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Zhang Z, Cai Y, Zheng N, Deng Y, Gao L, Wang Q, Xia X. Diverse models of cavity engineering in enzyme modification: Creation, filling, and reshaping. Biotechnol Adv 2024; 72:108346. [PMID: 38518963 DOI: 10.1016/j.biotechadv.2024.108346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 03/07/2024] [Accepted: 03/19/2024] [Indexed: 03/24/2024]
Abstract
Most enzyme modification strategies focus on designing the active sites or their surrounding structures. Interestingly, a large portion of the enzymes (60%) feature active sites located within spacious cavities. Despite recent discoveries, cavity-mediated enzyme engineering remains crucial for enhancing enzyme properties and unraveling folding-unfolding mechanisms. Cavity engineering influences enzyme stability, catalytic activity, specificity, substrate recognition, and docking. This article provides a comprehensive review of various cavity engineering models for enzyme modification, including cavity creation, filling, and reshaping. Additionally, it also discusses feasible tools for geometric analysis, functional assessment, and modification of cavities, and explores potential future research directions in this field. Furthermore, a promising universal modification strategy for cavity engineering that leverages state-of-the-art technologies and methodologies to tailor cavities according to the specific requirements of industrial production conditions is proposed.
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Affiliation(s)
- Zehua Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
| | - Yongchao Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
| | - Nan Zheng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
| | - Yu Deng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
| | - Ling Gao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
| | - Qiong Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
| | - Xiaole Xia
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China; College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, PR China.
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Abula A, Yang T, Zhang Y, Li T, Ji X. Enhancement of Escherichia coli Ribonuclease R Cytosine-Sensitive Activity by Single Amino Acid Substitution. Mol Biotechnol 2023; 65:108-115. [PMID: 35838865 DOI: 10.1007/s12033-022-00533-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 06/30/2022] [Indexed: 02/07/2023]
Abstract
Exoribonucleases are frequently used as nuclei acids detection tools for their sequences, modifications, and structures. Escherichia coli ribonuclease R (EcR) is the prototypical exoribonuclease of the RNase II/RNB family degrading RNA in the 3'-5' direction. Different from RNase II, EcR is capable of degrading structured RNA efficiently, which makes it a potential analysis tool for various RNA species. In this work, we examined the nuclease activity of EcR degrading a series of RNA substrates with various sequences. Our biochemical work reveals that EcR is significantly sensitive to cytosine compared with other bases when catalyzing RNA degradation. EcR shows higher cytosine sensitivity compared to its homolog RNase II when degrading RNAs, and the hydrolysis process of EcR is transiently halted and produces apparent intermediate product when the 1-nt upstream of C is A or U, or G. Furthermore, the substitution of glycine with proline (G273P) in EcR enhances its cytosine sensitivity. These findings expand our understanding of EcR enzymatic activities. The EcR G273P mutant bearing higher cytosine sensitivity could help enrich cytosine trails in RNAs and will have potential implications in the detection and analysis of various RNA species especially small RNAs in biological and clinical samples.
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Affiliation(s)
- Abudureyimu Abula
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, Jiangsu, People's Republic of China.,School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, 830054, Xinjiang, China
| | - Tingting Yang
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, Jiangsu, People's Republic of China
| | - Yingxin Zhang
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, Jiangsu, People's Republic of China
| | - Tinghan Li
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, Jiangsu, People's Republic of China
| | - Xiaoyun Ji
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, Jiangsu, People's Republic of China. .,Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, China. .,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 163 Xianlin Avenue, Nanjing, 210023, China. .,Ministry of Education, Engineering Research Center of Protein and Peptide Medicine, Nanjing, China.
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3
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Mori S, Kitta Y, Sakamoto H, Takamura E, Suye SI. Electrochemical characteristics of a gold nanoparticle-modified controlled enzyme-electrode contact junction electrode. Biotechnol Lett 2021; 43:1037-1042. [PMID: 33576902 DOI: 10.1007/s10529-021-03092-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 02/03/2021] [Indexed: 10/22/2022]
Abstract
Biodevices in which biomolecules such as enzymes and antibodies are immobilized on the surface of electrode materials are capable of converting chemical energy into electrical energy, and are expected to contribute to solving energy problems and developing medical measurements especially as biobatteries and biosensors. Device performance depends on the interface formed between the biomolecule layer and electrode material, and the interface is required to simultaneously achieve a highly efficient enzymatic reaction and electron transfer. However, when enzymes were immobilized on a material surface, the enzymes undergoes a structural change due to the interaction between the enzyme and the electrode surface, making it difficult to maximize the function of the enzyme molecule on the material surface. In this study, we postulate that the structural change of the enzyme would be reduced and the electrochemical performance improved by making the contact area between the enzyme and the electrode extremely small and adsorbing it as a point. Therefore, we aimed to develop a high-power biodevice that retains enzyme structure and activity by interposing gold nanoparticles (AuNPs) between the enzyme and the electrode. The enzymatic and electrochemical properties of pyrroloquinoline quinone-dependent glucose dehydrogenase adsorbed on AuNPs of 5-40 nm diameter were investigated. We found that the characteristics differed among the particles, and the enzyme adsorbed on 20 nm AuNPs showed the best electrochemical characteristics.
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Affiliation(s)
- Saki Mori
- Department of Advanced Interdisciplinary Science and Technology, Graduate School of Engineering, University of Fukui, Fukui, Japan
| | - Yohei Kitta
- Department of Frontier Fiber Technology and Science, Graduate School of Engineering, University of Fukui, Bunkyo 3-9-1, Fukui, 910-8507, Japan
| | - Hiroaki Sakamoto
- Department of Frontier Fiber Technology and Science, Graduate School of Engineering, University of Fukui, Bunkyo 3-9-1, Fukui, 910-8507, Japan.
| | - Eiichiro Takamura
- Department of Frontier Fiber Technology and Science, Graduate School of Engineering, University of Fukui, Bunkyo 3-9-1, Fukui, 910-8507, Japan
| | - Shin-Ichiro Suye
- Department of Frontier Fiber Technology and Science, Graduate School of Engineering, University of Fukui, Bunkyo 3-9-1, Fukui, 910-8507, Japan
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Guo L, Li J, Yuan Y, Gui Y, Zou F, Lu L, Cui B. Structural and functional modification of kudzu starch using α-amylase and transglucosidase. Int J Biol Macromol 2020; 169:67-74. [PMID: 33338525 DOI: 10.1016/j.ijbiomac.2020.12.099] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/01/2020] [Accepted: 12/12/2020] [Indexed: 11/16/2022]
Abstract
The large agglomeration of starch paste in hot water, and fast retrogradation tendency and low transparency of starch gel restrict widespread application of kudzu starch. To improve the above defects, kudzu starch was modified with sequentially α-amylase (AA) and transglucosidase (TG), the latter for varying times. The results indicated that, compared to kudzu starch, amylose content and molecular weight of AA/TG-treated starches reduced by 20.07% and 69.50%, respectively. The proportion of A chain increased by 68.68%, whereas B1, B2 and B3 chains decreased by 14.28%, 48.29% and 23.44%, respectively. The degree of branching dramatically increased by 128.3%. After AA→TG treatment, the changes of starch structure enhanced the functional properties of kudzu starch. The solubility, paste clarity and gelatinization temperature increased, whereas the relative crystallinity, viscosity, storage and loss moduli decreased. Overall, the AA→TG modification would be desirable to improve the functional properties of kudzu starch to expand more large-scale application.
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Affiliation(s)
- Li Guo
- State Key Laboratory of Biobased Material and Green Papermaking, School of Food Sciences and Engineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China
| | - Jiahao Li
- State Key Laboratory of Biobased Material and Green Papermaking, School of Food Sciences and Engineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China
| | - Yuhan Yuan
- Life Science and Technology College, Xinjiang University, Urumchi, China
| | - Yifan Gui
- State Key Laboratory of Biobased Material and Green Papermaking, School of Food Sciences and Engineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China
| | - Feixue Zou
- State Key Laboratory of Biobased Material and Green Papermaking, School of Food Sciences and Engineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China
| | - Lu Lu
- State Key Laboratory of Biobased Material and Green Papermaking, School of Food Sciences and Engineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China
| | - Bo Cui
- State Key Laboratory of Biobased Material and Green Papermaking, School of Food Sciences and Engineering, Qilu University of Technology, Shandong Academy of Sciences, Jinan, China.
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Huang J, Zhang Y, Ding F, Chen D, Wang Y, Jin X, Zhu X. Rational design of electroactive redox enzyme nanocapsules for high-performance biosensors and enzymatic biofuel cell. Biosens Bioelectron 2021; 174:112805. [PMID: 33257186 DOI: 10.1016/j.bios.2020.112805] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 12/24/2022]
Abstract
The potential application of biodevices based on enzymatic bioelectrocatalysis are limited by poor stability and electrochemical performance. To solve the limitation, modifying enzyme with functional polymer to tailor enzyme function is highly desirable. Herein, glucose oxidase (GOx) was chosen as a model enzyme, and according to the chemical structure of GOx cofactor (flavin adenine dinucleotide, FAD), we customize a biomimetic cofactor containing vinyl group (SFAD) for GOx, and prepared an GOx nanocapsule via in-situ polymerization. The characterization of particle size distribution, TEM, fluorescence and electrochemical performance indicated the successful formation of electroactive GOx nanocapsule with SFAD-containing polymeric network (n (GOx-SFAD-PAM)). The network can act as an electronic "highway" to link the active site with electrode, with capability to accelerate electron transfer as well as enhanced GOx stability. Further investigation of bioelectrocatalysis shows that n (GOx-SFAD-PAM)-based biosensor has low detection potential (-0.4 vs. Ag/AgCl), high sensitivity (64.97 μAmM-1cm-2), good anti-interference performance, quick response (3⁓5s) and excellent stability, and that n (GOx-SFAD-PAM)-based enzymatic biofuel cell (EBFC) has the high maximum power density (1011.21 μWcm-2), which is a 385-fold increase over that of native GOx-based EBFC (2.62 μWcm-2). This study suggests that novel enzyme nanocapsule with electroactive polymeric shell might provide a prospective solution for the performance improvement of enzymatic bioelectrocatalysis-based biodevices.
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Daskalova SM, Eisenhauer BM, Gao M, Feng X, Ji X, Cheng Q, Fahmi N, Khdour OM, Chen S, Hecht SM. An assay for DNA polymerase β lyase inhibitors that engage the catalytic nucleophile for binding. Bioorg Med Chem 2020; 28:115642. [PMID: 32773093 DOI: 10.1016/j.bmc.2020.115642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/03/2020] [Accepted: 07/05/2020] [Indexed: 11/16/2022]
Abstract
DNA polymerase β (Pol β) repairs cellular DNA damage. When such damage is inflicted upon the DNA in tumor cells treated with DNA targeted antitumor agents, Pol β thus diminishes their efficacy. Accordingly, this enzyme has long been a target for antitumor therapy. Although numerous inhibitors of the lyase activity of the enzyme have been reported, none has yet proven adequate for development as a therapeutic agent. In the present study, we developed a new strategy to identify lyase inhibitors that critically engage the lyase active site primary nucleophile Lys72 as part of the binding interface. This involves a parallel evaluation of the effect of the inhibitors on the wild-type DNA polymerase β (Pol β) and Pol β modified with a lysine analogue at position 72. A model panel of five structurally diverse lyase inhibitors identified in our previous studies (only one of which has been published) with unknown modes of binding were used for testing, and one compound, cis-9,10-epoxyoctadecanoic acid, was found to have the desired characteristics. This finding was further corroborated by in silico docking, demonstrating that the predominant mode of binding of the inhibitor involves an important electrostatic interaction between the oxygen atom of the epoxy group and Nε of the main catalytic nucleophile, Lys72. The strategy, which is designed to identify compounds that engage certain structural elements of the target enzyme, could find broader application for identification of ligands with predetermined sites of binding.
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Affiliation(s)
- Sasha M Daskalova
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Brian M Eisenhauer
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, VA 22904, United States
| | - Mingxuan Gao
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Xizhi Feng
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, VA 22904, United States
| | - Xun Ji
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Qi Cheng
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - NourEddine Fahmi
- Departments of Chemistry and Biology, University of Virginia, Charlottesville, VA 22904, United States
| | - Omar M Khdour
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Shengxi Chen
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States
| | - Sidney M Hecht
- Biodesign Center for BioEnergetics and School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, United States; Departments of Chemistry and Biology, University of Virginia, Charlottesville, VA 22904, United States
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Abstract
Recycling biomass is indispensable these days not only because fossil energy sources are gradually depleted, but also because pollution of the environment, caused by the increasing use of energy, must be reduced. This article intends to overview the results of plant biomass processing methods that are currently in use. Our aim was also to review published methods that are not currently in use. It is intended to explore the possibilities of new methods and enzymes to be used in biomass recycling. The results of this overview are perplexing in almost every area. Advances have been made in the pre-treatment of biomass and in the diversity and applications of the enzymes utilized. Based on molecular modeling, very little progress has been made in the modification of existing enzymes for altered function and adaptation for the environmental conditions during the processing of biomass. There are hardly any publications in which molecular modeling techniques are used to improve enzyme function and to adapt enzymes to various environmental conditions. Our view is that using modern computational, biochemical, and biotechnological methods would enable the purposeful design of enzymes that are more efficient and suitable for biomass processing.
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Affiliation(s)
- László Fülöp
- Department of Chemistry, Szent István University, Gödöllő, Hungary
| | - János Ecker
- Department of Chemistry, Szent István University, Gödöllő, Hungary
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Shukla P. Synthetic Biology Perspectives of Microbial Enzymes and Their Innovative Applications. Indian J Microbiol 2019; 59:401-409. [PMID: 31762501 DOI: 10.1007/s12088-019-00819-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 08/19/2019] [Indexed: 11/29/2022] Open
Abstract
Microbial enzymes are high in demand and there is focus on their efficient, cost effective and eco-friendly production. The relevant microbial enzymes for respective industries needs to be identified but the conventional technologies don't have much edge over it. So, there is more attention towards high throughput methods for production of efficient enzymes. The enzymes produced by microbes need to be modified to bear the extreme conditions of the industries in order to get prolific outcomes and here the synthetic biology tools may be augmented to modify such microbes and enzymes. These tools are applied to synthesize novel and efficient enzymes. Use of computational tools for enzyme modification has provided new avenues for faster and specific modification of enzymes in a shorter time period. This review focuses on few important enzymes and their modification through synthetic biology tools including genetic modification, nanotechnology, post translational modification.
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Affiliation(s)
- Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, Haryana 124001 India
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Wang D, Yan L, Ma X, Wang W, Zou M, Zhong J, Ding T, Ye X, Liu D. Ultrasound promotes enzymatic reactions by acting on different targets: Enzymes, substrates and enzymatic reaction systems. Int J Biol Macromol 2018; 119:453-461. [PMID: 30041035 DOI: 10.1016/j.ijbiomac.2018.07.133] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 07/18/2018] [Accepted: 07/20/2018] [Indexed: 12/24/2022]
Abstract
With the extensive application of enzyme-catalyzed reactions in numerous fields, improving enzymatic efficiency has attracted wide attention for reducing operating costs and increasing output. There are three targets throughout enzymatic reactions: the enzyme, substrate, and mixed reaction system. Ultrasound has been known to accelerate enzymatic reactions by acting on different targets. It can modify both enzyme and substrate macromolecules, which is helpful for enhancing enzyme activity and product yields. The synergistic effect of ultrasound and enzymes is widely reported to increase catalytic rates. The present review discusses the positive effect induced by ultrasound throughout the enzymatic process, including ultrasonic modification of enzymes, ultrasound assisted immobilization, ultrasonic pretreatment of substrates, and ultrasound assisted enzymatic reactions.
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Affiliation(s)
- Danli Wang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.
| | - Lufeng Yan
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Xiaobin Ma
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Wenjun Wang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Mingming Zou
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Jianjun Zhong
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China
| | - Tian Ding
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China; National Engineering Laboratory of Intelligent Food Technology and Equipment, Hangzhou 310058, China; Zhejiang Key Laboratory for Agro-Food Processing, Hangzhou 310058, China
| | - Xingqian Ye
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China; National Engineering Laboratory of Intelligent Food Technology and Equipment, Hangzhou 310058, China; Zhejiang Key Laboratory for Agro-Food Processing, Hangzhou 310058, China; Fuli Institute of Food Science, Zhejiang University, Hangzhou 310058, China
| | - Donghong Liu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China; National Engineering Laboratory of Intelligent Food Technology and Equipment, Hangzhou 310058, China; Zhejiang Key Laboratory for Agro-Food Processing, Hangzhou 310058, China; Fuli Institute of Food Science, Zhejiang University, Hangzhou 310058, China.
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Di Lorenzo G, Velho RV, Winter D, Thelen M, Ahmadi S, Schweizer M, De Pace R, Cornils K, Yorgan TA, Grüb S, Hermans-Borgmeyer I, Schinke T, Müller-Loennies S, Braulke T, Pohl S. Lysosomal Proteome and Secretome Analysis Identifies Missorted Enzymes and Their Nondegraded Substrates in Mucolipidosis III Mouse Cells. Mol Cell Proteomics 2018; 17:1612-1626. [PMID: 29773673 DOI: 10.1074/mcp.ra118.000720] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/27/2018] [Indexed: 11/06/2022] Open
Abstract
Targeting of soluble lysosomal enzymes requires mannose 6-phosphate (M6P) signals whose formation is initiated by the hexameric N-acetylglucosamine (GlcNAc)-1-phosphotransferase complex (α2β2γ2). Upon proteolytic cleavage by site-1 protease, the α/β-subunit precursor is catalytically activated but the functions of γ-subunits (Gnptg) in M6P modification of lysosomal enzymes are unknown. To investigate this, we analyzed the Gnptg expression in mouse tissues, primary cultured cells, and in Gnptg reporter mice in vivo, and found high amounts in the brain, eye, kidney, femur, vertebra and fibroblasts. Consecutively we performed comprehensive quantitative lysosomal proteome and M6P secretome analysis in fibroblasts of wild-type and Gnptgko mice mimicking the lysosomal storage disorder mucolipidosis III. Although the cleavage of the α/β-precursor was not affected by Gnptg deficiency, the GlcNAc-1-phosphotransferase activity was significantly reduced. We purified lysosomes and identified 29 soluble lysosomal proteins by SILAC-based mass spectrometry exhibiting differential abundance in Gnptgko fibroblasts which was confirmed by Western blotting and enzymatic activity analysis for selected proteins. A subset of these lysosomal enzymes show also reduced M6P modifications, fail to reach lysosomes and are secreted, among them α-l-fucosidase and arylsulfatase B. Low levels of these enzymes correlate with the accumulation of non-degraded fucose-containing glycostructures and sulfated glycosaminoglycans in Gnptgko lysosomes. Incubation of Gnptgko fibroblasts with arylsulfatase B partially rescued glycosaminoglycan storage. Combinatorial treatments with other here identified missorted enzymes of this degradation pathway might further correct glycosaminoglycan accumulation and will provide a useful basis to reveal mechanisms of selective, Gnptg-dependent formation of M6P residues on lysosomal proteins.
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Affiliation(s)
- Giorgia Di Lorenzo
- From the ‡Section Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Renata Voltolini Velho
- From the ‡Section Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Dominic Winter
- §Institute of Biochemistry and Molecular Biology, University of Bonn, Bonn, Germany
| | - Melanie Thelen
- §Institute of Biochemistry and Molecular Biology, University of Bonn, Bonn, Germany
| | - Shiva Ahmadi
- §Institute of Biochemistry and Molecular Biology, University of Bonn, Bonn, Germany
| | - Michaela Schweizer
- ¶Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Raffaella De Pace
- From the ‡Section Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kerstin Cornils
- ‖Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Timur Alexander Yorgan
- **Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Saskia Grüb
- From the ‡Section Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Irm Hermans-Borgmeyer
- ¶Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thorsten Schinke
- **Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Sven Müller-Loennies
- ‡‡Division Biophysics, Research Center Borstel, Leibniz Lung Center, 23845 Borstel, Germany
| | - Thomas Braulke
- From the ‡Section Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany;
| | - Sandra Pohl
- From the ‡Section Biochemistry, Children's Hospital, University Medical Center Hamburg-Eppendorf, Hamburg, Germany;
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Tudek B, Zdżalik-Bielecka D, Tudek A, Kosicki K, Fabisiewicz A, Speina E. Lipid peroxidation in face of DNA damage, DNA repair and other cellular processes. Free Radic Biol Med 2017; 107:77-89. [PMID: 27908783 DOI: 10.1016/j.freeradbiomed.2016.11.043] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 11/20/2016] [Accepted: 11/27/2016] [Indexed: 01/09/2023]
Abstract
Exocyclic adducts to DNA bases are formed as a consequence of exposure to certain environmental carcinogens as well as inflammation and lipid peroxidation (LPO). Complex family of LPO products gives rise to a variety of DNA adducts, which can be grouped in two classes: (i) small etheno-type adducts of strong mutagenic potential, and (ii) bulky, propano-type adducts, which block replication and transcription, and are lethal lesions. Etheno-DNA adducts are removed from the DNA by base excision repair (BER), AlkB and nucleotide incision repair enzymes (NIR), while substituted propano-type lesions by nucleotide excision repair (NER) and homologous recombination (HR). Changes of the level and activity of several enzymes removing exocyclic adducts from the DNA was reported during carcinogenesis. Also several beyond repair functions of these enzymes, which participate in regulation of cell proliferation and growth, as well as RNA processing was recently described. In addition, adducts of LPO products to proteins was reported during aging and age-related diseases. The paper summarizes pathways for exocyclic adducts removal and describes how proteins involved in repair of these adducts can modify pathological states of the organism.
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Affiliation(s)
- Barbara Tudek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland.
| | - Daria Zdżalik-Bielecka
- Laboratory of Cell Biology, International Institute of Molecular and Cell Biology, Ksiecia Trojdena 4, 02-109 Warsaw, Poland
| | - Agnieszka Tudek
- Department of Molecular Biology and Genetics, Aarhus University, C. F. Mollers Alle 3, 8000 Aarhus, Denmark
| | - Konrad Kosicki
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Anna Fabisiewicz
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Roentgena 5, Warsaw 02-781, Poland
| | - Elżbieta Speina
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
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Shin JH, Kim HU, Kim DI, Lee SY. Production of bulk chemicals via novel metabolic pathways in microorganisms. Biotechnol Adv 2013; 31:925-35. [PMID: 23280013 DOI: 10.1016/j.biotechadv.2012.12.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Revised: 12/09/2012] [Accepted: 12/23/2012] [Indexed: 02/05/2023]
Abstract
Metabolic engineering has been playing important roles in developing high performance microorganisms capable of producing various chemicals and materials from renewable biomass in a sustainable manner. Synthetic and systems biology are also contributing significantly to the creation of novel pathways and the whole cell-wide optimization of metabolic performance, respectively. In order to expand the spectrum of chemicals that can be produced biotechnologically, it is necessary to broaden the metabolic capacities of microorganisms. Expanding the metabolic pathways for biosynthesizing the target chemicals requires not only the enumeration of a series of known enzymes, but also the identification of biochemical gaps whose corresponding enzymes might not actually exist in nature; this issue is the focus of this paper. First, pathway prediction tools, effectively combining reactions that lead to the production of a target chemical, are analyzed in terms of logics representing chemical information, and designing and ranking the proposed metabolic pathways. Then, several approaches for potentially filling in the gaps of the novel metabolic pathway are suggested along with relevant examples, including the use of promiscuous enzymes that flexibly utilize different substrates, design of novel enzymes for non-natural reactions, and exploration of hypothetical proteins. Finally, strain optimization by systems metabolic engineering in the context of novel metabolic pathways constructed is briefly described. It is hoped that this review paper will provide logical ways of efficiently utilizing 'big' biological data to design and develop novel metabolic pathways for the production of various bulk chemicals that are currently produced from fossil resources.
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