 34879649 DOI: 10.1021/acs.jafc.1c05197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Fomitopsis palustris, a prominent wood decayer, is known to produce a variety of glycoside hydrolases (GHs). In this study, we characterized a fungal β-glycosidase belonging to subfamily 4 of GH family 30 (GH30). The recombinant protein (FpGH30) showed the highest hydrolytic activity toward p-nitrophenyl-β-d-fucopyranoside (pNPβFuc), followed by p-nitrophenyl-α-l-arabinopyranoside (pNPαAra) and p-nitrophenyl-β-d-galactopyranoside (pNPβGal). FpGH30 also exhibited transglycosylation activities, which catalyzed the transfer of glycosyl moieties to different glycosides and alkyl alcohols. When pNPβFuc, pNPβGal, and pNPαAra were used as substrates, self-condensation reactions occurred, leading to the production of the corresponding transglycosylated products with yields of 21, 26, and 25%, respectively. The enzyme was also able to catalyze the transfucosylation of pNP derivatives of β-d-glucose, β-d-mannose, and β-d-xylose and alkyl alcohols (C1-C6), producing the corresponding transfucosylated products and alkyl fucosides. Our study indicates that FpGH30 is the first characterized fungal β-glycosidase belonging to subfamily 4 of GH30 with transglycosylation activities.
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Affiliation(s)
- Ju-Hee Cha
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Minsun Hong
- Division of Biological Science and Technology, Yonsei University, Wonju 26493, Republic of Korea
| | - Chang-Jun Cha
- Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea
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15
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Functional and structural characterization of a GH3 β-N-acetylhexosaminidase from Akkermansia muciniphila involved in mucin degradation. Biochem Biophys Res Commun 2021; 589:186-191. [PMID: 34922201 DOI: 10.1016/j.bbrc.2021.12.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 12/07/2021] [Indexed: 01/06/2023]
Abstract
Akkermansia muciniphila is a probiotic that colonizes the outer layer of intestinal mucus and is negatively associated with metabolic disorders. Amuc_2109 protein, a β-N-acetylhexosaminidase from A. muciniphila, may be involved in the degradation of mucins and is associated with intestinal health. Here, we reported the crystal structure of Amuc_2109, which belongs to the GH family 3 enzymes and fell into the canonical (α/β)8 TIM barrel structure with GlcNAc bound to the active center. Biochemical assay characterization of Amuc_2109 revealed that Amuc_2109 is a GlcNAc-specific glycosidase active over a wide temperature and pH range, reflecting the survival advantage of Amuc_2109 in the intestinal environment. Our structural and biochemical results will contribute to the understanding of the catalytic mechanism of the GH3 β-N-acetylhexosaminidase and help to gain insight into the molecular mechanism of complex carbohydrate utilization and restoration of the intestinal barrier in A. muciniphila.
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16
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Hansen AL, Koivisto JM, Simonsen S, Dong Z, Crehuet R, Hansen DK, Willemoës M. Identification of a Catalytic Nucleophile-Activating Network in the endo -α -N-Acetylgalactosaminidase of Family GH101. Biochemistry 2021; 60:3398-3407. [PMID: 34694774 DOI: 10.1021/acs.biochem.1c00596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bifidobacterium longum endo-α-N-acetylgalactosaminidase (GH101), EngBF, is highly specific toward the mucin Core 1 glycan, Galβ1-3GalNAc. Apart from the side chains involved in the retaining mechanism of EngBF, Asp-682 is important for the activity. In the crystal structures of both EngBF and EngSP (from Streptococcus pneumoniae), we identified a conserved water molecule in proximity to Asp-682 and the homologue residue in EngSP. The water molecule also coordinates the catalytic nucleophile and three other residues conserved in GH101 enzymes; in EngBF, these residues are His-685, His-718, and Asn-720. With casein-glycomacropeptide as the substrate, the importance of Asp-682 was confirmed by the lack of a detectable activity for the D682N enzyme. The enzyme variants, H685A, H718A, H685Q, and H718Q, all displayed only a modestly reduction in kcat of up to 15 fold for the H718A variant. However, the double-substituted variants, H685A/H718A and H685Q/H718Q, had a greatly reduced kcat value by about 200 fold compared to that of wild-type EngBF. With the synthetic substrate, Galβ(1-3)GalNAcα1-para-nitrophenol, kcat of the double-substituted variants was only up to 30-fold reduced and was found to increase with pH. Compared to the pre-steady-state kinetics of wild-type EngBF, a burst of about the size of the enzyme concentration was absent with the double-substituted EngBF variants, indicating that the nucleophilic attack had become at least as slow as the hydrolysis of the enzyme intermediate. Together, the results indicate that not only Asp-682 but also the entire conserved network of His-685, His-718, and what we suggest is a catalytic water molecule is important in the activation of the catalytic nucleophile.
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Affiliation(s)
- Anders Lønstrup Hansen
- Linderstrøm-Lang Centre, Section for Biomolecular Sciences, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | - Johanna M Koivisto
- Linderstrøm-Lang Centre, Section for Biomolecular Sciences, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | - Signe Simonsen
- Linderstrøm-Lang Centre, Section for Biomolecular Sciences, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | - Zehui Dong
- Linderstrøm-Lang Centre, Section for Biomolecular Sciences, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | - Ramon Crehuet
- CSIC-Institute for Advanced Chemistry of Catalonia (IQAC), c/ Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Dennis K Hansen
- Linderstrøm-Lang Centre, Section for Biomolecular Sciences, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | - Martin Willemoës
- Linderstrøm-Lang Centre, Section for Biomolecular Sciences, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
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17
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Amin K, Tranchimand S, Benvegnu T, Abdel-Razzak Z, Chamieh H. Glycoside Hydrolases and Glycosyltransferases from Hyperthermophilic Archaea: Insights on Their Characteristics and Applications in Biotechnology. Biomolecules 2021; 11:1557. [PMID: 34827555 PMCID: PMC8615776 DOI: 10.3390/biom11111557] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/09/2021] [Accepted: 10/16/2021] [Indexed: 01/18/2023] Open
Abstract
Hyperthermophilic Archaea colonizing unnatural habitats of extremes conditions such as volcanoes and deep-sea hydrothermal vents represent an unmeasurable bioresource for enzymes used in various industrial applications. Their enzymes show distinct structural and functional properties and are resistant to extreme conditions of temperature and pressure where their mesophilic homologs fail. In this review, we will outline carbohydrate-active enzymes (CAZymes) from hyperthermophilic Archaea with specific focus on the two largest families, glycoside hydrolases (GHs) and glycosyltransferases (GTs). We will present the latest advances on these enzymes particularly in the light of novel accumulating data from genomics and metagenomics sequencing technologies. We will discuss the contribution of these enzymes from hyperthermophilic Archaea to industrial applications and put the emphasis on newly identifed enzymes. We will highlight their common biochemical and distinct features. Finally, we will overview the areas that remain to be explored to identify novel promising hyperthermozymes.
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Affiliation(s)
- Khadija Amin
- Laboratory of Applied Biotechnology, Azm Center for Research in Biotechnology and Its Applications, Lebanese University, Mitein Street, Tripoli P.O. Box 210, Lebanon; (K.A.); (Z.A.-R.)
- Univ Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR-UMR 6226, F-35000 Rennes, France; (S.T.); (T.B.)
| | - Sylvain Tranchimand
- Univ Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR-UMR 6226, F-35000 Rennes, France; (S.T.); (T.B.)
| | - Thierry Benvegnu
- Univ Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, ISCR-UMR 6226, F-35000 Rennes, France; (S.T.); (T.B.)
| | - Ziad Abdel-Razzak
- Laboratory of Applied Biotechnology, Azm Center for Research in Biotechnology and Its Applications, Lebanese University, Mitein Street, Tripoli P.O. Box 210, Lebanon; (K.A.); (Z.A.-R.)
- Faculty of Sciences, Lebanese University, Rafic Hariri Campus, Beirut P.O. Box 6573, Lebanon
| | - Hala Chamieh
- Laboratory of Applied Biotechnology, Azm Center for Research in Biotechnology and Its Applications, Lebanese University, Mitein Street, Tripoli P.O. Box 210, Lebanon; (K.A.); (Z.A.-R.)
- Faculty of Sciences, Lebanese University, Rafic Hariri Campus, Beirut P.O. Box 6573, Lebanon
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18
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Chen A, Wang D, Ji R, Li J, Gu S, Tang R, Ji C. Structural and Catalytic Characterization of TsBGL, a β-Glucosidase From Thermofilum sp. ex4484_79. Front Microbiol 2021; 12:723678. [PMID: 34659150 PMCID: PMC8517440 DOI: 10.3389/fmicb.2021.723678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/25/2021] [Indexed: 11/13/2022] Open
Abstract
Beta-glucosidase is an enzyme that catalyzes the hydrolysis of the glycosidic bonds of cellobiose, resulting in the production of glucose, which is an important step for the effective utilization of cellulose. In the present study, a thermostable β-glucosidase was isolated and purified from the Thermoprotei Thermofilum sp. ex4484_79 and subjected to enzymatic and structural characterization. The purified β-glucosidase (TsBGL) exhibited maximum activity at 90°C and pH 5.0 and displayed maximum specific activity of 139.2μmol/min/mgzne against p-nitrophenyl β-D-glucopyranoside (pNPGlc) and 24.3μmol/min/mgzen against cellobiose. Furthermore, TsBGL exhibited a relatively high thermostability, retaining 84 and 47% of its activity after incubation at 85°C for 1.5h and 90°C for 1.5h, respectively. The crystal structure of TsBGL was resolved at a resolution of 2.14Å, which revealed a classical (α/β)8-barrel catalytic domain. A structural comparison of TsBGL with other homologous proteins revealed that its catalytic sites included Glu210 and Glu414. We provide the molecular structure of TsBGL and the possibility of improving its characteristics for potential applications in industries.
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Affiliation(s)
- Anke Chen
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Dan Wang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Rui Ji
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Shaohua Gu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Rong Tang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Chaoneng Ji
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
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19
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Feng J, Xu S, Feng R, Kovalevsky A, Zhang X, Liu D, Wan Q. Identification and structural analysis of a thermophilic β-1,3-glucanase from compost. BIORESOUR BIOPROCESS 2021; 8:102. [PMID: 38650272 PMCID: PMC10992293 DOI: 10.1186/s40643-021-00449-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 09/24/2021] [Indexed: 11/10/2022] Open
Abstract
β-1,3-glucanase can specifically hydrolyze glucans to oligosaccharides and has potential applications in biotechnology. We used the metatranscriptomic technology to discover a thermophilic β-1,3-glucanase from compost. The phylogenetic study shows that it belongs to the family 16 glycoside hydrolase (GH16) and is most homologous with an enzyme from Streptomyces sioyaensis, an actinobacterium. It has the activity of 146.9 U/mg in the optimal reaction condition (75 °C and pH 5.5). Its catalytic domain was crystallized and diffracted to 1.14 Å resolution. The crystal structure shows a sandwich-like β-jelly-roll fold with two disulfide bonds. After analyzing the occurring frequencies of these cysteine residues, we designed two mutants (C160G and C180I) to study the role of these disulfide bonds. Both mutants have decreased their optimal temperature from 75 to 70 °C, which indicate that the disulfide bonds are important to maintain thermostability. Interestingly, the activity of C160G has increased ~ 17% to reach 171.4 U/mg. We speculate that the increased activity of C160G mutant is due to increased dynamics near the active site. Our studies give a good example of balancing the rigidity and flexibility for enzyme activity, which is helpful for protein engineering.
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Affiliation(s)
- Jianwei Feng
- College of Science, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Shenyuan Xu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, People's Republic of China
| | - Ruirui Feng
- College of Science, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Xia Zhang
- Department of Molecular Biology, Qingdao Vland Biotech Group Inc., Qingdao, Shandong, 266000, People's Republic of China
| | - Dongyang Liu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Qun Wan
- College of Science, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
- Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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20
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Maruyama S, Sawano K, Amaki S, Suzuki T, Narita S, Kimura K, Arakawa T, Yamada C, Ito Y, Dohmae N, Fujita K, Ishiwata A, Fushinobu S. Substrate complex structure, active site labeling and catalytic role of the zinc ion in cysteine glycosidase. Glycobiology 2021; 32:171-180. [PMID: 34735571 DOI: 10.1093/glycob/cwab103] [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] [Received: 06/27/2021] [Revised: 09/16/2021] [Accepted: 09/30/2021] [Indexed: 11/13/2022] Open
Abstract
β-l-Arabinofuranosidase HypBA1 from Bifidobacterium longum belongs to the glycoside hydrolase family 127. At the active site of HypBA1, a cysteine residue (Cys417) coordinates with a Zn2+ atom and functions as the catalytic nucleophile for the anomer-retaining hydrolytic reaction. In this study, the role of Zn2+ ion and cysteine in catalysis as well as the substrate-bound structure were studied based on biochemical and crystallographic approaches. The enzymatic activity of HypBA1 decreased after dialysis in the presence of EDTA and guanidine hydrochloride and was then recovered by the addition of Zn2+. The Michaelis complex structure was determined using a crystal of a mutant at the acid/base catalyst residue (E322Q) soaked in a solution containing the substrate p-nitrophenyl-β-l-arabinofuranoside. To investigate the covalent thioglycosyl enzyme intermediate structure, synthetic inhibitors of l-arabinofuranosyl haloacetamide derivatives with different anomer configurations were used to target the nucleophilic cysteine. In the crystal structure of HypBA1, β-configured l-arabinofuranosylamide formed a covalent link with Cys417, whereas α-configured l-arabinofuranosylamide was linked to a noncatalytic residue Cys415. Mass spectrometric analysis indicated that Cys415 was also reactive with the probe molecule. With the β-configured inhibitor, the arabinofuranoside moiety was correctly positioned at the subsite and the active site integrity was retained to successfully mimic the covalent intermediate state.
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Affiliation(s)
- Shun Maruyama
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kota Sawano
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Satoko Amaki
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takehiro Suzuki
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Satoru Narita
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Graduate School of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma, Saitama 337-8570, Japan
| | - Kenta Kimura
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Graduate School of Systems Engineering and Science, Shibaura Institute of Technology, 307 Fukasaku, Minuma, Saitama 337-8570, Japan
| | - Takatoshi Arakawa
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Chihaya Yamada
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yukishige Ito
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.,Graduate School of Science, Osaka University, 1-1 Machikaneyamacho, Toyonaka, Osaka 560-0043, Japan
| | - Naoshi Dohmae
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kiyotaka Fujita
- Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima 890-0065, Japan
| | - Akihiro Ishiwata
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Shinya Fushinobu
- Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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21
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Cayetano RDA, Park J, Kim GB, Jung JH, Kim SH. Enhanced anaerobic digestion of waste-activated sludge via bioaugmentation strategy-Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt2) analysis through hydrolytic enzymes and possible linkage to system performance. BIORESOURCE TECHNOLOGY 2021; 332:125014. [PMID: 33839513 DOI: 10.1016/j.biortech.2021.125014] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/13/2021] [Accepted: 03/13/2021] [Indexed: 06/12/2023]
Abstract
In this study, anaerobic digestion of waste-activated sludge was bioaugmented with hydrolytic bacteria, Bacteroidetes uniformis (Bacteroidetes, B) and Clostridium sp. (Firmicutes, F) at various dosages. Bioaugmentation resulted in enhanced methane conversion of waste-activated sludge. The highest methane yield of 298.1 mL CH4/g-COD, 85.2% COD conversion efficiency was obtained when Bacteroidetes uniformis and Clostridium sp. were augmented at 100 and 900 CFU/mL, respectively. The microbial community analysis demonstrated that bioaugmentation increased the proportion of Bacteroidetes, Firmicutes, and Proteobacteria. Furthermore, at the highest methane yield, the principal methanogenic pathway was altered from acetoclastic to a mixture of hydrogenotrophic and acetoclastic; the major species shifted from Methanosaeta concilii to Methanobacterium subterraneum. Predicted gene analysis revealed that increased expression of hydrolases resulted in enhanced methane conversion through bioaugmentation.
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Affiliation(s)
- Roent Dune A Cayetano
- School of Civil and Environmental Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Jungsu Park
- School of Civil and Environmental Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Gi-Beom Kim
- School of Civil and Environmental Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Ju-Hyeong Jung
- School of Civil and Environmental Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Sang-Hyoun Kim
- School of Civil and Environmental Engineering, Yonsei University, Seoul 03722, Republic of Korea.
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22
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Unconventional β-Glucosidases: A Promising Biocatalyst for Industrial Biotechnology. Appl Biochem Biotechnol 2021; 193:2993-3016. [PMID: 33871765 DOI: 10.1007/s12010-021-03568-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 04/08/2021] [Indexed: 10/21/2022]
Abstract
β-Glucosidases primarily catalyze removal of terminal glucosyl residues from a variety of glucoconjugates and also perform transglycosylation and reverse hydrolysis. These catalytic properties can be readily exploited for degradation of lignocellulosic biomass as well as for pharmaceutical, food and flavor industries. β-Glucosidases have been either isolated in the native form from the producer organism or recombinantly expressed and gaged for their biochemical properties and substrate specificities. Although almond and Aspergillus niger have been instantly recognizable sources of β-glucosidases utilized for various applications, an intricate pool of novel β-glucosidases from different sources can provide their potent replacements. Moreover, one can envisage the better efficacy of these novel candidates in biofuel and biorefinery industries facilitating efficient degradation of biomass. This article reviews properties of the novel β-glucosidases such as glucose tolerance and activation, substrate specificity, and thermostability which can be useful for their applications in lignocellulose degradation, food industry, and pharmaceutical industry in comparison with the β-glucosidases from the conventional sources. Such β-glucosidases have potential for encouraging white biotechnology.
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23
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Ishida T, Parks JM, Smith JC. Insight into the Catalytic Mechanism of GH11 Xylanase: Computational Analysis of Substrate Distortion Based on a Neutron Structure. J Am Chem Soc 2020; 142:17966-17980. [PMID: 32959658 DOI: 10.1021/jacs.0c02148] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The reaction mechanism of biomass decomposition by xylanases remains the subject of debate. To clarify the mechanism we investigated the glycosylation step of GH11 xylanase, an enzyme that catalyzes the hydrolysis of lignocellulosic hemicellulose (xylan). Making use of a recent neutron crystal structure, which revealed the protonation states of relevant residues, we used ab initio quantum mechanics/molecular mechanics (QM/MM) calculations to determine the detailed reaction mechanism of the glycosylation step. In particular, our focus is on the controversial question of whether or not an oxocarbenium ion intermediate is formed on the reaction pathway. The calculations support the validity of a basic retaining mechanism within a double-displacement scheme. The estimated free energy barrier of this reaction is ∼18 kcal/mol with QM/MM-CCSD(T)/6-31(+)G**//MP2/6-31+G**/AMBER calculations, and the rate-determining step of the glycosylation is scission of the glycosidic bond after proton transfer from the acidic Glu177. The estimated lifetime of the oxocarbenium ion intermediate (on the order of tens of ps) and the secondary kinetic isotope effect suggest that there is no accumulation of this intermediate on the reaction path, although the intermediate can be transiently formed. In the enzyme-substrate (ES) complex, the carbohydrate structure of the xylose residue at the -1 subsite has a rather distorted (skewed) geometry, and this xylose unit at the active site has an apparent half-chair conformation when the oxocarbenium ion intermediate is formed. The major catalytic role of the protein environment is to orient residues that take part in the initial proton transfer. Because of a fine alignment of catalytic residues, the enzyme can accelerate the glycosylation reaction without paying a reorganization energy penalty.
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Affiliation(s)
- Toyokazu Ishida
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 2, 1-1-1 Umezono, Tsukuba 305-8568, Japan
| | - Jerry M Parks
- Center for Molecular Biophysics (CMB), Biosciences Division, Oak Ridge National Laboratory (ORNL), 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
| | - Jeremy C Smith
- Center for Molecular Biophysics (CMB), Biosciences Division, Oak Ridge National Laboratory (ORNL), 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
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24
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Li Z, Liu W, Lyu Q. Biochemical Characterization of a Novel Endo-1,3-β-Glucanase from the Scallop Chlamys farreri. Mar Drugs 2020; 18:md18090466. [PMID: 32947865 PMCID: PMC7551256 DOI: 10.3390/md18090466] [Citation(s) in RCA: 3] [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: 08/26/2020] [Revised: 09/11/2020] [Accepted: 09/13/2020] [Indexed: 01/05/2023] Open
Abstract
Endo-1,3-β-glucanases derived from marine mollusks have attracted much attention in recent years because of their unique transglycosylation activity. In this study, a novel endo-1,3-β-glucanase from the scallop Chlamys farreri, named Lcf, was biochemically characterized. Unlike in earlier studies on marine mollusk endo-1,3-β-glucanases, Lcf was expressed in vitro first. Enzymatic analysis demonstrated that Lcf preferred to hydrolyze laminarihexaose than to hydrolyze laminarin. Furthermore, Lcf was capable of catalyzing transglycosylation reactions with different kinds of glycosyl acceptors. More interestingly, the transglycosylation specificity of Lcf was different from that of other marine mollusk endo-1,3-β-glucanases, although they share a high sequence identity. This study enhanced our understanding of the diverse enzymatic specificities of marine mollusk endo-1,3-β-glucanases, which facilitated development of a unique endo-1,3-β-glucanase tool in the synthesis of novel glycosides.
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Affiliation(s)
- Zhijian Li
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (Z.L.); (W.L.)
| | - Weizhi Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (Z.L.); (W.L.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, China
| | - Qianqian Lyu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China; (Z.L.); (W.L.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, China
- Correspondence:
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25
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Torgbo S, Sukyai P. Biodegradation and thermal stability of bacterial cellulose as biomaterial: The relevance in biomedical applications. Polym Degrad Stab 2020. [DOI: 10.1016/j.polymdegradstab.2020.109232] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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26
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Nutho B, Pengthaisong S, Tankrathok A, Lee VS, Ketudat Cairns JR, Rungrotmongkol T, Hannongbua S. Structural Basis of Specific Glucoimidazole and Mannoimidazole Binding by Os3BGlu7. Biomolecules 2020; 10:biom10060907. [PMID: 32549280 PMCID: PMC7356692 DOI: 10.3390/biom10060907] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/09/2020] [Accepted: 06/11/2020] [Indexed: 01/07/2023] Open
Abstract
β-Glucosidases and β-mannosidases hydrolyze substrates that differ only in the epimer of the nonreducing terminal sugar moiety, but most such enzymes show a strong preference for one activity or the other. Rice Os3BGlu7 and Os7BGlu26 β-glycosidases show a less strong preference, but Os3BGlu7 and Os7BGlu26 prefer glucosides and mannosides, respectively. Previous studies of crystal structures with glucoimidazole (GIm) and mannoimidazole (MIm) complexes and metadynamic simulations suggested that Os7BGlu26 hydrolyzes mannosides via the B2,5 transition state (TS) conformation preferred for mannosides and glucosides via their preferred 4H3/4E TS conformation. However, MIm is weakly bound by both enzymes. In the present study, we found that MIm was not bound in the active site of crystallized Os3BGlu7, but GIm was tightly bound in the -1 subsite in a 4H3/4E conformation via hydrogen bonds with the surrounding residues. One-microsecond molecular dynamics simulations showed that GIm was stably bound in the Os3BGlu7 active site and the glycone-binding site with little distortion. In contrast, MIm initialized in the B2,5 conformation rapidly relaxed to a E3/4H3 conformation and moved out into a position in the entrance of the active site, where it bound more stably despite making fewer interactions. The lack of MIm binding in the glycone site in protein crystals and simulations implies that the energy required to distort MIm to the B2,5 conformation for optimal active site residue interactions is sufficient to offset the energy of those interactions in Os3BGlu7. This balance between distortion and binding energy may also provide a rationale for glucosidase versus mannosidase specificity in plant β-glycosidases.
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Affiliation(s)
- Bodee Nutho
- Center of Excellence in Computational Chemistry (CECC), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Salila Pengthaisong
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; (S.P.); (A.T.)
- Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Anupong Tankrathok
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; (S.P.); (A.T.)
- Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Vannajan Sanghiran Lee
- Department of Chemistry, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia;
| | - James R. Ketudat Cairns
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand; (S.P.); (A.T.)
- Center for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
- Correspondence: (J.R.K.C.); (T.R.); (S.H.); Tel.: +66-4422-4304 (J.R.K.C.); +66-2218-5426 (T.R.); +66-2218-7602 (S.H.)
| | - Thanyada Rungrotmongkol
- Biocatalyst and Environmental Biotechnology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
- Correspondence: (J.R.K.C.); (T.R.); (S.H.); Tel.: +66-4422-4304 (J.R.K.C.); +66-2218-5426 (T.R.); +66-2218-7602 (S.H.)
| | - Supot Hannongbua
- Center of Excellence in Computational Chemistry (CECC), Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
- Correspondence: (J.R.K.C.); (T.R.); (S.H.); Tel.: +66-4422-4304 (J.R.K.C.); +66-2218-5426 (T.R.); +66-2218-7602 (S.H.)
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27
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García-Cano I, Rocha-Mendoza D, Kosmerl E, Zhang L, Jiménez-Flores R. Technically relevant enzymes and proteins produced by LAB suitable for industrial and biological activity. Appl Microbiol Biotechnol 2020; 104:1401-1422. [DOI: 10.1007/s00253-019-10322-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/06/2019] [Accepted: 12/15/2019] [Indexed: 12/19/2022]
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28
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Bamford NC, Le Mauff F, Subramanian AS, Yip P, Millán C, Zhang Y, Zacharias C, Forman A, Nitz M, Codée JDC, Usón I, Sheppard DC, Howell PL. Ega3 from the fungal pathogen Aspergillus fumigatus is an endo-α-1,4-galactosaminidase that disrupts microbial biofilms. J Biol Chem 2019; 294:13833-13849. [PMID: 31416836 DOI: 10.1074/jbc.ra119.009910] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 08/01/2019] [Indexed: 11/06/2022] Open
Abstract
Aspergillus fumigatus is an opportunistic fungal pathogen that causes both chronic and acute invasive infections. Galactosaminogalactan (GAG) is an integral component of the A. fumigatus biofilm matrix and a key virulence factor. GAG is a heterogeneous linear α-1,4-linked exopolysaccharide of galactose and GalNAc that is partially deacetylated after secretion. A cluster of five co-expressed genes has been linked to GAG biosynthesis and modification. One gene in this cluster, ega3, is annotated as encoding a putative α-1,4-galactosaminidase belonging to glycoside hydrolase family 114 (GH114). Herein, we show that recombinant Ega3 is an active glycoside hydrolase that disrupts GAG-dependent A. fumigatus and Pel polysaccharide-dependent Pseudomonas aeruginosa biofilms at nanomolar concentrations. Using MS and functional assays, we demonstrate that Ega3 is an endo-acting α-1,4-galactosaminidase whose activity depends on the conserved acidic residues, Asp-189 and Glu-247. X-ray crystallographic structural analysis of the apo Ega3 and an Ega3-galactosamine complex, at 1.76 and 2.09 Å resolutions, revealed a modified (β/α)8-fold with a deep electronegative cleft, which upon ligand binding is capped to form a tunnel. Our structural analysis coupled with in silico docking studies also uncovered the molecular determinants for galactosamine specificity and substrate binding at the -2 to +1 binding subsites. The findings in this study increase the structural and mechanistic understanding of the GH114 family, which has >600 members encoded by plant and opportunistic human pathogens, as well as in industrially used bacteria and fungi.
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Affiliation(s)
- Natalie C Bamford
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada.,Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - François Le Mauff
- Department of Microbiology and Immunology, Faculty of Medicine, McGill University, Montreal, Quebec H3A 2B4, Canada.,Infectious Disease and Immunity in Global Health, Research Institute of the McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada.,McGill Interdisciplinary Initiative in Infection and Immunity, Montreal, Quebec H3A 1Y2, Canada
| | - Adithya S Subramanian
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada.,Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Patrick Yip
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Claudia Millán
- Structural Biology, Instituto de Biología Molecular de Barcelona, CSIC, Carrer Baldiri Reixac 15, 3 A17, Barcelona 08028, Spain
| | - Yongzhen Zhang
- Leiden Institute of Chemistry, Leiden University, 2300RA Leiden, The Netherlands
| | - Caitlin Zacharias
- Department of Microbiology and Immunology, Faculty of Medicine, McGill University, Montreal, Quebec H3A 2B4, Canada.,Infectious Disease and Immunity in Global Health, Research Institute of the McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada.,McGill Interdisciplinary Initiative in Infection and Immunity, Montreal, Quebec H3A 1Y2, Canada
| | - Adam Forman
- Department of Chemistry, Faculty of Arts and Sciences, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Mark Nitz
- Department of Chemistry, Faculty of Arts and Sciences, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Jeroen D C Codée
- Leiden Institute of Chemistry, Leiden University, 2300RA Leiden, The Netherlands
| | - Isabel Usón
- Structural Biology, Instituto de Biología Molecular de Barcelona, CSIC, Carrer Baldiri Reixac 15, 3 A17, Barcelona 08028, Spain.,ICREA, Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys, 23, E-08003 Barcelona, Spain
| | - Donald C Sheppard
- Department of Microbiology and Immunology, Faculty of Medicine, McGill University, Montreal, Quebec H3A 2B4, Canada .,Infectious Disease and Immunity in Global Health, Research Institute of the McGill University Health Centre, Montreal, Quebec H4A 3J1, Canada.,McGill Interdisciplinary Initiative in Infection and Immunity, Montreal, Quebec H3A 1Y2, Canada
| | - P Lynne Howell
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada .,Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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29
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Chen JJ, Liang X, Wang F, Wen YH, Chen TJ, Liu WC, Gong T, Yang JL, Zhu P. Combinatorial mutation on the β-glycosidase specific to 7- β-xylosyltaxanes and increasing the mutated enzyme production by engineering the recombinant yeast. Acta Pharm Sin B 2019; 9:626-638. [PMID: 31193781 PMCID: PMC6542770 DOI: 10.1016/j.apsb.2018.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 11/08/2018] [Accepted: 11/18/2018] [Indexed: 11/20/2022] Open
Abstract
Taxol is a “blockbuster” antitumor drug produced by Taxus species with extremely low amount, while its analogue 7-β-xylosyl-10-deacetyltaxol is generally much higher in the plants. Both the fungal enzymes LXYL-P1−1 and LXYL-P1−2 can convert 7-β-xylosyl-10-deacetyltaxol into 10-deacetyltaxol for Taxol semi-synthesis. Of them, LXYL-P1−2 is twice more active than LXYL-P1−1, but there are only 11 significantly different amino acids in terms of the polarity and acidic-basic properties between them. In this study, single and multiple site-directed mutations at the 11 sites from LXYL-P1−1 to LXYL-P1−2 were performed to define the amino acids with upward bias in activities and to acquire variants with improved catalytic properties. Among all the 17 mutants, E12 (A72T/V91S) was the most active and even displayed 2.8- and 3-fold higher than LXYL-P1−2 on β-xylosidase and β-glucosidase activities. The possible mechanism for such improvement was proposed by homology modeling and molecular docking between E12 and 7-β-xylosyl-10-deacetyltaxol. The recombinant yeast GS115-P1E12-7 was constructed by introducing variant E12, the molecular chaperone gene pdi and the bacterial hemoglobin gene vhb. This engineered yeast rendered 4 times higher biomass enzyme activity than GS115-3.5K-P1−2 that had been used for demo-scale fermentation. Thus, GS115-P1E12-7 becomes a promising candidate to replace GS115-3.5K-P1−2 for industrial purpose.
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30
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Nomura T, Iwase H, Saka N, Takahashi N, Mikami B, Mizutani K. High-resolution crystal structures of the glycoside hydrolase family 45 endoglucanase EG27II from the snail Ampullaria crossean. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:426-436. [PMID: 30988259 DOI: 10.1107/s2059798319003000] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 02/27/2019] [Indexed: 11/10/2022]
Abstract
Although endogenous animal cellulases have great potential for industrial applications such as bioethanol production, few investigations have focused on these enzymes. In this study, the glycoside hydrolase family 45 (GH45) subfamily B endoglucanase EG27II from the snail Ampullaria crossean was expressed using a Pichia pastoris expression system and the crystal structure of the apo form was determined at 1.00 Å resolution; this is the highest resolution structure of an animal endoglucanase. The results showed that EG27II has a double-ψ six-stranded β-barrel and that the structure of EG27II more closely resembles those of subfamily C enzymes than those of subfamily A enzymes. The structure of EG27II complexed with cellobiose was also determined under cryoconditions and at room temperature at three pH values, pH 4.0, 5.5 and 8.0, and no structural changes were found to be associated with the change in pH. The structural comparison and catalytic activity measurements showed that Asp137 and Asn112 function as the catalytic acid and base, respectively, and that Asp27 is also an important residue for catalysis. These high-resolution structures of EG27II provide a large amount of information for structure-based enzyme modification and cell-surface engineering, which will advance biofuel production using animal-derived cellulases.
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Affiliation(s)
- Taisuke Nomura
- Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Hisamu Iwase
- Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Naoki Saka
- Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Nobuyuki Takahashi
- Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Bunzo Mikami
- Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Kimihiko Mizutani
- Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan
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31
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Sugano Y, Kuittinen S, Turunen O, Pappinen A. Amino acid-functionalized carbon nanotube framework as a biomimetic catalyst for cleavage of glycosidic bonds. BIOINSPIRATION & BIOMIMETICS 2019; 14:036007. [PMID: 30708363 DOI: 10.1088/1748-3190/ab03de] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In this work, carbon nanotubes (CNTs) functionalized by acidic amino acids were used as a framework, which aims to form a mimetic structure of an active site of the glycoside hydrolases. It was demonstrated that the glycosidic bonds of the disaccharides were cleaved by the fabricated biofunctionalized CNTs. It was implied that the number of carboxyl groups and their individual pKa values in the amino acids, and the distance between the NH2 and the side chain carboxyl groups of the amino acid are predominant factors for determining the reaction efficiency and the optimum pH. It was suggested that glutamic acid functionalized CNTs framework showed the highest efficiency in the cleavage of glycosidic bond of cellobiose than other acidic biomolecules. It was also suggested that the glutamic acid functionalized CNT framework showed preference to the types of glycosidic bonds in the following order: β-1,2-glycoside > β-1,4-glycoside > α-1,4-glycoside [Formula: see text] α-1,1-glycoside bond.
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Affiliation(s)
- Yasuhito Sugano
- Faculty of Science and Forestry, School of Forest Science, University of Eastern Finland, Yliopistonkatu 7, FI-80101 Joensuu, Finland. Faculty of Engineering, Department of Industrial Chemistry, Tokyo University of Science, Shinjuku-ku, 162-0826, Tokyo, Japan
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32
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Singh R, Weikert T, Basa S, Moerschbacher BM. Structural and biochemical insight into mode of action and subsite specificity of a chitosan degrading enzyme from Bacillus spec. MN. Sci Rep 2019; 9:1132. [PMID: 30718524 PMCID: PMC6362164 DOI: 10.1038/s41598-018-36213-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 11/14/2018] [Indexed: 12/14/2022] Open
Abstract
Chitosans, partially de-N-acetylated derivatives of chitin, are multifunctional biopolymers. In nature, biological activities of partially acetylated chitosan polymers are mediated in part by their oligomeric breakdown products, which are generated in situ by the action of chitosanolytic enzymes. Understanding chitosanolytic enzymes, therefore, can lead to the production of chitosan oligomers with fully defined structures that may confer specific bioactivities. To address whether defined oligomer products can be produced via chitosanolytic enzymes, we here characterized a GH8 family chitosanase from Bacillus spec. MN, determining its mode of action and product profiles. We found that the enzyme has higher activity towards polymers with lower degree of acetylation. Oligomeric products were dominated by GlcN3, GlcN3GlcNAc1, and GlcN4GlcNAc1. The product distribution from oligomers were GlcN3 > GlcN2. Modeling and simulations show that the binding site comprises subsites ranging from (-3) to (+3), and a putative (+4) subsite, with defined preferences for GlcN or GlcNAc at each subsite. Flexible loops at the binding site facilitate enzyme-substrate interactions and form a cleft at the active site which can open and close. The detailed insight gained here will help to engineer enzyme variants to produce tailored chitosan oligomers with defined structures that can then be used to probe their specific biological activities.
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Affiliation(s)
- Ratna Singh
- Institute for Biology and Biotechnology of Plants, University of Münster, Schlossplatz 8, 48143, Münster, Germany
| | - Tobias Weikert
- Institute for Biology and Biotechnology of Plants, University of Münster, Schlossplatz 8, 48143, Münster, Germany
| | - Sven Basa
- Institute for Biology and Biotechnology of Plants, University of Münster, Schlossplatz 8, 48143, Münster, Germany
| | - Bruno M Moerschbacher
- Institute for Biology and Biotechnology of Plants, University of Münster, Schlossplatz 8, 48143, Münster, Germany.
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33
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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.
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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
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34
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Iino T, Sakurai M, Furuta T. A novel ring-shaped reaction pathway with interconvertible intermediates in chitinase A as revealed by QM/MM simulation combined with a one-dimensional projection technique. Phys Chem Chem Phys 2019; 21:24956-24966. [DOI: 10.1039/c9cp05163e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Efficient sampling achieved by the use of a one-dimensional projection technique reveals the catalytic mechanism of chitinase A from Serratia marcescens.
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Affiliation(s)
- Tsubasa Iino
- Center for Biological Resources and Informatics
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Minoru Sakurai
- Center for Biological Resources and Informatics
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Tadaomi Furuta
- Center for Biological Resources and Informatics
- Tokyo Institute of Technology
- Yokohama
- Japan
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35
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Bissaro B, Várnai A, Røhr ÅK, Eijsink VGH. Oxidoreductases and Reactive Oxygen Species in Conversion of Lignocellulosic Biomass. Microbiol Mol Biol Rev 2018; 82:e00029-18. [PMID: 30257993 PMCID: PMC6298611 DOI: 10.1128/mmbr.00029-18] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Biomass constitutes an appealing alternative to fossil resources for the production of materials and energy. The abundance and attractiveness of vegetal biomass come along with challenges pertaining to the intricacy of its structure, evolved during billions of years to face and resist abiotic and biotic attacks. To achieve the daunting goal of plant cell wall decomposition, microorganisms have developed many (enzymatic) strategies, from which we seek inspiration to develop biotechnological processes. A major breakthrough in the field has been the discovery of enzymes today known as lytic polysaccharide monooxygenases (LPMOs), which, by catalyzing the oxidative cleavage of recalcitrant polysaccharides, allow canonical hydrolytic enzymes to depolymerize the biomass more efficiently. Very recently, it has been shown that LPMOs are not classical monooxygenases in that they can also use hydrogen peroxide (H2O2) as an oxidant. This discovery calls for a revision of our understanding of how lignocellulolytic enzymes are connected since H2O2 is produced and used by several of them. The first part of this review is dedicated to the LPMO paradigm, describing knowns, unknowns, and uncertainties. We then present different lignocellulolytic redox systems, enzymatic or not, that depend on fluxes of reactive oxygen species (ROS). Based on an assessment of these putatively interconnected systems, we suggest that fine-tuning of H2O2 levels and proximity between sites of H2O2 production and consumption are important for fungal biomass conversion. In the last part of this review, we discuss how our evolving understanding of redox processes involved in biomass depolymerization may translate into industrial applications.
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Affiliation(s)
- Bastien Bissaro
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Anikó Várnai
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Åsmund K Røhr
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Aas, Norway
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36
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Chuzel L, Ganatra MB, Rapp E, Henrissat B, Taron CH. Functional metagenomics identifies an exosialidase with an inverting catalytic mechanism that defines a new glycoside hydrolase family (GH156). J Biol Chem 2018; 293:18138-18150. [PMID: 30249617 PMCID: PMC6254351 DOI: 10.1074/jbc.ra118.003302] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 09/11/2018] [Indexed: 12/24/2022] Open
Abstract
Exosialidases are glycoside hydrolases that remove a single terminal sialic acid residue from oligosaccharides. They are widely distributed in biology, having been found in prokaryotes, eukaryotes, and certain viruses. Most characterized prokaryotic sialidases are from organisms that are pathogenic or commensal with mammals. However, in this study, we used functional metagenomic screening to seek microbial sialidases encoded by environmental DNA isolated from an extreme ecological niche, a thermal spring. Using recombinant expression of potential exosialidase candidates and a fluorogenic sialidase substrate, we discovered an exosialidase having no homology to known sialidases. Phylogenetic analysis indicated that this protein is a member of a small family of bacterial proteins of previously unknown function. Proton NMR revealed that this enzyme functions via an inverting catalytic mechanism, a biochemical property that is distinct from those of known exosialidases. This unique inverting exosialidase defines a new CAZy glycoside hydrolase family we have designated GH156.
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Affiliation(s)
- Léa Chuzel
- From New England Biolabs, Ipswich, Massachusetts 01938,; the Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany
| | | | - Erdmann Rapp
- the Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany,; glyXera GmbH, 39120 Magdeburg, Germany
| | - Bernard Henrissat
- the Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, F-13288 Marseille, France,; the Institut National de la Recherche Agronomique (INRA), Unité Sous Contrat (USC) 1408, Architecture et Fonction des Macromolécules Biologiques, 13288 Marseille, France, and; the Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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37
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You X, Qin Z, Yan Q, Yang S, Li Y, Jiang Z. Structural insights into the catalytic mechanism of a novel glycoside hydrolase family 113 β-1,4-mannanase from Amphibacillus xylanus. J Biol Chem 2018; 293:11746-11757. [PMID: 29871927 DOI: 10.1074/jbc.ra118.002363] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 05/25/2018] [Indexed: 11/06/2022] Open
Abstract
β-1,4-Mannanase degrades β-1,4-mannan polymers into manno-oligosaccharides with a low degree of polymerization. To date, only one glycoside hydrolase (GH) family 113 β-1,4-mannanase, from Alicyclobacillus acidocaldarius (AaManA), has been structurally characterized, and no complex structure of enzyme-manno-oligosaccharides from this family has been reported. Here, crystal structures of a GH family 113 β-1,4-mannanase from Amphibacillus xylanus (AxMan113A) and its complexes with mannobiose, mannotriose, mannopentaose, and mannahexaose were solved. AxMan113A had higher affinity for -1 and +1 mannoses, which explains why the enzyme can hydrolyze mannobiose. At least six subsites (-4 to +2) exist in the groove, but mannose units preferentially occupied subsites -4 to -1 because of steric hindrance formed by Lys-238 and Trp-239. Based on the structural information and bioinformatics, rational design was implemented to enhance hydrolysis activity. Enzyme activity of AxMan113A mutants V139C, N237W, K238A, and W239Y was improved by 93.7, 63.4, 112.9, and 36.4%, respectively, compared with the WT. In addition, previously unreported surface-binding sites were observed. Site-directed mutagenesis studies and kinetic data indicated that key residues near the surface sites play important roles in substrate binding and recognition. These first GH family 113 β-1,4-mannanase-manno-oligosaccharide complex structures may be useful in further studying the catalytic mechanism of GH family 113 members, and provide novel insight into protein engineering of GHs to improve their hydrolysis activity.
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Affiliation(s)
- Xin You
- From the Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Engineering, China Agricultural University, Beijing 100083
| | - Zhen Qin
- the School of Biotechnology, State Key Laboratory of Bioreactor Engineering, R&D Center of Separation and Extraction Technology in Fermentation Industry, East China University of Science and Technology, Shanghai 200237, and
| | - Qiaojuan Yan
- From the Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Engineering, China Agricultural University, Beijing 100083
| | - Shaoqing Yang
- the College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yanxiao Li
- From the Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Engineering, China Agricultural University, Beijing 100083
| | - Zhengqiang Jiang
- the College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
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38
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Borišek J, Pintar S, Ogrizek M, Turk D, Perdih A, Novič M. A Water-Assisted Catalytic Mechanism in Glycoside Hydrolases Demonstrated on the Staphylococcus aureus Autolysin E. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01064] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Jure Borišek
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Sara Pintar
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
- Jozef Stefan International Postgraduate School, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Mitja Ogrizek
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Dušan Turk
- Department of Biochemistry, Molecular and Structural Biology, Jozef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
- Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Andrej Perdih
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
| | - Marjana Novič
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
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39
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Lee IM, Tu IF, Yang FL, Ko TP, Liao JH, Lin NT, Wu CY, Ren CT, Wang AHJ, Chang CM, Huang KF, Wu SH. Structural basis for fragmenting the exopolysaccharide of Acinetobacter baumannii by bacteriophage ΦAB6 tailspike protein. Sci Rep 2017; 7:42711. [PMID: 28209973 PMCID: PMC5314372 DOI: 10.1038/srep42711] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 01/12/2017] [Indexed: 12/24/2022] Open
Abstract
With an increase in antibiotic-resistant strains, the nosocomial pathogen Acinetobacter baumannii has become a serious threat to global health. Glycoconjugate vaccines containing fragments of bacterial exopolysaccharide (EPS) are an emerging therapeutic to combat bacterial infection. Herein, we characterize the bacteriophage ΦAB6 tailspike protein (TSP), which specifically hydrolyzed the EPS of A. baumannii strain 54149 (Ab-54149). Ab-54149 EPS exhibited the same chemical structure as two antibiotic-resistant A. baumannii strains. The ΦAB6 TSP-digested products comprised oligosaccharides of two repeat units, typically with stoichiometric pseudaminic acid (Pse). The 1.48-1.89-Å resolution crystal structures of an N-terminally-truncated ΦAB6 TSP and its complexes with the semi-hydrolyzed products revealed a trimeric β-helix architecture that bears intersubunit carbohydrate-binding grooves, with some features unusual to the TSP family. The structures suggest that Pse in the substrate is an important recognition site for ΦAB6 TSP. A region in the carbohydrate-binding groove is identified as the determinant of product specificity. The structures also elucidated a retaining mechanism, for which the catalytic residues were verified by site-directed mutagenesis. Our findings provide a structural basis for engineering the enzyme to produce desired oligosaccharides, which is useful for the development of glycoconjugate vaccines against A. baumannii infection.
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Affiliation(s)
- I-Ming Lee
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan.,Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - I-Fan Tu
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Feng-Ling Yang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.,Core Facilities for Protein Structural Analysis (CFPSA), Academia Sinica, Taipei 115, Taiwan
| | - Jiahn-Haur Liao
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Nien-Tsung Lin
- Master program in Microbiology and Immunology, Tzu Chi University, Hualien 970, Taiwan
| | - Chung-Yi Wu
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Chien-Tai Ren
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Andrew H-J Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.,Core Facilities for Protein Structural Analysis (CFPSA), Academia Sinica, Taipei 115, Taiwan
| | - Ching-Ming Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Kai-Fa Huang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.,Core Facilities for Protein Structural Analysis (CFPSA), Academia Sinica, Taipei 115, Taiwan
| | - Shih-Hsiung Wu
- Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan.,Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.,Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
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40
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Kameshwar AKS, Qin W. Metadata Analysis of Phanerochaete chrysosporium Gene Expression Data Identified Common CAZymes Encoding Gene Expression Profiles Involved in Cellulose and Hemicellulose Degradation. Int J Biol Sci 2017; 13:85-99. [PMID: 28123349 PMCID: PMC5264264 DOI: 10.7150/ijbs.17390] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 10/10/2016] [Indexed: 01/04/2023] Open
Abstract
In literature, extensive studies have been conducted on popular wood degrading white rot fungus, Phanerochaete chrysosporium about its lignin degrading mechanisms compared to the cellulose and hemicellulose degrading abilities. This study delineates cellulose and hemicellulose degrading mechanisms through large scale metadata analysis of P. chrysosporium gene expression data (retrieved from NCBI GEO) to understand the common expression patterns of differentially expressed genes when cultured on different growth substrates. Genes encoding glycoside hydrolase classes commonly expressed during breakdown of cellulose such as GH-5,6,7,9,44,45,48 and hemicellulose are GH-2,8,10,11,26,30,43,47 were found to be highly expressed among varied growth conditions including simple customized and complex natural plant biomass growth mediums. Genes encoding carbohydrate esterase class enzymes CE (1,4,8,9,15,16) polysaccharide lyase class enzymes PL-8 and PL-14, and glycosyl transferases classes GT (1,2,4,8,15,20,35,39,48) were differentially expressed in natural plant biomass growth mediums. Based on these results, P. chrysosporium, on natural plant biomass substrates was found to express lignin and hemicellulose degrading enzymes more than cellulolytic enzymes except GH-61 (LPMO) class enzymes, in early stages. It was observed that the fate of P. chrysosporium transcriptome is significantly affected by the wood substrate provided. We believe, the gene expression findings in this study plays crucial role in developing genetically efficient microbe with effective cellulose and hemicellulose degradation abilities.
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Affiliation(s)
| | - Wensheng Qin
- Department of Biology, Lakehead University, 955 Oliver Road, Thunder Bay, Ontario, P7B 5E1, Canada
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41
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Mayes HB, Knott BC, Crowley MF, Broadbelt LJ, Ståhlberg J, Beckham GT. Who's on base? Revealing the catalytic mechanism of inverting family 6 glycoside hydrolases. Chem Sci 2016; 7:5955-5968. [PMID: 30155195 PMCID: PMC6091422 DOI: 10.1039/c6sc00571c] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 05/29/2016] [Indexed: 12/16/2022] Open
Abstract
In several important classes of inverting carbohydrate-active enzymes, the identity of the catalytic base remains elusive, including in family 6 Glycoside Hydrolase (GH6) enzymes, which are key components of cellulase cocktails for cellulose depolymerization. Despite many structural and kinetic studies with both wild-type and mutant enzymes, especially on the Trichoderma reesei (Hypocrea jecorina) GH6 cellulase (TrCel6A), the catalytic base in the single displacement inverting mechanism has not been definitively identified in the GH6 family. Here, we employ transition path sampling to gain insight into the catalytic mechanism, which provides unbiased atomic-level understanding of key order parameters involved in cleaving the strong glycosidic bond. Our hybrid quantum mechanics and molecular mechanics (QM/MM) simulations reveal a network of hydrogen bonding that aligns two active site water molecules that play key roles in hydrolysis: one water molecule drives the reaction by nucleophilic attack on the substrate and a second shuttles a proton to the putative base (D175) via a short water wire. We also investigated the case where the putative base is mutated to an alanine, an enzyme that is experimentally still partially active. The simulations predict that proton hopping along a water wire via a Grotthuss mechanism provides a mechanism of catalytic rescue. Further simulations reveal that substrate processive motion is 'driven' by strong electrostatic interactions with the protein at the product sites and that the -1 sugar adopts a 2SO ring configuration as it reaches its binding site. This work thus elucidates previously elusive steps in the processive catalytic mechanism of this important class of enzymes.
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Affiliation(s)
- Heather B Mayes
- Department of Chemical and Biological Engineering , Northwestern University , Evanston , IL 60208 , USA
- National Bioenergy Center , National Renewable Energy Laboratory , Golden , CO 80401 , USA .
| | - Brandon C Knott
- National Bioenergy Center , National Renewable Energy Laboratory , Golden , CO 80401 , USA .
| | - Michael F Crowley
- Biosciences Center , National Renewable Energy Laboratory , Golden , CO 80401 , USA
| | - Linda J Broadbelt
- Department of Chemical and Biological Engineering , Northwestern University , Evanston , IL 60208 , USA
| | - Jerry Ståhlberg
- Department of Chemistry and Biotechnology , Swedish University of Agricultural Sciences , SE-75007 , Uppsala , Sweden .
| | - Gregg T Beckham
- National Bioenergy Center , National Renewable Energy Laboratory , Golden , CO 80401 , USA .
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42
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Immobilization of Glycoside Hydrolase Families GH1, GH13, and GH70: State of the Art and Perspectives. Molecules 2016; 21:molecules21081074. [PMID: 27548117 PMCID: PMC6274110 DOI: 10.3390/molecules21081074] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 08/11/2016] [Accepted: 08/12/2016] [Indexed: 12/20/2022] Open
Abstract
Glycoside hydrolases (GH) are enzymes capable to hydrolyze the glycosidic bond between two carbohydrates or even between a carbohydrate and a non-carbohydrate moiety. Because of the increasing interest for industrial applications of these enzymes, the immobilization of GH has become an important development in order to improve its activity, stability, as well as the possibility of its reuse in batch reactions and in continuous processes. In this review, we focus on the broad aspects of immobilization of enzymes from the specific GH families. A brief introduction on methods of enzyme immobilization is presented, discussing some advantages and drawbacks of this technology. We then review the state of the art of enzyme immobilization of families GH1, GH13, and GH70, with special attention on the enzymes β-glucosidase, α-amylase, cyclodextrin glycosyltransferase, and dextransucrase. In each case, the immobilization protocols are evaluated considering their positive and negative aspects. Finally, the perspectives on new immobilization methods are briefly presented.
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43
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Abellán Flos M, García Moreno MI, Ortiz Mellet C, García Fernández JM, Nierengarten JF, Vincent SP. Potent Glycosidase Inhibition with Heterovalent Fullerenes: Unveiling the Binding Modes Triggering Multivalent Inhibition. Chemistry 2016; 22:11450-60. [DOI: 10.1002/chem.201601673] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Indexed: 12/24/2022]
Affiliation(s)
- Marta Abellán Flos
- Département de Chimie, Laboratoire de Chimie Bio-Organique; University of Namur (UNamur); rue de Bruxelles 61 5000 Namur Belgium
| | - M. Isabel García Moreno
- Departamento de Química Orgánica; Facultad de Química; Universidad de Sevilla; C/Prof. García González 1 41012 Sevilla Spain
| | - Carmen Ortiz Mellet
- Departamento de Química Orgánica; Facultad de Química; Universidad de Sevilla; C/Prof. García González 1 41012 Sevilla Spain
| | - Jose Manuel García Fernández
- Instituto de Investigaciones Químicas (IIQ); CSIC - Universidad de Sevilla; Av. Américo Vespucio 49, Isla de la Cartuja 41092 Sevilla Spain
| | - Jean-Francois Nierengarten
- Laboratoire de Chimie des Matériaux Moléculaires; Université de Strasbourg et CNRS (UMR 7509); Ecole Européenne de Chimie, Polymères et Matériaux; 25 rue Becquerel 67087 Strasbourg France
| | - Stéphane P. Vincent
- Département de Chimie, Laboratoire de Chimie Bio-Organique; University of Namur (UNamur); rue de Bruxelles 61 5000 Namur Belgium
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44
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Yu F, Smet M, Dehaen W, Sels BF. Water-soluble sulfonated hyperbranched poly(arylene oxindole) catalysts as functional biomimics of cellulases. Chem Commun (Camb) 2016; 52:2756-9. [DOI: 10.1039/c5cc08742b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new polymer acid catalyst, sulfonated hyperbranched poly(arylene oxindole), 5-OH–SHPAO, was prepared for selective cellulose hydrolysis.
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Affiliation(s)
- Feng Yu
- Department of Chemistry
- KU Leuven
- 3001 Leuven
- Belgium
- Centre for Surface Chemistry and Catalysis
| | - Mario Smet
- Department of Chemistry
- KU Leuven
- 3001 Leuven
- Belgium
| | - Wim Dehaen
- Department of Chemistry
- KU Leuven
- 3001 Leuven
- Belgium
| | - Bert F. Sels
- Centre for Surface Chemistry and Catalysis
- KU Leuven
- 3001 Leuven
- Belgium
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45
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Lin MG, Chi MC, Naveen V, Li YC, Lin LL, Hsiao CD. Bacillus licheniformistrehalose-6-phosphate hydrolase structures suggest keys to substrate specificity. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016; 72:59-70. [DOI: 10.1107/s2059798315020756] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 11/02/2015] [Indexed: 11/10/2022]
Abstract
Trehalose-6-phosphate hydrolase (TreA) belongs to glycoside hydrolase family 13 (GH13) and catalyzes the hydrolysis of trehalose 6-phosphate (T6P) to yield glucose and glucose 6-phosphate. The products of this reaction can be further metabolized by the energy-generating glycolytic pathway. Here, crystal structures ofBacillus licheniformisTreA (BlTreA) and its R201Q mutant complexed withp-nitrophenyl-α-D-glucopyranoside (R201Q–pPNG) are presented at 2.0 and 2.05 Å resolution, respectively. The overall structure ofBlTreA is similar to those of other GH13 family enzymes. However, detailed structural comparisons revealed that the catalytic site ofBlTreA contains a long loop that adopts a different conformation from those of other GH13 family members. Unlike the homologous regions ofBacillus cereusoligo-1,6-glucosidase (BcOgl) andErwinia rhaponticiisomaltulose synthase (NX-5), the surface potential of theBlTreA active site exhibits a largely positive charge contributed by the four basic residues His281, His282, Lys284 and Lys292. Mutation of these residues resulted in significant decreases in the enzymatic activity ofBlTreA. Strikingly, the281HHLK284motif and Lys292 play critical roles in substrate discrimination byBlTreA.
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46
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Mhlongo SI, den Haan R, Viljoen-Bloom M, van Zyl WH. Lignocellulosic hydrolysate inhibitors selectively inhibit/deactivate cellulase performance. Enzyme Microb Technol 2015; 81:16-22. [DOI: 10.1016/j.enzmictec.2015.07.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 07/01/2015] [Accepted: 07/23/2015] [Indexed: 12/01/2022]
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Structural Insight of a Trimodular Halophilic Cellulase with a Family 46 Carbohydrate-Binding Module. PLoS One 2015; 10:e0142107. [PMID: 26562160 PMCID: PMC4643050 DOI: 10.1371/journal.pone.0142107] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 10/16/2015] [Indexed: 01/08/2023] Open
Abstract
Cellulases are the key enzymes used in the biofuel industry. A typical cellulase contains a catalytic domain connected to a carbohydrate-binding module (CBM) through a flexible linker. Here we report the structure of an atypical trimodular cellulase which harbors a catalytic domain, a CBM46 domain and a rigid CBM_X domain between them. The catalytic domain shows the features of GH5 family, while the CBM46 domain has a sandwich-like structure. The catalytic domain and the CBM46 domain form an extended substrate binding cleft, within which several tryptophan residues are well exposed. Mutagenesis assays indicate that these residues are essential for the enzymatic activities. Gel affinity electrophoresis shows that these tryptophan residues are involved in the polysaccharide substrate binding. Also, electrostatic potential analysis indicates that almost the entire solvent accessible surface of CelB is negatively charged, which is consistent with the halophilic nature of this enzyme.
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48
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Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography. Proc Natl Acad Sci U S A 2015; 112:12384-9. [PMID: 26392527 DOI: 10.1073/pnas.1504986112] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Glycoside hydrolase (GH) enzymes apply acid/base chemistry to catalyze the decomposition of complex carbohydrates. These ubiquitous enzymes accept protons from solvent and donate them to substrates at close to neutral pH by modulating the pKa values of key side chains during catalysis. However, it is not known how the catalytic acid residue acquires a proton and transfers it efficiently to the substrate. To better understand GH chemistry, we used macromolecular neutron crystallography to directly determine protonation and ionization states of the active site residues of a family 11 GH at multiple pD (pD=pH+0.4) values. The general acid glutamate (Glu) cycles between two conformations, upward and downward, but is protonated only in the downward orientation. We performed continuum electrostatics calculations to estimate the pKa values of the catalytic Glu residues in both the apo- and substrate-bound states of the enzyme. The calculated pKa of the Glu increases substantially when the side chain moves down. The energy barrier required to rotate the catalytic Glu residue back to the upward conformation, where it can protonate the glycosidic oxygen of the substrate, is 4.3 kcal/mol according to free energy simulations. These findings shed light on the initial stage of the glycoside hydrolysis reaction in which molecular motion enables the general acid catalyst to obtain a proton from the bulk solvent and deliver it to the glycosidic oxygen.
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Sousa SF, Ramos MJ, Lim C, Fernandes PA. Relationship between Enzyme/Substrate Properties and Enzyme Efficiency in Hydrolases. ACS Catal 2015. [DOI: 10.1021/acscatal.5b00923] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Sérgio F. Sousa
- UCIBIO,
REQUIMTE, Departamento de Química e Bioquímica, Faculdade
de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- UCIBIO,
REQUIMTE, Departamento de Química e Bioquímica, Faculdade
de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Carmay Lim
- Institute
of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
- Department
of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Pedro A. Fernandes
- UCIBIO,
REQUIMTE, Departamento de Química e Bioquímica, Faculdade
de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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50
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Flannelly DF, Aoki TG, Aristilde L. Short-time dynamics of pH-dependent conformation and substrate binding in the active site of beta-glucosidases: A computational study. J Struct Biol 2015; 191:352-64. [PMID: 26160737 DOI: 10.1016/j.jsb.2015.07.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 06/17/2015] [Accepted: 07/03/2015] [Indexed: 12/25/2022]
Abstract
The complete degradation of cellulose to glucose is essential to carbon turnover in terrestrial ecosystems and to engineered biofuel production. A rate-limiting step in this pathway is catalyzed by beta-glucosidase (BG) enzymes, which convert cellulobiose into two glucose molecules. The activity of these enzymes has been shown to vary with solution pH. However, it is not well understood how pH influences the enzyme conformation required for catalytic action on the substrate. A structural understanding of this pH effect is important for predicting shifts in BG activity in bioreactors and environmental matrices, in addition to informing targeted protein engineering. Here we applied molecular dynamics simulations to explore conformational and substrate binding dynamics in two well-characterized BGs of bacterial (Clostridium cellulovorans) and fungal (Trichoderma reesei) origins as a function of pH. The enzymes were simulated in an explicit solvated environment, with NaCl as electrolytes, at their prominent ionization states obtained at pH 5, 6, 7, and 7.5. Our findings indicated that pH-dependent changes in the ionization states of non-catalytic residues localized outside of the immediate active site led to pH-dependent disruption of the active site conformation. This disruption interferes with favorable H-bonding interactions with catalytic residues required to initiate catalysis on the substrate. We also identified specific non-catalytic residues that are involved in stabilizing the substrate at the optimal pH for enzyme activity. The simulations further revealed the dynamics of water-bridging interactions both outside and inside the substrate binding cleft during structural changes in the enzyme-substrate complex. These findings provide new structural insights into the pH-dependent substrate binding specificity in BGs.
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Affiliation(s)
- David F Flannelly
- The Institute for Comparative and Environmental Toxicology, College of Agricultural and Life Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Thalia G Aoki
- Department of Biological and Environmental Engineering, College of Agricultural and Life Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Ludmilla Aristilde
- The Institute for Comparative and Environmental Toxicology, College of Agricultural and Life Sciences, Cornell University, Ithaca, NY 14853, USA; Department of Biological and Environmental Engineering, College of Agricultural and Life Sciences, Cornell University, Ithaca, NY 14853, USA.
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