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Feng Y, Lyu X, Cong Y, Miao T, Fang B, Zhang C, Shen Q, Matthews M, Fisher AJ, Zhang JZH, Zhang L, Yang R. A precise swaying map for how promiscuous cellobiose-2-epimerase operate bi-reaction. Int J Biol Macromol 2023; 253:127093. [PMID: 37758108 DOI: 10.1016/j.ijbiomac.2023.127093] [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: 08/09/2023] [Revised: 09/24/2023] [Accepted: 09/24/2023] [Indexed: 10/02/2023]
Abstract
Promiscuous enzymes play a crucial role in organism survival and new reaction mining. However, comprehensive mapping of the catalytic and regulatory mechanisms hasn't been well studied due to the characteristic complexity. The cellobiose 2-epimerase from Caldicellulosiruptor saccharolyticus (CsCE) with complex epimerization and isomerization was chosen to comprehensively investigate the promiscuous mechanisms. Here, the catalytic frame of ring-opening, cis-enediol mediated catalysis and ring-closing was firstly determined. To map the full view of promiscuous CE, the structure of CsCE complex with the isomerized product glucopyranosyl-β1,4-fructose was determined. Combined with computational calculation, the promiscuity was proved a precise cooperation of the double subsites, loop rearrangement, and intermediate swaying. The flexible loop was like a gear, whose structural reshaping regulates the sway of the intermediates between the two subsites of H377-H188 and H377-H247, and thus regulates the catalytic directions. The different protonated states of cis-enediol intermediate catalyzed by H188 were the key point for the catalysis. The promiscuous enzyme tends to utilize all elements at hand to carry out the promiscuous functions.
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Affiliation(s)
- Yinghui Feng
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China; State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, 214122 Wuxi, China
| | - Xiaomei Lyu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, 214122 Wuxi, China; Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yalong Cong
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Tingwei Miao
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Bohuan Fang
- Department of Micro/Nano Electronics, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chuanxi Zhang
- Department of Micro/Nano Electronics, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiang Shen
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
| | - Melissa Matthews
- Okinawa Institute of Science and Technology, Onna, Okinawa 904-0495, Japan; Department of Chemistry, University of California Davis, Davis, CA 95616, United States; Department of Molecular and Cellular Biology, University of California Davis, Davis, CA 95616, United States
| | - Andrew J Fisher
- Department of Chemistry, University of California Davis, Davis, CA 95616, United States; Department of Molecular and Cellular Biology, University of California Davis, Davis, CA 95616, United States
| | - John Z H Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China; NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China; Department of Chemistry, New York University, New York, NY 10003, United States
| | - Lujia Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China; NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China.
| | - Ruijin Yang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, 214122 Wuxi, China; Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, Jiangnan University, Wuxi, Jiangsu 214122, China.
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Goh KM, Shahar S, Chan KG, Chong CS, Amran SI, Sani MH, Zakaria II, Kahar UM. Current Status and Potential Applications of Underexplored Prokaryotes. Microorganisms 2019; 7:E468. [PMID: 31635256 PMCID: PMC6843859 DOI: 10.3390/microorganisms7100468] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/05/2019] [Accepted: 10/08/2019] [Indexed: 12/20/2022] Open
Abstract
Thousands of prokaryotic genera have been published, but methodological bias in the study of prokaryotes is noted. Prokaryotes that are relatively easy to isolate have been well-studied from multiple aspects. Massive quantities of experimental findings and knowledge generated from the well-known prokaryotic strains are inundating scientific publications. However, researchers may neglect or pay little attention to the uncommon prokaryotes and hard-to-cultivate microorganisms. In this review, we provide a systematic update on the discovery of underexplored culturable and unculturable prokaryotes and discuss the insights accumulated from various research efforts. Examining these neglected prokaryotes may elucidate their novelties and functions and pave the way for their industrial applications. In addition, we hope that this review will prompt the scientific community to reconsider these untapped pragmatic resources.
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Affiliation(s)
- Kian Mau Goh
- Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia.
| | - Saleha Shahar
- Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia.
| | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Institute of Biological Science, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia.
- International Genome Centre, Jiangsu University, ZhenJiang 212013, China.
| | - Chun Shiong Chong
- Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia.
| | - Syazwani Itri Amran
- Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia.
| | - Mohd Helmi Sani
- Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia.
| | - Iffah Izzati Zakaria
- Malaysia Genome Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, Kajang 43000, Selangor, Malaysia.
| | - Ummirul Mukminin Kahar
- Malaysia Genome Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, Kajang 43000, Selangor, Malaysia.
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Chen Q, Xiao Y, Zhang W, Zhang T, Jiang B, Stressler T, Fischer L, Mu W. Current research on cellobiose 2-epimerase: Enzymatic properties, mechanistic insights, and potential applications in the dairy industry. Trends Food Sci Technol 2018. [DOI: 10.1016/j.tifs.2018.09.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Berini F, Casciello C, Marcone GL, Marinelli F. Metagenomics: novel enzymes from non-culturable microbes. FEMS Microbiol Lett 2017; 364:4329276. [DOI: 10.1093/femsle/fnx211] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/02/2017] [Indexed: 01/02/2023] Open
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Chen Q, Levin R, Zhang W, Zhang T, Jiang B, Stressler T, Fischer L, Mu W. Characterisation of a novel cellobiose 2-epimerase from thermophilic Caldicellulosiruptor obsidiansis for lactulose production. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2017; 97:3095-3105. [PMID: 27873314 DOI: 10.1002/jsfa.8148] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 11/17/2016] [Accepted: 11/17/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND Lactulose, a bioactive lactose derivative, has been widely used in food and pharmaceutical industries. Isomerisation of lactose to lactulose by cellobiose 2-epimerase (CE) has recently attracted increasing attention, since CE produces lactulose with high yield from lactose as a single substrate. In this study, a new lactulose-producing CE from Caldicellulosiruptor obsidiansis was extensively characterised. RESULTS The recombinant enzyme exhibited maximal activity at pH 7.5 and 70 °C. It displayed high thermostability with Tm of 86.7 °C. The half-life was calculated to be 8.1, 2.8 and 0.6 h at 75, 80, and 85 °C, respectively. When lactose was used as substrate, epilactose was rapidly produced in a short period, and afterwards both epilactose and lactose were steadily isomerised to lactulose, with a final ratio of 35:11:54 for lactose:epilactose:lactulose. When the reverse reaction was investigated using lactulose as substrate, both lactose and epilactose appeared to be steadily produced from the start. CONCLUSION The recombinant CE showed both epimerisation and isomerisation activities against lactose, making it an alternative promising biocatalyst candidate for lactulose production. © 2016 Society of Chemical Industry.
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Affiliation(s)
- Qiuming Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Roman Levin
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- University of Hohenheim, Institute of Food Science and Biotechnology, Department of Biotechnology and Enzyme Science, Garbenstr. 25, 70599, Stuttgart, Germany
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Tao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Bo Jiang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, 214122, China
| | - Timo Stressler
- University of Hohenheim, Institute of Food Science and Biotechnology, Department of Biotechnology and Enzyme Science, Garbenstr. 25, 70599, Stuttgart, Germany
| | - Lutz Fischer
- University of Hohenheim, Institute of Food Science and Biotechnology, Department of Biotechnology and Enzyme Science, Garbenstr. 25, 70599, Stuttgart, Germany
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, 214122, China
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Kuschel B, Seitl I, Glück C, Mu W, Jiang B, Stressler T, Fischer L. Hidden Reaction: Mesophilic Cellobiose 2-Epimerases Produce Lactulose. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:2530-2539. [PMID: 28252294 DOI: 10.1021/acs.jafc.6b05599] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Lactulose (4-O-β-d-galactopyranosyl-d-fructofuranose) is a prebiotic sugar derived from the milk sugar lactose (4-O-β-d-galactopyranosyl-d-glucopyranose). In our study we observed for the first time that known cellobiose 2-epimerases (CEs; EC 5.1.3.11) from mesophilic microorganisms were generally able to catalyze the isomerization reaction of lactose into lactulose. Commonly, CEs catalyze the C2-epimerization of d-glucose and d-mannose moieties at the reducing end of β-1,4-glycosidic-linked oligosaccharides. Thus, epilactose (4-O-β-d-galactopyranosyl-d-mannopyranose) is formed with lactose as substrate. So far, only four CEs, exclusively from thermophilic microorganisms, have been reported to additionally catalyze the isomerization reaction of lactose into lactulose. The specific isomerization activity of the seven CEs in this study ranged between 8.7 ± 0.1 and 1300 ± 37 pkat/mg. The results indicate that very likely all CEs are able to catalyze both the epimerization as well as the isomerization reaction, whereby the latter is performed at a comparatively much lower reaction rate.
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Affiliation(s)
- Beatrice Kuschel
- Department of Biotechnology and Enzyme Science, Institute of Food Science and Biotechnology, University of Hohenheim , Garbenstrasse 25, D-70599, Stuttgart, Germany
| | - Ines Seitl
- Department of Biotechnology and Enzyme Science, Institute of Food Science and Biotechnology, University of Hohenheim , Garbenstrasse 25, D-70599, Stuttgart, Germany
| | - Claudia Glück
- Department of Biotechnology and Enzyme Science, Institute of Food Science and Biotechnology, University of Hohenheim , Garbenstrasse 25, D-70599, Stuttgart, Germany
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University , Wuxi, Jiangsu 214122, China
| | - Bo Jiang
- State Key Laboratory of Food Science and Technology, Jiangnan University , Wuxi, Jiangsu 214122, China
| | - Timo Stressler
- Department of Biotechnology and Enzyme Science, Institute of Food Science and Biotechnology, University of Hohenheim , Garbenstrasse 25, D-70599, Stuttgart, Germany
| | - Lutz Fischer
- Department of Biotechnology and Enzyme Science, Institute of Food Science and Biotechnology, University of Hohenheim , Garbenstrasse 25, D-70599, Stuttgart, Germany
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Reaction investigation of lactulose-producing cellobiose 2-epimerases under operational relevant conditions. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.11.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Saburi W. Functions, structures, and applications of cellobiose 2-epimerase and glycoside hydrolase family 130 mannoside phosphorylases. Biosci Biotechnol Biochem 2016; 80:1294-305. [PMID: 27031293 DOI: 10.1080/09168451.2016.1166934] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Carbohydrate isomerases/epimerases are essential in carbohydrate metabolism, and have great potential in industrial carbohydrate conversion. Cellobiose 2-epimerase (CE) reversibly epimerizes the reducing end d-glucose residue of β-(1→4)-linked disaccharides to d-mannose residue. CE shares catalytic machinery with monosaccharide isomerases and epimerases having an (α/α)6-barrel catalytic domain. Two histidine residues act as general acid and base catalysts in the proton abstraction and addition mechanism. β-Mannoside hydrolase and 4-O-β-d-mannosyl-d-glucose phosphorylase (MGP) were found as neighboring genes of CE, meaning that CE is involved in β-mannan metabolism, where it epimerizes β-d-mannopyranosyl-(1→4)-d-mannose to β-d-mannopyranosyl-(1→4)-d-glucose for further phosphorolysis. MGPs form glycoside hydrolase family 130 (GH130) together with other β-mannoside phosphorylases and hydrolases. Structural analysis of GH130 enzymes revealed an unusual catalytic mechanism involving a proton relay and the molecular basis for substrate and reaction specificities. Epilactose, efficiently produced from lactose using CE, has superior physiological functions as a prebiotic oligosaccharide.
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Affiliation(s)
- Wataru Saburi
- a Research Faculty of Agriculture , Hokkaido University , Sapporo , Japan
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