1
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Tang R, Xing K, Tu J, Wang X, Xu L, Chen W, Cheng Y, Xu Z. Application and Cytotoxicity Evaluation of Fe-MIL-101 Nanozyme in Milk. Appl Biochem Biotechnol 2024:10.1007/s12010-024-05015-0. [PMID: 39158664 DOI: 10.1007/s12010-024-05015-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2024] [Indexed: 08/20/2024]
Abstract
In this study, we used Fe-MIL-101 nanozyme to convert lactose into lactitol, and it was proved that Fe-MIL-101 nanozyme has lactase-like activity. Due to the potential health effects of nanomaterials, we evaluated the cytotoxicity of Fe-MIL-101 nanozyme. To reduce the potential toxicity of the nanozyme, we applied centrifugation and membrane filtration. When the membrane aperture size was 100 nm, the residual content of Fe-MIL-101 nanozyme was 14.09 μg/mL. The residual content of Fe-MIL-101 nanozyme was reduced by optimizing time, temperature, and Fe-MIL-101 nanozyme-to-substrate ratio. It was showed that the concentration of Fe was 38.47 mg/kg and the concentration of H2BDC was 0 mg/kg under optimized conditions (110℃, 2 h of reaction and the ratio of Fe-MIL-101 nanozyme to substrate is 1:20). The result met the national standard of China. Experiments measuring cytotoxicity, oxidative stress, and cell membrane damage revealed that less than 20 μg/mL Fe-MIL-101 nanozyme had no significant cytotoxicity. Our study findings showed that Fe-MIL-101 nanozyme reduced lactose content in milk.
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Affiliation(s)
- Ruicong Tang
- Hunan Provincial Key Laboratory of Cytochemistry, School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha, 410114, Hunan, China
| | - Keyu Xing
- Hunan Provincial Key Laboratory of Cytochemistry, School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha, 410114, Hunan, China
| | - Jia Tu
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, 410004, Hunan, China
| | - Xufeng Wang
- Hunan Provincial Key Laboratory of Cytochemistry, School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha, 410114, Hunan, China
| | - Liguang Xu
- School of Food Science and Technology, Jiangnan University, Wuxi, 214000, Jiangsu, China
| | - Wei Chen
- MOE, School of Food and Biological Engineering, Engineering Research Center of Bio-Process, Hefei University of Technology, Hefei, 230009, Anhui, China
| | - Yunhui Cheng
- Hunan Provincial Key Laboratory of Cytochemistry, School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha, 410114, Hunan, China
| | - Zhou Xu
- Hunan Provincial Key Laboratory of Cytochemistry, School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha, 410114, Hunan, China.
- State Key Laboratory of Utilization of Woody Oil Resource, Hunan Academy of Forestry, Changsha, 410004, Hunan, China.
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2
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Zhu F, Hu S, Zhao W, Mei L. A Novel Method for γ-Aminobutyric Acid Biosynthesis Using Glutamate Decarboxylase Entrapped in Polyvinyl Alcohol-Sodium Alginate Capsules. Molecules 2023; 28:6844. [PMID: 37836687 PMCID: PMC10574615 DOI: 10.3390/molecules28196844] [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: 09/04/2023] [Revised: 09/23/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
γ-aminobutyric acid (GABA) has essential physiological functions in the human body. A novel method using glutamate decarboxylase (GAD) entrapped in polyvinyl alcohol (PVA)-sodium alginate (SA) capsules provides a green biological strategy for GABA synthesis. In this investigation, the stability range of immobilized GAD was effectively broadened, and immobilized GAD could be repeatedly used as a batch and fixed-bed column catalyst. The immobilized enzymes were stable and retained 89% of their activity in a pH range of 4.0-5.6, while there was an approximately 50% decrease in free GAD activity in the pH range of 4.8 ± 0.4. The immobilized GAD affinity to the substrate improved, and this was evidenced by the apparent decrease in Km to 13.3 mmol/L from the 30.9 mmol/L for free GAD. The immobilized GAD retained >90.6% activity after eight cycles and a near-100% enzyme activity retention after 120 h of a continuous fixed-bed column catalyst operation. This study has thus presented an effective PVA-SA-GAD immobilization method that could be used to continuously scale-up GABA biosynthesis.
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Affiliation(s)
- Fei Zhu
- Department of Food Science, Zhejiang Pharmaceutical University, Ningbo 315000, China
| | - Sheng Hu
- School of Biological and Chemical Engineering, NingboTech University, Ningbo 315000, China
| | - Weirui Zhao
- School of Biological and Chemical Engineering, NingboTech University, Ningbo 315000, China
| | - Lehe Mei
- College of Chemical and Biochemical Engineering, Zhejiang University, Hangzhou 310058, China
- Jinhua Advanced Research Institute, Jinhua 321019, China
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3
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DeChellis A, Nemmaru B, Sammond D, Douglass J, Patil N, Reste O, Chundawat SPS. Supercharging carbohydrate-binding module alone enhances endocellulase thermostability, binding, and activity on cellulosic biomass. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.09.557007. [PMID: 37745483 PMCID: PMC10515785 DOI: 10.1101/2023.09.09.557007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Lignocellulosic biomass recalcitrance to enzymatic degradation necessitates high enzyme loadings incurring large processing costs for industrial-scale biofuels or biochemicals production. Manipulating surface charge interactions to minimize non-productive interactions between cellulolytic enzymes and plant cell wall components (e.g., lignin or cellulose) via protein supercharging has been hypothesized to improve biomass biodegradability, but with limited demonstrated success to date. Here we characterize the effect of introducing non-natural enzyme surface mutations and net charge on cellulosic biomass hydrolysis activity by designing a library of supercharged family-5 endoglucanase Cel5A and its native family-2a carbohydrate binding module (CBM) originally belonging to an industrially relevant thermophilic microbe Thermobifida fusca . A combinatorial library of 33 mutant constructs containing different CBM and Cel5A designs spanning a net charge range of -52 to 37 was computationally designed using Rosetta macromolecular modelling software. Activity for all mutants was rapidly characterized as soluble cell lysates and promising mutants (containing mutations either on the CBM, Cel5A catalytic domain, or both CBM and Cel5A domains) were then purified and systematically characterized. Surprisingly, often endocellulases with mutations on the CBM domain alone resulted in improved activity on cellulosic biomass, with three top-performing supercharged CBM mutants exhibiting between 2-5-fold increase in activity, compared to native enzyme, on both pretreated biomass enriched in lignin (i.e., corn stover) and isolated crystalline/amorphous cellulose. Furthermore, we were able to clearly demonstrate that endocellulase net charge can be selectively fine-tuned using protein supercharging protocol for targeting distinct substrates and maximizing biocatalytic activity. Additionally, several supercharged CBM containing endocellulases exhibited a 5-10 °C increase in optimal hydrolysis temperature, compared to native enzyme, which enabled further increase in hydrolytic yield at higher operational reaction temperatures. This study demonstrates the first successful implementation of enzyme supercharging of cellulolytic enzymes to increase hydrolytic activity towards complex lignocellulosic biomass derived substrates.
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4
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Gantz M, Neun S, Medcalf EJ, van Vliet LD, Hollfelder F. Ultrahigh-Throughput Enzyme Engineering and Discovery in In Vitro Compartments. Chem Rev 2023; 123:5571-5611. [PMID: 37126602 PMCID: PMC10176489 DOI: 10.1021/acs.chemrev.2c00910] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Novel and improved biocatalysts are increasingly sourced from libraries via experimental screening. The success of such campaigns is crucially dependent on the number of candidates tested. Water-in-oil emulsion droplets can replace the classical test tube, to provide in vitro compartments as an alternative screening format, containing genotype and phenotype and enabling a readout of function. The scale-down to micrometer droplet diameters and picoliter volumes brings about a >107-fold volume reduction compared to 96-well-plate screening. Droplets made in automated microfluidic devices can be integrated into modular workflows to set up multistep screening protocols involving various detection modes to sort >107 variants a day with kHz frequencies. The repertoire of assays available for droplet screening covers all seven enzyme commission (EC) number classes, setting the stage for widespread use of droplet microfluidics in everyday biochemical experiments. We review the practicalities of adapting droplet screening for enzyme discovery and for detailed kinetic characterization. These new ways of working will not just accelerate discovery experiments currently limited by screening capacity but profoundly change the paradigms we can probe. By interfacing the results of ultrahigh-throughput droplet screening with next-generation sequencing and deep learning, strategies for directed evolution can be implemented, examined, and evaluated.
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Affiliation(s)
- Maximilian Gantz
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Stefanie Neun
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Elliot J Medcalf
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Liisa D van Vliet
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
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5
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Tan Z, Li J, Hou J, Gonzalez R. Designing artificial pathways for improving chemical production. Biotechnol Adv 2023; 64:108119. [PMID: 36764336 DOI: 10.1016/j.biotechadv.2023.108119] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
Abstract
Metabolic engineering exploits manipulation of catalytic and regulatory elements to improve a specific function of the host cell, often the synthesis of interesting chemicals. Although naturally occurring pathways are significant resources for metabolic engineering, these pathways are frequently inefficient and suffer from a series of inherent drawbacks. Designing artificial pathways in a rational manner provides a promising alternative for chemicals production. However, the entry barrier of designing artificial pathway is relatively high, which requires researchers a comprehensive and deep understanding of physical, chemical and biological principles. On the other hand, the designed artificial pathways frequently suffer from low efficiencies, which impair their further applications in host cells. Here, we illustrate the concept and basic workflow of retrobiosynthesis in designing artificial pathways, as well as the most currently used methods including the knowledge- and computer-based approaches. Then, we discuss how to obtain desired enzymes for novel biochemistries, and how to trim the initially designed artificial pathways for further improving their functionalities. Finally, we summarize the current applications of artificial pathways from feedstocks utilization to various products synthesis, as well as our future perspectives on designing artificial pathways.
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Affiliation(s)
- Zaigao Tan
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China; School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; Department of Bioengineering, Shanghai Jiao Tong University, Shanghai, China.
| | - Jian Li
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China; School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; Department of Bioengineering, Shanghai Jiao Tong University, Shanghai, China
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Ramon Gonzalez
- Department of Chemical, Biological, and Materials Engineering, University of South Florida, Tampa, FL, USA.
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6
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Benítez-Mateos AI, Paradisi F. Halomonas elongata: a microbial source of highly stable enzymes for applied biotechnology. Appl Microbiol Biotechnol 2023; 107:3183-3190. [PMID: 37052635 PMCID: PMC10160191 DOI: 10.1007/s00253-023-12510-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/14/2023]
Abstract
Extremophilic microorganisms, which are resistant to extreme levels of temperature, salinity, pH, etc., have become popular tools for biotechnological applications. Due to their availability and cost-efficacy, enzymes from extremophiles are getting the attention of researchers and industries in the field of biocatalysis to catalyze diverse chemical reactions in a selective and sustainable manner. In this mini-review, we discuss the advantages of Halomonas elongata as moderate halophilic bacteria to provide suitable enzymes for biotechnology. While enzymes from H. elongata are more resistant to the presence of salt compared to their mesophilic counterparts, they are also easier to produce in heterologous hosts compared with more extremophilic microorganisms. Herein, a set of different enzymes (hydrolases, transferases, and oxidoreductases) from H. elongata are showcased, highlighting their interesting properties as more efficient and sustainable biocatalysts. With this, we aim to improve the visibility of halotolerant enzymes and their uncommon properties to integrate biocatalysis in industrial set-ups. KEYPOINTS: • Production and use of halotolerant enzymes can be easier than strong halophilic ones. • Enzymes from halotolerant organisms are robust catalysts under harsh conditions. • Halomonas elongata has shown a broad enzyme toolbox with biotechnology applications.
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Affiliation(s)
- Ana I Benítez-Mateos
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.
| | - Francesca Paradisi
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.
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7
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Wang S, Lei H, Ji Z. Exploring Oxidoreductases from Extremophiles for Biosynthesis in a Non-Aqueous System. Int J Mol Sci 2023; 24:ijms24076396. [PMID: 37047370 PMCID: PMC10094897 DOI: 10.3390/ijms24076396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 03/19/2023] [Accepted: 03/27/2023] [Indexed: 04/14/2023] Open
Abstract
Organic solvent tolerant oxidoreductases are significant for both scientific research and biomanufacturing. However, it is really challenging to obtain oxidoreductases due to the shortages of natural resources and the difficulty to obtained it via protein modification. This review summarizes the recent advances in gene mining and structure-functional study of oxidoreductases from extremophiles for non-aqueous reaction systems. First, new strategies combining genome mining with bioinformatics provide new insights to the discovery and identification of novel extreme oxidoreductases. Second, analysis from the perspectives of amino acid interaction networks explain the organic solvent tolerant mechanism, which regulate the discrete structure-functional properties of extreme oxidoreductases. Third, further study by conservation and co-evolution analysis of extreme oxidoreductases provides new perspectives and strategies for designing robust enzymes for an organic media reaction system. Furthermore, the challenges and opportunities in designing biocatalysis non-aqueous systems are highlighted.
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Affiliation(s)
- Shizhen Wang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Xiamen Key Laboratory of Synthetic Biotechnology, Xiamen University, Xiamen 361005, China
| | - Hangbin Lei
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zhehui Ji
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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8
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Han J, Zhang T, Zhou Z, Zhang H. Development of a novel ultrasound- and biocrosslinking-enhanced immobilization strategy with application to food enzymes. Food Chem 2023; 417:135810. [PMID: 36917903 DOI: 10.1016/j.foodchem.2023.135810] [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: 11/09/2022] [Revised: 02/23/2023] [Accepted: 02/25/2023] [Indexed: 03/08/2023]
Abstract
The increasing demand for greener food production makes biocatalysts more desirable than traditional production approaches. One limiting factor for biocatalyst efficiency is the immobilization strategy. In this work, a novel immobilization method was developed with the tyrosine-tag crosslinking mechanism. The immobilization efficiency was further enhanced with ultrasound treatment. Such a strategy was proven to be efficient with food enzyme lipase, d-amino acid oxidase and glucose dehydrogenase when they were immobilized on macroporous resins, amino resins, epoxy resins, and multiwalled carbon nanotubes. For lipase, glucose dehydrogenase and d-amino acid oxidase, the immobilization yield on macroporous resins increased by 20.4%, 21.1% and 24.1%, respectively. In addition, the immobilized enzymes had enhanced reusability, with a high degree of activity (more than 85%) detected after six cycles. Furthermore, the enzyme electrochemical sensors constructed by enzyme crosslinking have higher sensitivity, with peak currents 4-8 times those of sensors with uncrosslinked enzymes. The enzyme immobilization strategy developed in this study paves the way for better application of biocatalysts in the food industry.
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Affiliation(s)
- Juan Han
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, MOE Key Laboratory of Molecular Biophysics, Wuhan 430074, China
| | - Ting Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, MOE Key Laboratory of Molecular Biophysics, Wuhan 430074, China
| | - Zhuoyue Zhou
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, MOE Key Laboratory of Molecular Biophysics, Wuhan 430074, China
| | - Houjin Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, MOE Key Laboratory of Molecular Biophysics, Wuhan 430074, China.
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9
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Jin C, Fan S, Zhuang Z, Zhou Y. Single-atom nanozymes: From bench to bedside. NANO RESEARCH 2023; 16:1992-2002. [PMID: 36405985 PMCID: PMC9643943 DOI: 10.1007/s12274-022-5060-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/12/2022] [Accepted: 09/14/2022] [Indexed: 05/06/2023]
Abstract
Single-atom nanozymes (SANs) are the new emerging catalytic nanomaterials with enzyme-mimetic activities, which have many extraordinary merits, such as low-cost preparation, maximum atom utilization, ideal catalytic activity, and optimized selectivity. With these advantages, SANs have received extensive research attention in the fields of chemistry, energy conversion, and environmental purification. Recently, a growing number of studies have shown the great promise of SANs in biological applications. In this article, we present the most recent developments of SANs in anti-infective treatment, cancer diagnosis and therapy, biosensing, and antioxidative therapy. This text is expected to better guide the readers to understand the current state and future clinical possibilities of SANs in medical applications.
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Affiliation(s)
- Chanyuan Jin
- Second Dental Center, Peking University School and Hospital of Stomatology, Beijing, 100101 China
| | - Sanjun Fan
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210 USA
| | - Zechao Zhuang
- Department of Chemistry, Tsinghua University, Beijing, 100084 China
| | - Yongsheng Zhou
- Department of Prosthodontics, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices & Beijing Key Laboratory of Digital Stomatology, Beijing, 100081 China
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10
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Thirumalai A, Ganapathy Raman P, Jayavelu T, Subramanian R. Bridging the gap between maleate hydratase, citraconase and isopropylmalate isomerase: Insights into the single broad-specific enzyme. Enzyme Microb Technol 2023; 162:110140. [DOI: 10.1016/j.enzmictec.2022.110140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 09/23/2022] [Accepted: 10/08/2022] [Indexed: 11/13/2022]
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11
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Li F, Chen Y, Anton M, Nielsen J. GotEnzymes: an extensive database of enzyme parameter predictions. Nucleic Acids Res 2022; 51:D583-D586. [PMID: 36169223 PMCID: PMC9825421 DOI: 10.1093/nar/gkac831] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/08/2022] [Accepted: 09/26/2022] [Indexed: 01/29/2023] Open
Abstract
Enzyme parameters are essential for quantitatively understanding, modelling, and engineering cells. However, experimental measurements cover only a small fraction of known enzyme-compound pairs in model organisms, much less in other organisms. Artificial intelligence (AI) techniques have accelerated the pace of exploring enzyme properties by predicting these in a high-throughput manner. Here, we present GotEnzymes, an extensive database with enzyme parameter predictions by AI approaches, which is publicly available at https://metabolicatlas.org/gotenzymes for interactive web exploration and programmatic access. The first release of this data resource contains predicted turnover numbers of over 25.7 million enzyme-compound pairs across 8099 organisms. We believe that GotEnzymes, with the readily-predicted enzyme parameters, would bring a speed boost to biological research covering both experimental and computational fields that involve working with candidate enzymes.
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Affiliation(s)
- Feiran Li
- Correspondence may also be addressed to Feiran Li.
| | | | | | - Jens Nielsen
- To whom correspondence should be addressed. Tel: +46 31 772 3804;
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12
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Application Prospects and Opportunities of Inorganic Nanomaterials for Enzyme Immobilization in the Food Processing Industry. Curr Opin Food Sci 2022. [DOI: 10.1016/j.cofs.2022.100909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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13
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Mesbah NM. Industrial Biotechnology Based on Enzymes From Extreme Environments. Front Bioeng Biotechnol 2022; 10:870083. [PMID: 35480975 PMCID: PMC9036996 DOI: 10.3389/fbioe.2022.870083] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 03/21/2022] [Indexed: 12/22/2022] Open
Abstract
Biocatalysis is crucial for a green, sustainable, biobased economy, and this has driven major advances in biotechnology and biocatalysis over the past 2 decades. There are numerous benefits to biocatalysis, including increased selectivity and specificity, reduced operating costs and lower toxicity, all of which result in lower environmental impact of industrial processes. Most enzymes available commercially are active and stable under a narrow range of conditions, and quickly lose activity at extremes of ion concentration, temperature, pH, pressure, and solvent concentrations. Extremophilic microorganisms thrive under extreme conditions and produce robust enzymes with higher activity and stability under unconventional circumstances. The number of extremophilic enzymes, or extremozymes, currently available are insufficient to meet growing industrial demand. This is in part due to difficulty in cultivation of extremophiles in a laboratory setting. This review will present an overview of extremozymes and their biotechnological applications. Culture-independent and genomic-based methods for study of extremozymes will be presented.
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Affiliation(s)
- Noha M Mesbah
- Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
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14
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Wang Y, Chen Y, Jiang L, Huang H. Improvement of the enzymatic detoxification activity towards mycotoxins through structure-based engineering. Biotechnol Adv 2022; 56:107927. [PMID: 35182727 DOI: 10.1016/j.biotechadv.2022.107927] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/09/2022] [Accepted: 02/14/2022] [Indexed: 12/11/2022]
Abstract
Mycotoxin contamination of food and feed is posing a serious threat to the global food safety and public health. Biological detoxification mediated by enzymes has emerged as a promising approach, as they can specifically degrade mycotoxins into non-toxic ones. However, the low degradation efficiency and stability limit their further application. To optimize the enzymes for mycotoxin removal, modification strategies that combine computational design with their structural data have been developed. Accordingly, this review will comprehensively summarize the recent trends in structure-based engineering to improve the enzyme catalytic efficiency, selectivity and stability in mycotoxins detoxification, which also provides perspectives in obtaining innovative and effective biocatalysts for mycotoxins degradation.
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Affiliation(s)
- Yanxia Wang
- College of Food Science and Light Industry, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Yao Chen
- College of Food Science and Light Industry, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China
| | - Ling Jiang
- College of Food Science and Light Industry, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing 211816, China.
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210046, China; College of Pharmaceutical Science, Nanjing Tech University, Nanjing 211816, China.
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15
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Dong W, Wang K, Zhao L, Li T, Wang Q, Ding Z. Selective immobilization of his-tagged phosphomannose isomerase on Ni chelated nanoparticles with good reusability and activity. Chembiochem 2021; 23:e202100497. [PMID: 34958513 DOI: 10.1002/cbic.202100497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 12/02/2021] [Indexed: 11/06/2022]
Abstract
In this paper, self-stable precipitation polymerization was used to prepare the enzyme-immobilized microsphere composite. Phosphomannose isomerase (PMI) with His-tag was successfully immobilized on Ni 2+ charged pyridine-derived particles. The maximum amount of PMI immobilized on such particles was ~ 184 mg/g. Compared with the free enzymes, the activity of the immobilized enzymes has been significantly improved. In addition, the immoblized enzymes showed a much better thermostability than free enzymes. At the same time, the immobilized enzymes can be reused for multiple reaction cycles. We have observed that the enzyme activity did not decrease significantly after 6 cycles of repeating usages. We conclude that the pyridine-derived particles can be used to selectively immobilize His-tagged enzymes, which can couple the enzyme purification and catalysis steps and improve the efficiency of enzyme-catalyzed industrial processes.
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Affiliation(s)
- Weifu Dong
- Jiangnan University, School of Chemical and Material Engineering, Lihu Road 1800, 214122, Wuxi, CHINA
| | - Kangjing Wang
- Jiangnan University, school of chemical and material engineering, CHINA
| | - Liting Zhao
- Jiangnan University, School of Biotechnology, CHINA
| | - Ting Li
- Jiangnan University, school of chemical and material engineering, CHINA
| | - Qian Wang
- University of South Carolina, Chemistry and Biochemistry, UNITED STATES
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16
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Catalyst Replacement Policy on Multienzymatic Systems: Theoretical Study in the One-Pot Sequential Batch Production of Lactofructose Syrup. Catalysts 2021. [DOI: 10.3390/catal11101167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
One-pot systems are an interesting proposal to carry out multi-enzymatic reactions, though this strategy implies establishing an optimal balance between the activity and operability of the involved enzymes. This is crucial for enzymes with marked differences in their operational stability, such as one-pot production of lactofructose syrup from cheese whey permeate, which involves two enzymes—β-galactosidase (β-gal) and glucose isomerase (GI). The aim of this work was to study the behavior of one-pot sequential batch production of lactofructose syrup considering both enzymes immobilized individually, in order to evaluate and design a strategy of replacement of the catalysts according to their stabilities. To this end, the modelling and simulation of the process was carried out, considering simultaneously the kinetics of both reactions and the kinetics of inactivation of both enzymes. For the latter, it was also considered the modulating effect that sugars present in the medium may have on the stability of β-gal, which is the less stable enzyme. At the simulated reaction conditions of 40 °C, pH 7, and 0.46 (IUGI/IUβ-gal), the results showed that considering the stability of β-gal under non-reactive conditions, meaning in absence of the effect of modulation, it is necessary to carry out four replacements of β-gal for each cycle of use of GI. On the other hand, when considering the modulation caused by the sugars on the β-gal stability, the productivity increases up to 23% in the case of the highest modulation factor studied (η = 0.8). This work shows the feasibility of conducting a one-pot operation with immobilized enzymes of quite different operational stability, and that a proper strategy of biocatalyst replacement increases the productivity of the process.
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Jang WD, Kim GB, Kim Y, Lee SY. Applications of artificial intelligence to enzyme and pathway design for metabolic engineering. Curr Opin Biotechnol 2021; 73:101-107. [PMID: 34358728 DOI: 10.1016/j.copbio.2021.07.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 07/16/2021] [Accepted: 07/17/2021] [Indexed: 01/07/2023]
Abstract
Metabolic engineering for developing industrial strains capable of overproducing bioproducts requires good understanding of cellular metabolism, including metabolic reactions and enzymes. However, metabolic pathways and enzymes involved are still unknown for many products of interest, which presents a key challenge in their biological production. This challenge can be partly overcome by constructing novel biosynthetic pathways through enzyme and pathway design approaches. With the increase in bio-big data, data-driven approaches using artificial intelligence (AI) techniques are allowing more advanced protein and pathway design. In this paper, we review recent studies on AI-aided protein engineering and design, focusing on directed evolution that uses AI approaches to efficiently construct mutant libraries. Also, recent works of AI-aided pathway design strategies, including template-based and template-free approaches, are discussed.
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Affiliation(s)
- Woo Dae Jang
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; KAIST Institute for the BioCentury, KAIST Institute for Artificial Intelligence, BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Gi Bae Kim
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Yeji Kim
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; KAIST Institute for the BioCentury, KAIST Institute for Artificial Intelligence, BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
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Strategies towards Reduction of Cellulases Consumption: Debottlenecking the Economics of Lignocellulosics Valorization Processes. POLYSACCHARIDES 2021. [DOI: 10.3390/polysaccharides2020020] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Lignocellulosic residues have been receiving growing interest as a promising source of polysaccharides, which can be converted into a variety of compounds, ranging from biofuels to bioplastics. Most of these can replace equivalent products traditionally originated from petroleum, hence representing an important environmental advantage. Lignocellulosic materials are theoretically unlimited, cheaper and may not compete with food crops. However, the conversion of these materials to simpler sugars usually requires cellulolytic enzymes. Being still associated with a high cost of production, cellulases are commonly considered as one of the main obstacles in the economic valorization of lignocellulosics. This work provides a brief overview of some of the most studied strategies that can allow an important reduction of cellulases consumption, hence improving the economy of lignocellulosics conversion. Cellulases recycling is initially discussed regarding the main processes to recover active enzymes and the most important factors that may affect enzyme recyclability. Similarly, the potential of enzyme immobilization is analyzed with a special focus on the contributions that some elements of the process can offer for prolonged times of operation and improved enzyme stability and robustness. Finally, the emergent concept of consolidated bioprocessing (CBP) is also described in the particular context of a potential reduction of cellulases consumption.
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Ruth JC, Spormann AM. Enzyme Electrochemistry for Industrial Energy Applications—A Perspective on Future Areas of Focus. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00708] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- John C. Ruth
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Alfred M. Spormann
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
- Department of Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
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