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Qin Z, Yuan B, Qu G, Sun Z. Rational enzyme design by reducing the number of hotspots and library size. Chem Commun (Camb) 2024. [PMID: 39210728 DOI: 10.1039/d4cc01394h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Biocatalysts that are eco-friendly, sustainable, and highly specific have great potential for applications in the production of fine chemicals, food, detergents, biofuels, pharmaceuticals, and more. However, due to factors such as low activity, narrow substrate scope, poor thermostability, or incorrect selectivity, most natural enzymes cannot be directly used for large-scale production of the desired products. To overcome these obstacles, protein engineering methods have been developed over decades and have become powerful and versatile tools for adapting enzymes with improved catalytic properties or new functions. The vastness of the protein sequence space makes screening a bottleneck in obtaining advantageous mutated enzymes in traditional directed evolution. In the realm of mathematics, there are two major constraints in the protein sequence space: (1) the number of residue substitutions (M); and (2) the number of codons encoding amino acids as building blocks (N). This feature review highlights protein engineering strategies to reduce screening efforts from two dimensions by reducing the numbers M and N, and also discusses representative seminal studies of rationally engineered natural enzymes to deliver new catalytic functions.
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Affiliation(s)
- Zongmin Qin
- University of Chinese Academy of Sciences, Beijing 100049, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Bo Yuan
- University of Chinese Academy of Sciences, Beijing 100049, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin 300308, China
| | - Ge Qu
- University of Chinese Academy of Sciences, Beijing 100049, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin 300308, China
| | - Zhoutong Sun
- University of Chinese Academy of Sciences, Beijing 100049, China
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin 300308, China
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2
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Zhang W, Shao ZQ, Wang ZX, Ye YF, Li SF, Wang YJ. Advances in aldo-keto reductases immobilization for biocatalytic synthesis of chiral alcohols. Int J Biol Macromol 2024; 274:133264. [PMID: 38901517 DOI: 10.1016/j.ijbiomac.2024.133264] [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: 02/23/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 06/22/2024]
Abstract
Chiral alcohols are essential building blocks of numerous pharmaceuticals and fine chemicals. Aldo-keto reductases (AKRs) constitute a superfamily of oxidoreductases that catalyze the reduction of aldehydes and ketones to their corresponding alcohols using NAD(P)H as a coenzyme. Knowledge about the crucial roles of AKRs immobilization in the biocatalytic synthesis of chiral alcohols is expanding. Herein, we reviewed the characteristics of various AKRs immobilization approaches, the applications of different immobilization materials, and the prospects of continuous flow bioreactor construction by employing these immobilized biocatalysts for synthesizing chiral alcohols. Finally, the opportunities and ongoing challenges for AKR immobilization are discussed and the outlook for this emerging area is analyzed.
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Affiliation(s)
- Wen Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Zi-Qing Shao
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Zhi-Xiu Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Yuan-Fan Ye
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Shu-Fang Li
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Ya-Jun Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, PR China; Engineering Research Center of Bioconversion and Biopurification of the Ministry of Education, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, PR China; The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, PR China.
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3
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Birch-Price Z, Hardy FJ, Lister TM, Kohn AR, Green AP. Noncanonical Amino Acids in Biocatalysis. Chem Rev 2024; 124:8740-8786. [PMID: 38959423 PMCID: PMC11273360 DOI: 10.1021/acs.chemrev.4c00120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/05/2024]
Abstract
In recent years, powerful genetic code reprogramming methods have emerged that allow new functional components to be embedded into proteins as noncanonical amino acid (ncAA) side chains. In this review, we will illustrate how the availability of an expanded set of amino acid building blocks has opened a wealth of new opportunities in enzymology and biocatalysis research. Genetic code reprogramming has provided new insights into enzyme mechanisms by allowing introduction of new spectroscopic probes and the targeted replacement of individual atoms or functional groups. NcAAs have also been used to develop engineered biocatalysts with improved activity, selectivity, and stability, as well as enzymes with artificial regulatory elements that are responsive to external stimuli. Perhaps most ambitiously, the combination of genetic code reprogramming and laboratory evolution has given rise to new classes of enzymes that use ncAAs as key catalytic elements. With the framework for developing ncAA-containing biocatalysts now firmly established, we are optimistic that genetic code reprogramming will become a progressively more powerful tool in the armory of enzyme designers and engineers in the coming years.
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Affiliation(s)
| | | | | | | | - Anthony P. Green
- Manchester Institute of Biotechnology,
School of Chemistry, University of Manchester, Manchester M1 7DN, U.K.
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4
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Zhou L, Tao C, Shen X, Sun X, Wang J, Yuan Q. Unlocking the potential of enzyme engineering via rational computational design strategies. Biotechnol Adv 2024; 73:108376. [PMID: 38740355 DOI: 10.1016/j.biotechadv.2024.108376] [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: 12/27/2023] [Revised: 04/27/2024] [Accepted: 05/08/2024] [Indexed: 05/16/2024]
Abstract
Enzymes play a pivotal role in various industries by enabling efficient, eco-friendly, and sustainable chemical processes. However, the low turnover rates and poor substrate selectivity of enzymes limit their large-scale applications. Rational computational enzyme design, facilitated by computational algorithms, offers a more targeted and less labor-intensive approach. There has been notable advancement in employing rational computational protein engineering strategies to overcome these issues, it has not been comprehensively reviewed so far. This article reviews recent developments in rational computational enzyme design, categorizing them into three types: structure-based, sequence-based, and data-driven machine learning computational design. Case studies are presented to demonstrate successful enhancements in catalytic activity, stability, and substrate selectivity. Lastly, the article provides a thorough analysis of these approaches, highlights existing challenges and potential solutions, and offers insights into future development directions.
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Affiliation(s)
- Lei Zhou
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Chunmeng Tao
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiaolin Shen
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xinxiao Sun
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jia Wang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Qipeng Yuan
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
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Lu J, Lv X, Yu W, Zhang J, Lu J, Liu Y, Li J, Du G, Chen J, Liu L. Reshaping Phosphatase Substrate Preference for Controlled Biosynthesis Using a "Design-Build-Test-Learn" Framework. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2309852. [PMID: 38504470 PMCID: PMC11165480 DOI: 10.1002/advs.202309852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/29/2024] [Indexed: 03/21/2024]
Abstract
Biosynthesis is the application of enzymes in microbial cell factories and has emerged as a promising alternative to chemical synthesis. However, natural enzymes with limited catalytic performance often need to be engineered to meet specific needs through a time-consuming trial-and-error process. This study presents a quantum mechanics (QM)-incorporated design-build-test-learn (DBTL) framework to rationally design phosphatase BT4131, an enzyme with an ambiguous substrate spectrum involved in N-acetylglucosamine (GlcNAc) biosynthesis. First, mutant M1 (L129Q) is designed using force field-based methods, resulting in a 1.4-fold increase in substrate preference (kcat/Km) toward GlcNAc-6-phosphate (GlcNAc6P). QM calculations indicate that the shift in substrate preference is caused by a 13.59 kcal mol-1 reduction in activation energy. Furthermore, an iterative computer-aided design is conducted to stabilize the transition state. As a result, mutant M4 (I49Q/L129Q/G172L) with a 9.5-fold increase in kcat-GlcNAc6P/Km-GlcNAc6P and a 59% decrease in kcat-Glc6P/Km-Glc6P is highly desirable compared to the wild type in the GlcNAc-producing chassis. The GlcNAc titer increases to 217.3 g L-1 with a yield of 0.597 g (g glucose)-1 in a 50-L bioreactor, representing the highest reported level. Collectively, this DBTL framework provides an easy yet fascinating approach to the rational design of enzymes for industrially viable biocatalysts.
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Affiliation(s)
- Jiangong Lu
- Key Laboratory of Carbohydrate Chemistry and BiotechnologyMinistry of EducationJiangnan UniversityWuxi214122China
- Science Center for Future FoodsJiangnan UniversityWuxi214122China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and BiotechnologyMinistry of EducationJiangnan UniversityWuxi214122China
- Science Center for Future FoodsJiangnan UniversityWuxi214122China
| | - Wenwen Yu
- Key Laboratory of Carbohydrate Chemistry and BiotechnologyMinistry of EducationJiangnan UniversityWuxi214122China
- Science Center for Future FoodsJiangnan UniversityWuxi214122China
| | - Jianing Zhang
- Key Laboratory of Carbohydrate Chemistry and BiotechnologyMinistry of EducationJiangnan UniversityWuxi214122China
- Science Center for Future FoodsJiangnan UniversityWuxi214122China
| | - Jianxing Lu
- Shandong Runde Biotechnology co., LTDTaian271200China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and BiotechnologyMinistry of EducationJiangnan UniversityWuxi214122China
- Science Center for Future FoodsJiangnan UniversityWuxi214122China
| | - Jianghua Li
- Science Center for Future FoodsJiangnan UniversityWuxi214122China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and BiotechnologyMinistry of EducationJiangnan UniversityWuxi214122China
- Science Center for Future FoodsJiangnan UniversityWuxi214122China
| | - Jian Chen
- Science Center for Future FoodsJiangnan UniversityWuxi214122China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and BiotechnologyMinistry of EducationJiangnan UniversityWuxi214122China
- Science Center for Future FoodsJiangnan UniversityWuxi214122China
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Scheele R, Weber Y, Nintzel FEH, Herger M, Kaminski TS, Hollfelder F. Ultrahigh Throughput Evolution of Tryptophan Synthase in Droplets via an Aptamer Sensor. ACS Catal 2024; 14:6259-6271. [PMID: 38660603 PMCID: PMC11036396 DOI: 10.1021/acscatal.4c00230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/29/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024]
Abstract
Tryptophan synthase catalyzes the synthesis of a wide array of noncanonical amino acids and is an attractive target for directed evolution. Droplet microfluidics offers an ultrahigh throughput approach to directed evolution (up to 107 experiments per day), enabling the search for biocatalysts in wider regions of sequence space with reagent consumption minimized to the picoliter volume (per library member). While the majority of screening campaigns in this format on record relied on an optically active reaction product, a new assay is needed for tryptophan synthase. Tryptophan is not fluorogenic in the visible light spectrum and thus falls outside the scope of conventional droplet microfluidic readouts, which are incompatible with UV light detection at high throughput. Here, we engineer a tryptophan DNA aptamer into a sensor to quantitatively report on tryptophan production in droplets. The utility of the sensor was validated by identifying five-fold improved tryptophan synthases from ∼100,000 protein variants. More generally, this work establishes the use of DNA-aptamer sensors with a fluorogenic read-out in widening the scope of droplet microfluidic evolution.
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Affiliation(s)
- Remkes
A. Scheele
- Department
of Biochemistry, University of Cambridge, Cambridge CB2 1GA, U.K.
| | - Yanik Weber
- Department
of Biochemistry, University of Cambridge, Cambridge CB2 1GA, U.K.
| | | | - Michael Herger
- Department
of Biochemistry, University of Cambridge, Cambridge CB2 1GA, U.K.
| | - Tomasz S. Kaminski
- Department
of Biochemistry, University of Cambridge, Cambridge CB2 1GA, U.K.
- Department
of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Florian Hollfelder
- Department
of Biochemistry, University of Cambridge, Cambridge CB2 1GA, U.K.
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7
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Su G, Ran L, Liu C, Qin Z, Teng H, Wu S. Directed Evolution and Immobilization of Lactobacillus brevis Alcohol Dehydrogenase for Chemo-Enzymatic Synthesis of Rivastigmine. Chemistry 2024:e202400454. [PMID: 38568868 DOI: 10.1002/chem.202400454] [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: 01/31/2024] [Revised: 03/21/2024] [Accepted: 04/02/2024] [Indexed: 04/05/2024]
Abstract
Rivastigmine is one of the several pharmaceuticals widely prescribed for the treatment of Alzheimer's disease. However, its practical synthesis still faces many issues, such as the involvement of toxic metals and harsh reaction conditions. Herein, we report a chemo-enzymatic synthesis of Rivastigmine. The key chiral intermediate was synthesized by an engineered alcohol dehydrogenase from Lactobacillus brevis (LbADH). A semi-rational approach was employed to improve its catalytic activity and thermal stability. Several LbADH variants were obtained with a remarkable increase in activity and melting temperature. Exploration of the substrate scope of these variants demonstrated improved activities toward various ketones, especially acetophenone analogs. To further recycle and reuse the biocatalyst, one LbADH variant and glucose dehydrogenase were co-immobilized on nanoparticles. By integrating enzymatic and chemical steps, Rivastigmine was successfully synthesized with an overall yield of 66 %. This study offers an efficient chemo-enzymatic route for Rivastigmine and provides several efficient LbADH variants with a broad range of potential applications.
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Affiliation(s)
- Guorong Su
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, 430070, P.R. China
| | - Lu Ran
- College of Chemistry, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, 430070, P.R. China
| | - Chang Liu
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, 430070, P.R. China
| | - Zhaoyang Qin
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, 430070, P.R. China
| | - Huailong Teng
- College of Chemistry, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, 430070, P.R. China
| | - Shuke Wu
- National Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, 430070, P.R. China
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Khodakarami Fard Z, Shirazinejad A, Mohammadi M, Hashemi SMB. Molecular Cloning of the Extracellular Lipases of Bacillus Amyloliquefaciens Isolated from Agrifood Wastes. IRANIAN JOURNAL OF BIOTECHNOLOGY 2024; 22:e3797. [PMID: 39220339 PMCID: PMC11364930 DOI: 10.30498/ijb.2024.417315.3797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 03/09/2024] [Indexed: 09/04/2024]
Abstract
Background The lipase enzyme (EC: 3.1.1.3) is one of the most important catalysts in food, dairy, detergent, and textile industries. Objective This study was performed to identify, isolate and characterize of lipase producing bacterial strain from agrifood wastes and to identify and characterize of their lipase genes. Materials and Methods In the present study, two lipase-producing isolates were identified from the effluent of Golbahar meat products and Soveyda vegetable oil factories using in silico and in vitro approaches. Results The results of morphological, biochemical, and molecular characterizations showed that both lipase-producing isolates belong to the Bacillus amyloliquefaciens species. Phylogenetic analysis confirmed the results of phenotypic, biochemical, and molecular characterizations. The results showed differences between LipA and LipB in the Golbahar and Soveyda isolates. Three different amino acids (residues 14, 100, and 165) were observed in LipA and one different amino acid (residue 102) was detected in LipB extracellular lipases. The protein molecular weight of the two extracted lipases ranged from 20 to 25 kDa. The identified extracellular lipases also had different physicochemical features. The maximum lipase activity of the Golbahar and Soveyda isolates was observed at 45 °C and at the pH of 8, but the Golbahar isolates exhibited higher lipase activity compared to the Soveyda isolates. The Golbahar and Soveyda isolates exhibited different activities in the presence of some ions, inhibitors, denaturing agents, and organic solvents and the Golbahar isolates showed better lipase activity than the Soveyda isolates. Conclusions In this study, two extracellular lipase-producing isolates of B. amyloliquefaciens were identified from different food industries, and their characteristics were investigated. The results of various investigations showed that the lipases produced by the Golbahar isolate have better characteristics than the lipases of the Soveyda isolate. The Golbahar lipases have a suitable temperature and pH activity range and maintain their activity in the presence of some ions, inhibitors, denaturing agents, and organic solvents. After further investigation, the Golbahar isolate lipase can be used in various industries. In addition, this lipase can be used enzyme engineering processes and its activity can be arbitrarily changed by targeted mutations. The results of this study can increase our knowledge of extracellular lipases and may turn out to have industrial applications.
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Affiliation(s)
- Zahra Khodakarami Fard
- Department of Food Science and Technology, Sarvestan Branch, Islamic Azad University, Sarvestan, Iran
| | - Alireza Shirazinejad
- Department of Food Science and Technology, Sarvestan Branch, Islamic Azad University, Sarvestan, Iran
| | - Mohsen Mohammadi
- Department of Pharmacognosy and Pharmaceutical Biotechnology, Faculty of Pharmacy, Lorestan University of Medical Sciences, Khorramabad, Iran
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Lin F, Li W, Wang D, Hu G, Qin Z, Xia X, Hu L, Liu X, Luo R. Advances in succinic acid production: the enhancement of CO 2 fixation for the carbon sequestration benefits. Front Bioeng Biotechnol 2024; 12:1392414. [PMID: 38605985 PMCID: PMC11007169 DOI: 10.3389/fbioe.2024.1392414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 03/18/2024] [Indexed: 04/13/2024] Open
Abstract
Succinic acid (SA), one of the 12 top platform chemicals produced from biomass, is a precursor of various high value-added derivatives. Specially, 1 mol CO2 is assimilated in 1 mol SA biosynthetic route under anaerobic conditions, which helps to achieve carbon reduction goals. In this review, methods for enhanced CO2 fixation in SA production and utilization of waste biomass for SA production are reviewed. Bioelectrochemical and bioreactor coupling systems constructed with off-gas reutilization to capture CO2 more efficiently were highlighted. In addition, the techno-economic analysis and carbon sequestration benefits for the synthesis of bio-based SA from CO2 and waste biomass are analyzed. Finally, a droplet microfluidics-based high-throughput screening technique applied to the future bioproduction of SA is proposed as a promising approach.
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Affiliation(s)
| | | | - Dan Wang
- Department of Chemical Engineering, School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, China
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10
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Schulke S, Nolten M, Schwaab G, Havenith M. Studying Local Electrostatics by Terahertz Spectroscopy Using Amines as a Probe. Chemphyschem 2024; 25:e202300389. [PMID: 37897334 DOI: 10.1002/cphc.202300389] [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: 06/05/2023] [Revised: 09/20/2023] [Accepted: 10/26/2023] [Indexed: 10/30/2023]
Abstract
In a previous study[1] we could show that a large amplitude mode of the zwitterion glycine can serve as a sensitive probe for protonation and allows to deduce local pKa values. Here we show that the underlying concept is more general: We present the results of a pH dependent measurement of Terahertz-FTIR (THz-FTIR) spectra of solvated amines, i. e. Diethylamine (DEA), Triethylamine (TEA), and Diisopropylamine (DiPA). We show that amines serve as a sensitive, label free probe for local protonation. Protonation of the amines yield intensity changes which can be quantified by precise THz spectroscopy (30 cm-1 -450 cm-1 ). A detailed analysis allows us to correlate the titration spectra of solvated amines in the THz range with pKa values. This demonstrates the potential of THz spectroscopy to probe the charge state of biomolecules in water in a label free manner.
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Affiliation(s)
- Simon Schulke
- Physical Chemistry 2, Ruhr-Univeristy Bochum, Universitaetsstraße 150, 44801, Bochum, Germany
| | - Melinda Nolten
- Physical Chemistry 2, Ruhr-Univeristy Bochum, Universitaetsstraße 150, 44801, Bochum, Germany
| | - Gerhard Schwaab
- Physical Chemistry 2, Ruhr-Univeristy Bochum, Universitaetsstraße 150, 44801, Bochum, Germany
| | - Martina Havenith
- Physical Chemistry 2, Ruhr-Univeristy Bochum, Universitaetsstraße 150, 44801, Bochum, Germany
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11
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Cascelli N, Gotor-Fernández V, Lavandera I, Sannia G, Lettera V. Spectrophotometric Assay for the Detection of 2,5-Diformylfuran and Its Validation through Laccase-Mediated Oxidation of 5-Hydroxymethylfurfural. Int J Mol Sci 2023; 24:16861. [PMID: 38069183 PMCID: PMC10706692 DOI: 10.3390/ijms242316861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/18/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023] Open
Abstract
Modern biocatalysis requires fast, sensitive, and efficient high-throughput screening methods to screen enzyme libraries in order to seek out novel biocatalysts or enhanced variants for the production of chemicals. For instance, the synthesis of bio-based furan compounds like 2,5-diformylfuran (DFF) from 5-hydroxymethylfurfural (HMF) via aerobic oxidation is a crucial process in industrial chemistry. Laccases, known for their mild operating conditions, independence from cofactors, and versatility with various substrates, thanks to the use of chemical mediators, are appealing candidates for catalyzing HMF oxidation. Herein, Schiff-based polymers based on the coupling of DFF and 1,4-phenylenediamine (PPD) have been used in the set-up of a novel colorimetric assay for detecting the presence of DFF in different reaction mixtures. This method may be employed for the fast screening of enzymes (Z' values ranging from 0.68 to 0.72). The sensitivity of the method has been proved, and detection (8.4 μM) and quantification (25.5 μM) limits have been calculated. Notably, the assay displayed selectivity for DFF and enabled the measurement of kinetics in DFF production from HMF using three distinct laccase-mediator systems.
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Affiliation(s)
- Nicoletta Cascelli
- Biopox srl, Viale Maria Bakunin 12, 80125 Napoli, Italy; (N.C.); (G.S.)
- Organic and Inorganic Chemistry Department, University of Oviedo, Avenida Julián Clavería 8, 33006 Oviedo, Spain; (V.G.-F.); (I.L.)
| | - Vicente Gotor-Fernández
- Organic and Inorganic Chemistry Department, University of Oviedo, Avenida Julián Clavería 8, 33006 Oviedo, Spain; (V.G.-F.); (I.L.)
| | - Iván Lavandera
- Organic and Inorganic Chemistry Department, University of Oviedo, Avenida Julián Clavería 8, 33006 Oviedo, Spain; (V.G.-F.); (I.L.)
| | - Giovanni Sannia
- Biopox srl, Viale Maria Bakunin 12, 80125 Napoli, Italy; (N.C.); (G.S.)
| | - Vincenzo Lettera
- Biopox srl, Viale Maria Bakunin 12, 80125 Napoli, Italy; (N.C.); (G.S.)
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, Via P. Bucci Cubo 12/D, 87036 Cosenza, Italy
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12
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Ting WW, Ng IS. Tunable T7 Promoter Orthogonality on T7RNAP for cis-Aconitate Decarboxylase Evolution via Base Editor and Screening from Itaconic Acid Biosensor. ACS Synth Biol 2023; 12:3020-3029. [PMID: 37750409 PMCID: PMC10595973 DOI: 10.1021/acssynbio.3c00344] [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: 06/05/2023] [Indexed: 09/27/2023]
Abstract
The deaminase-fused T7 RNA polymerase (T7RNAP) presents a promising toolkit for in vivo target-specific enzyme evolution, offering the unique advantage of simultaneous DNA modification and screening. Previous studies have reported the mutation efficiency of base editors relying on different resources. In contrast, the mechanism underlying the T7RNAP/T7 system is well-understood. Therefore, this study aimed to establish a new platform, termed dT7-Muta, by tuning the binding efficiency between T7RNAP and the T7 promoter for gene mutagenesis. The strategy for proof-of-concept involves alterations in the fluorescence distribution through dT7-Muta and screening of the mutants via flow cytometry. The cis-aconitate decarboxylase from Aspergillus terreus (AtCadA) was evolved and screened via an itaconate-induced biosensor as proof-of-function of enzyme evolution. First, the degenerated codons were designed within the binding and initial region of T7 promoters (dT7s), including upstream (U), central (C), and downstream (D) regions. Three strength variants of dT7 promoter from each design, i.e., strong (S), medium (M), and weak (W), were used for evaluation. Mutation using dT7s of varying strength resulted in a broader fluorescence distribution in sfGFP mutants from the promoters CW and DS. On the other hand, broader fluorescence distribution was observed in the AtCadA mutants from the original promoter T7, UW, and DS, with the highest fluorescence and itaconic acid titer at 860 a.u. and 0.51 g/L, respectively. The present platform introduces a novel aspect of the deaminase-based mutagenesis, emphasizing the potential of altering the binding efficiency between T7RNAP and the T7 promoter for further efforts in enzyme evolution.
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Affiliation(s)
- Wan-Wen Ting
- Department of Chemical
Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | - I-Son Ng
- Department of Chemical
Engineering, National Cheng Kung University, Tainan 70101, Taiwan
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13
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Wang CN, Qiu S, Fan FF, Lyu CJ, Hu S, Zhao WR, Mei JQ, Mei LH, Huang J. Enhancing the organic solvent resistance of ω-amine transaminase for enantioselective synthesis of (R)-(+)-1(1-naphthyl)-ethylamine. Biotechnol J 2023; 18:e2300120. [PMID: 37337619 DOI: 10.1002/biot.202300120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/28/2023] [Accepted: 06/14/2023] [Indexed: 06/21/2023]
Abstract
BACKGROUND Biocatalysis in high-concentration organic solvents has been applied to produce various industrial products with many advantages. However, using enzymes in organic solvents often suffers from inactivation or decreased catalytic activity and stability. An R-selective ω-amine transaminase from Aspergillus terreus (AtATA) exhibited activity toward 1-acetylnaphthalene. However, AtATA displayed unsatisfactory organic solvent resistance, which is required to enhance the solubility of the hydrophobic substrate 1-acetylnaphthalene. So, improving the tolerance of enzymes in organic solvents is essential. MAIN METHODS AND RESULTS The method of regional random mutation combined with combinatorial mutation was used to improve the resistance of AtATA in organic solvents. Enzyme surface areas are structural elements that undergo reversible conformational transitions, thus affecting the stability of the enzyme in organic solvents. Herein, three surface areas containing three loops were selected as potential mutation regions. And the "best" mutant T23I/T200K/P260S (M3) was acquired. In different concentrations of dimethyl sulfoxide (DMSO), the catalytic efficiency (kcat /Km ) toward 1-acetylnaphthalene and the stability (half-life t1/2 ) were higher than the wild-type (WT) of AtATA. The results of decreased Root Mean Square Fluctuation (RMSF) values via 20-ns molecular dynamics (MD) simulations under 15%, 25%, 35%, and 45% DMSO revealed that mutant M3 had lower flexibility, acquiring a more stable protein structure and contributing to its organic solvents stability than WT. Furthermore, M3 was applied to convert 1-acetylnaphthalene for synthesizing (R)-(+)-1(1-naphthyl)-ethylamine ((R)-NEA), which was an intermediate of Cinacalcet Hydrochloride for the treatment of secondary hyperthyroidism and hypercalcemia. Moreover, in a 20-mL scale-up experiment, 10 mM 1-acetylnaphthalene can be converted to (R)-NEA with 85.2% yield and a strict R-stereoselectivity (enantiomeric excess (e.e.) value >99.5%) within 10 h under 25% DMSO. CONCLUSION The beneficial mutation sites were identified to tailor AtATA's organic solvents stability via regional random mutation. The "best" mutant T23I/T200K/P260S (M3) holds great potential application for the synthesis of (R)-NEA.
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Affiliation(s)
- Chun-Ning Wang
- Key Laboratory of Chemical and Biological Processing Technology for Farm Products of Zhejiang Province, Zhejiang Provincial Collaborative Innovation Center of Agricultural Biological Resources Biochemical Manufacturing, School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Shuai Qiu
- Key Laboratory of Chemical and Biological Processing Technology for Farm Products of Zhejiang Province, Zhejiang Provincial Collaborative Innovation Center of Agricultural Biological Resources Biochemical Manufacturing, School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Fang-Fang Fan
- Key Laboratory of Chemical and Biological Processing Technology for Farm Products of Zhejiang Province, Zhejiang Provincial Collaborative Innovation Center of Agricultural Biological Resources Biochemical Manufacturing, School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Chang-Jiang Lyu
- Key Laboratory of Chemical and Biological Processing Technology for Farm Products of Zhejiang Province, Zhejiang Provincial Collaborative Innovation Center of Agricultural Biological Resources Biochemical Manufacturing, School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
| | - Sheng Hu
- School of Biological and Chemical Engineering, Ningbo Tech University, Ningbo, China
| | - Wei-Rui Zhao
- School of Biological and Chemical Engineering, Ningbo Tech University, Ningbo, China
| | - Jia-Qi Mei
- Hangzhou Huadong Medicine Group Co. Ltd, Hangzhou, China
| | - Le-He Mei
- School of Biological and Chemical Engineering, Ningbo Tech University, Ningbo, China
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- Jinhua Advanced Research Institute, Jinhua, China
| | - Jun Huang
- Key Laboratory of Chemical and Biological Processing Technology for Farm Products of Zhejiang Province, Zhejiang Provincial Collaborative Innovation Center of Agricultural Biological Resources Biochemical Manufacturing, School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, China
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14
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Christensen S, Wernersson C, André I. Facile Method for High-throughput Identification of Stabilizing Mutations. J Mol Biol 2023; 435:168209. [PMID: 37479080 DOI: 10.1016/j.jmb.2023.168209] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/13/2023] [Accepted: 07/13/2023] [Indexed: 07/23/2023]
Abstract
Characterizing the effects of mutations on stability is critical for understanding the function and evolution of proteins and improving their biophysical properties. High throughput folding and abundance assays have been successfully used to characterize missense mutations associated with reduced stability. However, screening for increased thermodynamic stability is more challenging since such mutations are rarer and their impact on assay readout is more subtle. Here, a multiplex assay for high throughput screening of protein folding was developed by combining deep mutational scanning, fluorescence-activated cell sorting, and deep sequencing. By analyzing a library of 2000 variants of Adenylate kinase we demonstrate that the readout of the method correlates with stability and that mutants with up to 13 °C increase in thermal melting temperature could be identified with low false positive rate. The discovery of many stabilizing mutations also enabled the analysis of general substitution patterns associated with increased stability in Adenylate kinase. This high throughput method to identify stabilizing mutations can be combined with functional screens to identify mutations that improve both stability and activity.
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Affiliation(s)
- Signe Christensen
- Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Camille Wernersson
- Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Ingemar André
- Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden.
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15
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Tei R, Bagde SR, Fromme JC, Baskin JM. Activity-based directed evolution of a membrane editor in mammalian cells. Nat Chem 2023; 15:1030-1039. [PMID: 37217787 PMCID: PMC10525039 DOI: 10.1038/s41557-023-01214-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 04/24/2023] [Indexed: 05/24/2023]
Abstract
Cellular membranes contain numerous lipid species, and efforts to understand the biological functions of individual lipids have been stymied by a lack of approaches for controlled modulation of membrane composition in situ. Here we present a strategy for editing phospholipids, the most abundant lipids in biological membranes. Our membrane editor is based on a bacterial phospholipase D (PLD), which exchanges phospholipid head groups through hydrolysis or transphosphatidylation of phosphatidylcholine with water or exogenous alcohols. Exploiting activity-dependent directed enzyme evolution in mammalian cells, we have developed and structurally characterized a family of 'superPLDs' with up to a 100-fold enhancement in intracellular activity. We demonstrate the utility of superPLDs for both optogenetics-enabled editing of phospholipids within specific organelle membranes in live cells and biocatalytic synthesis of natural and unnatural designer phospholipids in vitro. Beyond the superPLDs, activity-based directed enzyme evolution in mammalian cells is a generalizable approach to engineer additional chemoenzymatic biomolecule editors.
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Affiliation(s)
- Reika Tei
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Saket R Bagde
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - J Christopher Fromme
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Jeremy M Baskin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA.
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16
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Imam H, Hill K, Reid A, Mix S, Marr PC, Marr AC. Supramolecular Ionic Liquid Gels for Enzyme Entrapment. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2023; 11:6829-6837. [PMID: 37180026 PMCID: PMC10170508 DOI: 10.1021/acssuschemeng.3c00517] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 04/21/2023] [Indexed: 05/15/2023]
Abstract
Reported herein is an entrapment method for enzyme immobilization that does not require the formation of new covalent bonds. Ionic liquid supramolecular gels are formed containing enzymes that can be shaped into gel beads and act as recyclable immobilized biocatalysts. The gel was formed from two components, a hydrophobic phosphonium ionic liquid and a low molecular weight gelator derived from the amino acid phenylalanine. Gel-entrapped lipase from Aneurinibacillus thermoaerophilus was recycled for 10 runs over 3 days without loss of activity and retained activity for at least 150 days. The procedure does not form covalent bonds upon gel formation, which is supramolecular, and no bonds are formed between the enzyme and the solid support.
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Affiliation(s)
- Hasan
T. Imam
- School
of Chemistry and Chemical Engineering, Queen’s
University Belfast, UK, David Keir Building, Stranmillis Road, Belfast, Northern Ireland, United Kingdom BT9 5AG
| | - Kyle Hill
- School
of Chemistry and Chemical Engineering, Queen’s
University Belfast, UK, David Keir Building, Stranmillis Road, Belfast, Northern Ireland, United Kingdom BT9 5AG
| | - Andrew Reid
- School
of Chemistry and Chemical Engineering, Queen’s
University Belfast, UK, David Keir Building, Stranmillis Road, Belfast, Northern Ireland, United Kingdom BT9 5AG
| | - Stefan Mix
- Department
of Biocatalysis, Almac Bioscience, Almac
Group, Almac House, 20 Seagoe Industrial Estate, Craigavon, Belfast, Northern Ireland, United Kingdom BT63 5QD
| | - Patricia C. Marr
- School
of Chemistry and Chemical Engineering, Queen’s
University Belfast, UK, David Keir Building, Stranmillis Road, Belfast, Northern Ireland, United Kingdom BT9 5AG
- E-mail:
| | - Andrew C. Marr
- School
of Chemistry and Chemical Engineering, Queen’s
University Belfast, UK, David Keir Building, Stranmillis Road, Belfast, Northern Ireland, United Kingdom BT9 5AG
- E-mail:
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17
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Wu Y, Xie Y, Feng Y, Xu Z, Ban S, Song H. Diversity-Oriented Biosynthesis Yields l-Kynurenine Derivative-Based Neurological Drug Candidate Collection. ACS Synth Biol 2023; 12:608-617. [PMID: 36749842 DOI: 10.1021/acssynbio.2c00647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Natural product libraries with a remarkable range of biological activities play pivotal roles in drug discoveries due to their extraordinary structural complexity and immense diversity. l-Kynurenine (l-Kyn)-based derivatives are privileged pharmacophores that exhibit diverse therapeutic implications in neurological disorders. However, the difficulty in obtaining l-Kyn analogues with different skeletal structures has recently led to a decline in its medicinal research. Herein, we report a two-step, one-pot protocol for diversity-oriented biosynthesis of a collection of previously intractable l-Kyn-like compounds. The success of these challenging transformations mainly depends on unlocking the new catalytic scope of tryptophan 2,3-dioxygenases, followed by rational site-directed mutagenesis to modify the substrate domains further. As a result, 18 kynurenine analogues with diverse molecular scaffolds can be rapidly assembled in a predictable manner with 20-83% isolated yields, which not only fill the voids of the catalytic profile of tryptophan 2,3-dioxygenases with an array of substituent groups (e.g., F, Cl, Br, I, CH3, OCH3, and NO2) but also update the current understanding of its substrate spectrum. Our work highlights the great potential of existing enzymes in addressing long-standing synthetic challenges for facilitating the development or discovery of new drug candidates. Furthermore, our approach enables translating the reaction parameters from Eppendorf tubes to 1 L scale, affording l-4-Cl-Kyn and l-5-Cl-Kyn both on a gram scale with more than 80% isolated yields, and provides a promising alternative to further industrial applications.
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Affiliation(s)
- Yunbin Wu
- College of Chemistry & Molecular Science, Wuhan University, Wuhan, Hubei Province 430072, China
| | - Yongze Xie
- College of Chemistry & Molecular Science, Wuhan University, Wuhan, Hubei Province 430072, China
| | - Yinyin Feng
- College of Chemistry & Molecular Science, Wuhan University, Wuhan, Hubei Province 430072, China
| | - Zhiqin Xu
- School of Pharmacy, Shanxi Medical University, Taiyuan, Shanxi Province 030001, China
| | - Shurong Ban
- School of Pharmacy, Shanxi Medical University, Taiyuan, Shanxi Province 030001, China
| | - Heng Song
- College of Chemistry & Molecular Science, Wuhan University, Wuhan, Hubei Province 430072, China.,Wuhan University Shenzhen Research Institute, Shenzhen, Guangdong Province 518000, China
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18
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Liang B, Zhang X, Meng C, Wang L, Yang J. Directed evolution of tripartite ATP-independent periplasmic transporter for 3-Hydroxypropionate biosynthesis. Appl Microbiol Biotechnol 2023; 107:663-676. [PMID: 36525041 DOI: 10.1007/s00253-022-12330-1] [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: 08/17/2022] [Revised: 10/28/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022]
Abstract
Our previous study's introduction of the malonic acid assimilation pathway into Escherichia coli enabled biosynthesis of 3-Hydroxypropionate (3-HP) from malonate. However, the relatively low uptake activity of tripartite ATP-independent periplasmic (TRAP) malonic acid transporter (MatPQM) is considered rate-limiting in malonate utilization. Here, to improve the transport performance of this importer, MatP variants were obtained via directed evolution and a novel developed enzyme-inhibition-based high throughput screening approach. This plate chromogenic screening method is based on the fact that malonic acid inhibits both of succinate dehydrogenase activity and further the capability of the reduction of methylene-blue to methylene-white. The best mutant E103G/S194G/Y218H/L235P/N272S showed twofold increased transport efficiency compared to the wild-type. ITC assay and structural analysis revealed that increased binding affinity of the mutant to the ligand was the reason for improved uptake activity of MatPQM. Finally, the engineered strain harboring the evolved mutant produced 20.08 g/L 3-HP with the yield of 0.87 mol/mol malonate in a bioreactor. Therefore, the well-established directed evolution strategy can be regarded as the reference work for other TRAP-type transporters engineering. And, this transporter mutant with enhanced malonic acid uptake activity has broad applications in the microbial biosynthesis of malonyl-CoA-derived valuable compounds in bacteria. KEY POINTS: • We reported directed evolution of a TRAP-type malonic acid transporter. • We found the enhanced malonate uptake activity of mutant lies in improved affinity. • We enhanced 3-HP bioproduction with high yield by employing the best mutant.
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Affiliation(s)
- Bo Liang
- College of Food Science & Engineering, Qingdao Special Food Research Institute, Qingdao Agricultural University, Qingdao, China
- Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Xinping Zhang
- College of Food Science & Engineering, Qingdao Special Food Research Institute, Qingdao Agricultural University, Qingdao, China
- Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Chenfei Meng
- College of Food Science & Engineering, Qingdao Special Food Research Institute, Qingdao Agricultural University, Qingdao, China
- Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Lu Wang
- College of Food Science & Engineering, Qingdao Special Food Research Institute, Qingdao Agricultural University, Qingdao, China
- Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Jianming Yang
- College of Food Science & Engineering, Qingdao Special Food Research Institute, Qingdao Agricultural University, Qingdao, China.
- Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China.
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19
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Sürmeli Y, Şanlı-Mohamed G. Engineering of xylanases for the development of biotechnologically important characteristics. Biotechnol Bioeng 2023; 120:1171-1188. [PMID: 36715367 DOI: 10.1002/bit.28339] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 12/19/2022] [Accepted: 01/26/2023] [Indexed: 01/31/2023]
Abstract
Xylanases are the main biocatalysts used for the reduction of the xylan backbone from hemicellulose, randomly splitting off β-1,4-glycosidic linkages between xylopyranosyl residues. Xylanase market has been annually estimated at 500 million US Dollars and they are potentially used in broad industrial process ranges such as paper pulp biobleaching, xylo-oligosaccharide production, and biofuel manufacture from lignocellulose. The highly stable xylanases are preferred in the downstream procedure of industrial processes because they can tolerate severe conditions. Almost all native xylanases can not endure adverse conditions thus they are industrially not proper to be utilized. Protein engineering is a powerful technology for developing xylanases, which can effectively work in adverse conditions and can meet requirements for industrial processes. This study considered state-of-the-art strategies of protein engineering for creating the xylanase gene diversity, high-throughput screening systems toward upgraded traits of the xylanases, and the prediction and comprehensive analysis of the target mutations in xylanases by in silico methods. Also, key molecular factors have been elucidated for industrial characteristics (alkaliphilic enhancement, thermal stability, and catalytic performance) of GH11 family xylanases. The present review explores industrial characteristics improved by directed evolution, rational design, and semi-rational design as protein engineering approaches for pulp bleaching process, xylooligosaccharides production, and biorefinery & bioenergy production.
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Affiliation(s)
- Yusuf Sürmeli
- Department of Agricultural Biotechnology, Tekirdağ Namık Kemal University, Tekirdağ, Turkey
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20
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Ó'Fágáin C. Protein Stability: Enhancement and Measurement. Methods Mol Biol 2023; 2699:369-419. [PMID: 37647007 DOI: 10.1007/978-1-0716-3362-5_18] [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] [Indexed: 09/01/2023]
Abstract
This chapter defines protein stability, emphasizes its importance, and surveys the field of protein stabilization, with summary reference to a selection of 2014-2021 publications. One can enhance stability, particularly by protein engineering strategies but also by chemical modification and by other means. General protocols are set out on how to measure a given protein's (i) kinetic thermal stability and (ii) oxidative stability and (iii) how to undertake chemical modification of a protein in solution.
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Affiliation(s)
- Ciarán Ó'Fágáin
- School of Biotechnology, Dublin City University, Dublin, Ireland.
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21
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Biosynthesis of alkanes/alkenes from fatty acids or derivatives (triacylglycerols or fatty aldehydes). Biotechnol Adv 2022; 61:108045. [DOI: 10.1016/j.biotechadv.2022.108045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/22/2022] [Accepted: 09/24/2022] [Indexed: 11/27/2022]
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22
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Morellon-Sterling R, Bolivar JM, Fernandez-Lafuente R. Switch off/switch on of a cysteinyl protease as a way to preserve the active catalytic group by modification with a reversible covalent thiol modifier: Immobilization of ficin on vinyl-sulfone activated supports. Int J Biol Macromol 2022; 220:1155-1162. [PMID: 36037909 DOI: 10.1016/j.ijbiomac.2022.08.155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/11/2022] [Accepted: 08/23/2022] [Indexed: 11/05/2022]
Abstract
The immobilization of ficin (a cysteinyl proteases) on vinyl sulfone agarose produced its almost full inactivation. It was observed that the incubation of the free and immobilized enzyme in β-mercaptoethanol produced a 20 % of enzyme activity recovery, suggesting that the inactivation due to the immobilization could be a consequence of the modification of the catalytic Cys. To prevent the enzyme inactivation during the immobilization, switching off of ficin via Cys reaction with dipyridyl-disulfide was implemented, giving a reversible disulfide bond that produced a fully inactive enzyme. The switch on of ficin activity was implemented by incubation in 1 M β-mercaptoethanol. Using this strategy to immobilize the enzyme on vinyl sulfone agarose beads, the expressed activity of the immobilized ficin could be boosted up to 80 %. The immobilized enzyme presented a thermal stabilization similar to that obtained using ficin-glyoxyl-agarose beads. This procedure may be extended to many enzymes containing critical Cys, to permit their immobilization or chemical modification.
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Affiliation(s)
- Roberto Morellon-Sterling
- Departamento de Biocatálisis, ICP-CSIC, Marie Curie 2, Campus UAM-CSIC Cantoblanco, 28049 Madrid, Spain; Student of Departamento de Biología Molecular, Universidad Autónoma de Madrid, Darwin 2, Campus UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Juan M Bolivar
- FQPIMA Group, Chemical and Materials Engineering Department, Faculty of Chemical Sciences, Complutense University of Madrid, Complutense Ave., Madrid 28040, Spain
| | - Roberto Fernandez-Lafuente
- Departamento de Biocatálisis, ICP-CSIC, Marie Curie 2, Campus UAM-CSIC Cantoblanco, 28049 Madrid, Spain; Center of Excellence in Bionanoscience Research, External Scientific Advisory Academics, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
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23
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Song S, Jiang Y, Chen R, Su W, Liang W, Yang D, Li J, Zhang W, Gao S, Yuan B, Qu G, Sun Z. Whole-cell Biotransformation of Penicillin G by a Three-enzyme Co-expression System with Engineered Deacetoxycephalosporin C Synthase. Chembiochem 2022; 23:e202200179. [PMID: 35384232 DOI: 10.1002/cbic.202200179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/06/2022] [Indexed: 11/10/2022]
Abstract
Deacetoxycephalosporin C synthase (DAOCS) catalyzes the tranformation of penicillin G to phenylacetyl-7-aminodeacetoxycephalosporanic acid (G-7-ADCA) in dependence on 2-oxoglutarate (2OG). However, the low activity of DAOCS and the expense of 2OG restricted the practical application in the production of G-7-ADCA. Herein, a rational design campaign was performed on a DAOCS from Streptomyces clavuligerus (scDAOCS) in the quest to construct novel expandases. The resulting mutants showed 25~58% increase in activity compared to the template. The dominant DAOCS variants were then embeded into a three-enzyme co-expression system, consisting of a catalase and a L-glutamic oxidase for the generation of 2OG, to convert penicillin G into G-7-ADCA in E. coli . The engineered whole-cell enzyme cascade was applied on an up scaled reaction, exhibiting a yield of G-7-ADCA up to 39.21 mM (14.6 g·L -1 ) with a conversion of 78.42 mol%. This work highlights the potential of the integrated whole-cell system that may inspire further research on green and efficient production of 7-ADCA.
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Affiliation(s)
- Shiyi Song
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences, TIB, CHINA
| | - Yingying Jiang
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences, TIB, CHINA
| | - Ruidong Chen
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences, TIB, CHINA
| | - Wencheng Su
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences, TIB, 32 West 7th Avenue, Tianjin Airport Economic Area, 300308, Tianjin, CHINA
| | - Weinan Liang
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences, TIB, CHINA
| | - Dameng Yang
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences, TIB, 32 West 7th Avenue, Tianjin Airport Economic Area, 300308, CHINA
| | - Jincheng Li
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences, TIB, CHINA
| | - Wuyuan Zhang
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences, TIB, CHINA
| | - Shushan Gao
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences, TIB, CHINA
| | - Bo Yuan
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences, TIB, CHINA
| | - Ge Qu
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences, TIB, CHINA
| | - Zhoutong Sun
- Tianjin Institute of Industrial Biotechnology Chinese Academy of Sciences, National Enyzme Engineering Lab, 32 West 7th Avenue, Tianjin Airport Economic Area, 300308, Tianjin, CHINA
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24
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Nicholls BT, Oblinsky DG, Kurtoic SI, Grosheva D, Ye Y, Scholes GD, Hyster TK. Engineering a Non‐Natural Photoenzyme for Improved Photon Efficiency**. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202113842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Bryce T. Nicholls
- Department of Chemistry and Chemical Biology Cornell University Ithaca NY 14853 USA
- Department of Chemistry Princeton University Princeton NJ 08544 USA
| | | | - Sarah I. Kurtoic
- Department of Chemistry Princeton University Princeton NJ 08544 USA
| | - Daria Grosheva
- Department of Chemistry Princeton University Princeton NJ 08544 USA
| | - Yuxuan Ye
- Department of Chemistry and Chemical Biology Cornell University Ithaca NY 14853 USA
| | | | - Todd K. Hyster
- Department of Chemistry and Chemical Biology Cornell University Ithaca NY 14853 USA
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25
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Nicholls BT, Oblinsky DG, Kurtoic SI, Grosheva D, Ye Y, Scholes GD, Hyster TK. Engineering a Non-Natural Photoenzyme for Improved Photon Efficiency. Angew Chem Int Ed Engl 2022; 61:e202113842. [PMID: 34739168 DOI: 10.1002/anie.202113842] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Indexed: 11/08/2022]
Abstract
Photoenzymes are biological catalysts that use light to convert starting materials into products. These catalysts require photon absorption for each turnover, making quantum efficiency an important optimization parameter. Flavin-dependent "ene"-reductases (EREDs) display latent photoenzymatic activity for synthetically valuable hydroalkylations; however, protein engineering has not been used to optimize this non-natural function. We describe a protein engineering platform for the high throughput optimization of photoenzymes. A single round of engineering results in improved catalytic function toward the synthesis of γ, δ, ϵ-lactams, and acyclic amides. Mechanistic studies show that key mutations can alter the enzyme's excited state dynamics, enhance its photon efficiency, and ultimately increase catalyst performance. Transient absorption spectroscopy reveals that engineered variants display dramatically decreased radical lifetimes, indicating an evolution toward a concerted mechanism.
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Affiliation(s)
- Bryce T Nicholls
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Daniel G Oblinsky
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Sarah I Kurtoic
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Daria Grosheva
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Yuxuan Ye
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Gregory D Scholes
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Todd K Hyster
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA
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26
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Wang H, Zhong YY, Xiao YC, Chen FE. Chemical and chemoenzymatic stereoselective synthesis of β-nucleosides and their analogues. Org Chem Front 2022. [DOI: 10.1039/d1qo01936h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
β-Nucleosides are fundamental building blocks of biological systems that are widely used as therapeutic agents for treating cancer and viral infections among others. In the last two years, nucleoside analogues...
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27
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Ajeje SB, Hu Y, Song G, Peter SB, Afful RG, Sun F, Asadollahi MA, Amiri H, Abdulkhani A, Sun H. Thermostable Cellulases / Xylanases From Thermophilic and Hyperthermophilic Microorganisms: Current Perspective. Front Bioeng Biotechnol 2021; 9:794304. [PMID: 34976981 PMCID: PMC8715034 DOI: 10.3389/fbioe.2021.794304] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/02/2021] [Indexed: 12/13/2022] Open
Abstract
The bioconversion of lignocellulose into monosaccharides is critical for ensuring the continual manufacturing of biofuels and value-added bioproducts. Enzymatic degradation, which has a high yield, low energy consumption, and enhanced selectivity, could be the most efficient and environmentally friendly technique for converting complex lignocellulose polymers to fermentable monosaccharides, and it is expected to make cellulases and xylanases the most demanded industrial enzymes. The widespread nature of thermophilic microorganisms allows them to proliferate on a variety of substrates and release substantial quantities of cellulases and xylanases, which makes them a great source of thermostable enzymes. The most significant breakthrough of lignocellulolytic enzymes lies in lignocellulose-deconstruction by enzymatic depolymerization of holocellulose into simple monosaccharides. However, commercially valuable thermostable cellulases and xylanases are challenging to produce in high enough quantities. Thus, the present review aims at giving an overview of the most recent thermostable cellulases and xylanases isolated from thermophilic and hyperthermophilic microbes. The emphasis is on recent advancements in manufacturing these enzymes in other mesophilic host and enhancement of catalytic activity as well as thermostability of thermophilic cellulases and xylanases, using genetic engineering as a promising and efficient technology for its economic production. Additionally, the biotechnological applications of thermostable cellulases and xylanases of thermophiles were also discussed.
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Affiliation(s)
- Samaila Boyi Ajeje
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yun Hu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Guojie Song
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Sunday Bulus Peter
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Richmond Godwin Afful
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Fubao Sun
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Mohammad Ali Asadollahi
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Hamid Amiri
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Ali Abdulkhani
- Department of Wood and Paper Science and Technology, Faculty of Natural Resources, University of Tehran, Karaj, Iran
| | - Haiyan Sun
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
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28
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Juma WP, Nyoni D, Brady D, Bode ML. The Application of Biocatalysis in the Preparation and Resolution of Morita-Baylis-Hillman Adducts and Their Derivatives. Chembiochem 2021; 23:e202100527. [PMID: 34822736 DOI: 10.1002/cbic.202100527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/25/2021] [Indexed: 12/16/2022]
Abstract
The Morita-Baylis-Hillman (MBH) reaction affords highly functionalised allylic alcohols containing a new stereogenic centre. These MBH adducts are very versatile and have been transformed into a large range of products, some of which have medicinal potential. Several examples of asymmetric syntheses of MBH adducts have been reported, although a generally applicable method remains to be developed. Biocatalytic approaches for the synthesis and enzymatic kinetic resolution of MBH adducts have been reported, and are discussed in detail in this review. Enzymes able to catalyse the asymmetric MBH reaction have been identified, but selectivity and efficiency have generally been low. Lipases, esterases and nitrile-converting enzymes have all been successfully applied in the resolution of MBH adducts, with excellent selectivity being realised in most cases.
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Affiliation(s)
- Wanyama Peter Juma
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Private Bag 3, PO WITS, 2050, Johannesburg, South Africa
| | - Dubekile Nyoni
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Private Bag 3, PO WITS, 2050, Johannesburg, South Africa
| | - Dean Brady
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Private Bag 3, PO WITS, 2050, Johannesburg, South Africa
| | - Moira L Bode
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Private Bag 3, PO WITS, 2050, Johannesburg, South Africa
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29
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Zhu HQ, Tang XL, Zheng RC, Zheng YG. Recent advancements in enzyme engineering via site-specific incorporation of unnatural amino acids. World J Microbiol Biotechnol 2021; 37:213. [PMID: 34741210 DOI: 10.1007/s11274-021-03177-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 10/23/2021] [Indexed: 11/28/2022]
Abstract
With increased attention to excellent biocatalysts, evolving methods based on nature or unnatural amino acid (UAAs) mutagenesis have become an important part of enzyme engineering. The emergence of powerful method through expanding the genetic code allows to incorporate UAAs with unique chemical functionalities into proteins, endowing proteins with more structural and functional features. To date, over 200 diverse UAAs have been incorporated site-specifically into proteins via this methodology and many of them have been widely exploited in the field of enzyme engineering, making this genetic code expansion approach possible to be a promising tool for modulating the properties of enzymes. In this context, we focus on how this robust method to specifically incorporate UAAs into proteins and summarize their applications in enzyme engineering for tuning and expanding the functional properties of enzymes. Meanwhile, we aim to discuss how the benefits can be achieved by using the genetically encoded UAAs. We hope that this method will become an integral part of the field of enzyme engineering in the future.
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Affiliation(s)
- Hang-Qin Zhu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Xiao-Ling Tang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Ren-Chao Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China. .,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.,Engineering Research Center of Bioconversion and Biopurification of Ministry of Education, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
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30
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Modulating Glycoside Hydrolase Activity between Hydrolysis and Transfer Reactions Using an Evolutionary Approach. Molecules 2021; 26:molecules26216586. [PMID: 34770995 PMCID: PMC8587830 DOI: 10.3390/molecules26216586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 01/02/2023] Open
Abstract
The proteins within the CAZy glycoside hydrolase family GH13 catalyze the hydrolysis of polysaccharides such as glycogen and starch. Many of these enzymes also perform transglycosylation in various degrees, ranging from secondary to predominant reactions. Identifying structural determinants associated with GH13 family reaction specificity is key to modifying and designing enzymes with increased specificity towards individual reactions for further applications in industrial, chemical, or biomedical fields. This work proposes a computational approach for decoding the determinant structural composition defining the reaction specificity. This method is based on the conservation of coevolving residues in spatial contacts associated with reaction specificity. To evaluate the algorithm, mutants of α-amylase (TmAmyA) and glucanotransferase (TmGTase) from Thermotoga maritima were constructed to modify the reaction specificity. The K98P/D99A/H222Q variant from TmAmyA doubled the transglycosydation/hydrolysis (T/H) ratio while the M279N variant from TmGTase increased the hydrolysis/transglycosidation ratio five-fold. Molecular dynamic simulations of the variants indicated changes in flexibility that can account for the modified T/H ratio. An essential contribution of the presented computational approach is its capacity to identify residues outside of the active center that affect the reaction specificity.
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31
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Imam HT, Krasňan V, Rebroš M, Marr AC. Applications of Ionic Liquids in Whole-Cell and Isolated Enzyme Biocatalysis. Molecules 2021; 26:4791. [PMID: 34443378 PMCID: PMC8399596 DOI: 10.3390/molecules26164791] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/04/2021] [Accepted: 08/05/2021] [Indexed: 11/16/2022] Open
Abstract
Ionic liquids have unique chemical properties that have fascinated scientists in many fields. The effects of adding ionic liquids to biocatalysts are many and varied. The uses of ionic liquids in biocatalysis include improved separations and phase behaviour, reduction in toxicity, and stabilization of protein structures. As the ionic liquid state of the art has progressed, concepts of what can be achieved in biocatalysis using ionic liquids have evolved and more beneficial effects have been discovered. In this review ionic liquids for whole-cell and isolated enzyme biocatalysis will be discussed with an emphasis on the latest developments, and a look to the future.
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Affiliation(s)
- Hasan Tanvir Imam
- School of Chemistry and Chemical Engineering, Queen’s University Belfast, David Keir Building, Stranmillis Road, Belfast BT9 5AG, UK;
| | - Vladimír Krasňan
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 812 37 Bratislava, Slovakia;
| | - Martin Rebroš
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 812 37 Bratislava, Slovakia;
| | - Andrew Craig Marr
- School of Chemistry and Chemical Engineering, Queen’s University Belfast, David Keir Building, Stranmillis Road, Belfast BT9 5AG, UK;
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32
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Xu Y, Wu Y, Lv X, Sun G, Zhang H, Chen T, Du G, Li J, Liu L. Design and construction of novel biocatalyst for bioprocessing: Recent advances and future outlook. BIORESOURCE TECHNOLOGY 2021; 332:125071. [PMID: 33826982 DOI: 10.1016/j.biortech.2021.125071] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Bioprocess, a biocatalysis-based technology, is becoming popular in many research fields and widely applied in industrial manufacturing. However, low bioconversion, low productivity, and high costs during industrial processes are usually the limitation in bioprocess. Therefore, many biocatalyst strategies have been developed to meet these challenges in recent years. In this review, we firstly discuss protein engineering strategies, which are emerged for improving the biocatalysis activity of biocatalysts. Then, we summarize metabolic engineering strategies that are promoting the development of microbial cell factories. Next, we illustrate the necessity of using the combining strategy of protein engineering and metabolic engineering for efficient biocatalysts. Lastly, future perspectives about the development and application of novel biocatalyst strategies are discussed. This review provides theoretical guidance for the development of efficient, sustainable, and economical bioprocesses mediated by novel biocatalysts.
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Affiliation(s)
- Yameng Xu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China
| | - Yaokang Wu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China
| | - Guoyun Sun
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China
| | - Hongzhi Zhang
- Shandong Runde Biotechnology Co., Ltd., Tai'an 271000, PR China
| | - Taichi Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China.
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33
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Immobilization of the Peroxygenase from Agrocybe aegerita. The Effect of the Immobilization pH on the Features of an Ionically Exchanged Dimeric Peroxygenase. Catalysts 2021. [DOI: 10.3390/catal11050560] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
This paper outlines the immobilization of the recombinant dimeric unspecific peroxygenase from Agrocybe aegerita (rAaeUPO). The enzyme was quite stable (remaining unaltered its activity after 35 h at 47 °C and pH 7.0). Phosphate destabilized the enzyme, while glycerol stabilized it. The enzyme was not immobilized on glyoxyl-agarose supports, while it was immobilized albeit in inactive form on vinyl-sulfone-activated supports. rAaeUPO immobilization on glutaraldehyde pre-activated supports gave almost quantitative immobilization yield and retained some activity, but the biocatalyst was very unstable. Its immobilization via anion exchange on PEI supports also produced good immobilization yields, but the rAaeUPO stability dropped. However, using aminated agarose, the enzyme retained stability and activity. The stability of the immobilized enzyme strongly depended on the immobilization pH, being much less stable when rAaeUPO was adsorbed at pH 9.0 than when it was immobilized at pH 7.0 or pH 5.0 (residual activity was almost 0 for the former and 80% for the other preparations), presenting stability very similar to that of the free enzyme. This is a very clear example of how the immobilization pH greatly affects the final biocatalyst performance.
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