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Zhang X, Zhang X, Shi H, Zhang H, Zhang J, Yue C, Li D, Yao L, Tang C. Combining Flexible Region Design and Automatic Design to Enhance the Thermal Stability and Catalytic Efficiency of Leucine Dehydrogenase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 38838197 DOI: 10.1021/acs.jafc.4c02152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Leucine dehydrogenase (LeuDH, EC 1.4.1.9) can reversibly catalyze the oxidative deamination of l-leucine and some other specific α-amino acids to form the corresponding α-ketoacids. This reaction has great significance in the field of food additives and the pharmaceutical industry. The LeuDH from Exiguobacterium sibiricum (EsLeuDH) has high catalytic efficiency but limited thermal stability, hindering its widespread industrial application. In this study, a mutant N5F/I12L/A352Y of EsLeuDH (referred to as M2) was developed with enhanced thermal stability and catalytic activity through rational modification. The M2 mutant exhibits a half-life at 60 °C (t1/2(60 °C)) of 975.7 min and a specific activity of 69.6 U mg-1, which is 5.4 and 2.1 times higher than those of EsLeuDH, respectively. This research may facilitate the utilization of EsLeuDH at elevated temperatures, enhancing its potential for industrial applications. The findings offer a practical and efficient approach for optimizing LeuDH and other industrial enzymes.
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Affiliation(s)
- Xiang Zhang
- College of Life Science, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan 473061, People's Republic of China
| | - Xichuan Zhang
- College of Life Science, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan 473061, People's Republic of China
| | - Hongling Shi
- College of Life Science, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan 473061, People's Republic of China
| | - Huimin Zhang
- College of Animal Science and Technology, Yangzhou University, 88 South Daxue Road, Yangzhou, Jiangsu 225009, People's Republic of China
| | - Jianhui Zhang
- Postdoctoral Innovation Training Base, She Dian Lao Jiu Co. Ltd., 2 Liquor Avenue, Nanyang, Henan 473300, People's Republic of China
| | - Chao Yue
- College of Life Science, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan 473061, People's Republic of China
| | - Dandan Li
- College of Life Science, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan 473061, People's Republic of China
| | - Lunguang Yao
- College of Life Science, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan 473061, People's Republic of China
| | - Cunduo Tang
- College of Life Science, Nanyang Normal University, 1638 Wolong Road, Nanyang, Henan 473061, People's Republic of China
- Postdoctoral Innovation Training Base, She Dian Lao Jiu Co. Ltd., 2 Liquor Avenue, Nanyang, Henan 473300, People's Republic of China
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2
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Skeate JG, Pomeroy EJ, Slipek NJ, Jones BJ, Wick BJ, Chang JW, Lahr WS, Stelljes EM, Patrinostro X, Barnes B, Zarecki T, Krueger JB, Bridge JE, Robbins GM, McCormick MD, Leerar JR, Wenzel KT, Hornberger KM, Walker K, Smedley D, Largaespada DA, Otto N, Webber BR, Moriarity BS. Evolution of the clinical-stage hyperactive TcBuster transposase as a platform for robust non-viral production of adoptive cellular therapies. Mol Ther 2024; 32:1817-1834. [PMID: 38627969 DOI: 10.1016/j.ymthe.2024.04.024] [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: 08/31/2023] [Revised: 03/06/2024] [Accepted: 04/12/2024] [Indexed: 06/09/2024] Open
Abstract
Cellular therapies for the treatment of human diseases, such as chimeric antigen receptor (CAR) T and natural killer (NK) cells have shown remarkable clinical efficacy in treating hematological malignancies; however, current methods mainly utilize viral vectors that are limited by their cargo size capacities, high cost, and long timelines for production of clinical reagent. Delivery of genetic cargo via DNA transposon engineering is a more timely and cost-effective approach, yet has been held back by less efficient integration rates. Here, we report the development of a novel hyperactive TcBuster (TcB-M) transposase engineered through structure-guided and in vitro evolution approaches that achieves high-efficiency integration of large, multicistronic CAR-expression cassettes in primary human cells. Our proof-of-principle TcB-M engineering of CAR-NK and CAR-T cells shows low integrated vector copy number, a safe insertion site profile, robust in vitro function, and improves survival in a Burkitt lymphoma xenograft model in vivo. Overall, TcB-M is a versatile, safe, efficient and open-source option for the rapid manufacture and preclinical testing of primary human immune cell therapies through delivery of multicistronic large cargo via transposition.
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Affiliation(s)
- Joseph G Skeate
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Emily J Pomeroy
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Nicholas J Slipek
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Bryce J Wick
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jae-Woong Chang
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Walker S Lahr
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Erin M Stelljes
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | | | | | | | - Joshua B Krueger
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Jacob E Bridge
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gabrielle M Robbins
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Madeline D McCormick
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | | | | | | | | | | | - David A Largaespada
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Neil Otto
- Bio-Techne, Minneapolis, MN 55413, USA
| | - Beau R Webber
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Branden S Moriarity
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA.
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3
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Wang J, Lu X, Zhuge B, Zong H. Enhancing the catalytic efficiency of M32 carboxypeptidase by semi-rational design and its applications in food taste improvement. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024. [PMID: 38666395 DOI: 10.1002/jsfa.13558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/02/2024] [Accepted: 04/26/2024] [Indexed: 05/09/2024]
Abstract
BACKGROUND Carboxypeptidase is an exopeptidase that hydrolyzes amino acids at the C-terminal end of the peptide chain and has a wide range of applications in food. However, in industrial applications, the relatively low catalytic efficiency of carboxypeptidases is one of the main limiting factors for industrialization. RESULTS The study has enhanced the catalytic efficiency of Bacillus megaterium M32 carboxypeptidase (BmeCPM32) through semi-rational design. Firstly, the specific activity of the optimal mutant, BmeCPM32-M2, obtained through single-site mutagenesis and combinatorial mutagenesis, was 2.2-fold higher than that of the wild type (187.9 versus 417.8 U mg-1), and the catalytic efficiency was 2.9-fold higher (110.14 versus 325.75 s-1 mmol-1). Secondly, compared to the wild type, BmeCPM32-M2 exhibited a 1.8-fold increase in half-life at 60 °C, with no significant changes in its enzymatic properties (optimal pH, optimal temperature). Finally, BmeCPM32-M2 significantly increased the umami intensity of soy protein isolate hydrolysate by 55% and reduced bitterness by 83%, indicating its potential in developing tasty protein components. CONCLUSION Our research has revealed that the strategy based on protein sequence evolution and computational residue mutation energy led to an improved catalytic efficiency of BmeCPM32. Molecular dynamics simulations have revealed that a smaller substrate binding pocket and increased enzyme-substrate affinity are the reasons for the enhanced catalytic efficiency. Furthermore the number of hydrogen bonds and solvent and surface area may contribute to the improvement of thermostability. Finally, the de-bittering effect of BmeCPM32-M2 in soy protein isolate hydrolysate suggests its potential in developing palatable protein components. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Jinjiang Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xinyao Lu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Bin Zhuge
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Hong Zong
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
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4
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Xu K, Ma C, Wu C, Wu D. The molecular modification, expression, and the antibacterial effects studies of human lysozyme. Biosci Biotechnol Biochem 2024; 88:546-554. [PMID: 38409797 DOI: 10.1093/bbb/zbae023] [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: 11/30/2023] [Accepted: 02/14/2024] [Indexed: 02/28/2024]
Abstract
Human lysozyme (hLYZ) has attracted considerable research attention due to its natural and efficient antibacterial abilities and widespread uses. In this study, hLYZ was modified to enhance its enzyme activity and expressed in a Pichia pastoris expression system. A combination mutant HZM(2R-K)-N88D/V110S demonstrated the highest enzyme activity (6213 ± 164 U/mL) in shake flasks, which was 4.07-fold higher when compared with the original strain. Moreover, the recombinant P. pastoris was inducted in a 3 L bioreactor plus methanol/sorbitol co-feeding. After 120 h induction, the antibacterial activity of hLYZ reached 2.23 ± 0.12 × 105 U/mL, with the specific activity increasing to 1.89 × 105 U/mg, which is currently the highest specific activity obtained through recombinant expression of hLYZ. Also, hLYZ supernatants showed 2-fold inhibitory effects toward Staphylococcus aureus and Micrococcus lysodeikticus when compared with HZM(2R-K). Our research generated a hLYZ mutant with high antibacterial capabilities and provided a method for screening of high-quality enzymes.
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Affiliation(s)
- Kewei Xu
- SINOPEC Key Laboratory of Petroleum Accumulation Mechanisms, Wuxi, Jiangsu, China
- Wuxi Research Institute of Petroleum Geology, Research Institute of Petroleum Exploration & Production, SINOPEC, Wuxi, Jiangsu, China
| | - Chuanyuan Ma
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Changyun Wu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Dan Wu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
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5
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Yang J, Liang K, Ke H, Zhang Y, Meng Q, Gao L, Fan J, Li G, Zhou H, Xiao J, Lei X. Enzymatic Degradation of Deoxynivalenol with the Engineered Detoxification Enzyme Fhb7. JACS AU 2024; 4:619-634. [PMID: 38425922 PMCID: PMC10900206 DOI: 10.1021/jacsau.3c00696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 03/02/2024]
Abstract
In the era of global climate change, the increasingly severe Fusarium head blight (FHB) and deoxynivalenol (DON) contamination have caused economic losses and brought food and feed safety concerns. Recently, an FHB resistance gene Fhb7 coding a glutathione-S transferase (GST) to degrade DON by opening the critical toxic epoxide moiety was identified and opened a new window for wheat breeding and DON detoxification. However, the poor stability of Fhb7 and the elusiveness of the catalytic mechanism hinder its practical application. Herein, we report the first structure of Fhb7 at 2.41 Å and reveal a unique catalytic mechanism of epoxide opening transformation in GST family proteins. Furthermore, variants V29P and M10 showed that 5.5-fold and 266.7-fold longer half-life time than wild-type, respectively, were identified. These variants offer broad substrate scope, and the engineered biosafe Bacillus subtilis overexpressing the variants shows excellent DON degradation performance, exhibiting potential at bacterium engineering to achieve DON detoxification in the feed and biomedicine industry. This work provides a profound mechanistic insight into the enzymatic activities of Fhb7 and paves the way for further utilizing Fhb7-related enzymes in crop breeding and DON detoxification by synthetic biology.
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Affiliation(s)
- Jun Yang
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic
Chemistry and Molecular Engineering of Ministry of Education, Department
of Chemical Biology, College of Chemistry and Molecular Engineering,
and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Academy
for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Kai Liang
- School
of Life Sciences, Peking University, Beijing 100871, China
| | - Han Ke
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic
Chemistry and Molecular Engineering of Ministry of Education, Department
of Chemical Biology, College of Chemistry and Molecular Engineering,
and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yuebin Zhang
- Laboratory
of Molecular Modeling and Design, State Key Laboratory of Molecular
Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Qian Meng
- Analytical
Research Center for Organic and Biological Molecules, State Key Laboratory
of Drug Research, Shanghai Institute of
Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Lei Gao
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic
Chemistry and Molecular Engineering of Ministry of Education, Department
of Chemical Biology, College of Chemistry and Molecular Engineering,
and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Junping Fan
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic
Chemistry and Molecular Engineering of Ministry of Education, Department
of Chemical Biology, College of Chemistry and Molecular Engineering,
and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Guohui Li
- Laboratory
of Molecular Modeling and Design, State Key Laboratory of Molecular
Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Hu Zhou
- Analytical
Research Center for Organic and Biological Molecules, State Key Laboratory
of Drug Research, Shanghai Institute of
Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
- University
of Chinese Academy of Sciences, Number 19A Yuquan Road, Beijing 100049, China
| | - Junyu Xiao
- School
of Life Sciences, Peking University, Beijing 100871, China
- Academy
for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Xiaoguang Lei
- Beijing
National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic
Chemistry and Molecular Engineering of Ministry of Education, Department
of Chemical Biology, College of Chemistry and Molecular Engineering,
and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Academy
for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Institute
for Cancer Research, Shenzhen Bay Laboratory, Shenzhen 518107, China
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6
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Fauser F, Kadam BN, Arangundy-Franklin S, Davis JE, Vaidya V, Schmidt NJ, Lew G, Xia DF, Mureli R, Ng C, Zhou Y, Scarlott NA, Eshleman J, Bendaña YR, Shivak DA, Reik A, Li P, Davis GD, Miller JC. Compact zinc finger architecture utilizing toxin-derived cytidine deaminases for highly efficient base editing in human cells. Nat Commun 2024; 15:1181. [PMID: 38360922 PMCID: PMC10869815 DOI: 10.1038/s41467-024-45100-w] [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: 06/14/2023] [Accepted: 01/15/2024] [Indexed: 02/17/2024] Open
Abstract
Nucleobase editors represent an emerging technology that enables precise single-base edits to the genomes of eukaryotic cells. Most nucleobase editors use deaminase domains that act upon single-stranded DNA and require RNA-guided proteins such as Cas9 to unwind the DNA prior to editing. However, the most recent class of base editors utilizes a deaminase domain, DddAtox, that can act upon double-stranded DNA. Here, we target DddAtox fragments and a FokI-based nickase to the human CIITA gene by fusing these domains to arrays of engineered zinc fingers (ZFs). We also identify a broad variety of Toxin-Derived Deaminases (TDDs) orthologous to DddAtox that allow us to fine-tune properties such as targeting density and specificity. TDD-derived ZF base editors enable up to 73% base editing in T cells with good cell viability and favorable specificity.
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Affiliation(s)
| | | | | | | | | | | | - Garrett Lew
- Sangamo Therapeutics, Inc., Brisbane, CA, USA
| | - Danny F Xia
- Sangamo Therapeutics, Inc., Brisbane, CA, USA
| | | | - Colman Ng
- Sangamo Therapeutics, Inc., Brisbane, CA, USA
| | | | | | | | | | | | | | - Patrick Li
- Sangamo Therapeutics, Inc., Brisbane, CA, USA
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7
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Xue Y, Ji X, Li Z, Ma F, Jiang J, Huang Y. NADH-dependent formate dehydrogenase mutants for efficient carbon dioxide fixation. BIORESOURCE TECHNOLOGY 2024; 393:130027. [PMID: 37977496 DOI: 10.1016/j.biortech.2023.130027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/14/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
Bioconversion of CO2 to high-valuable products is a globally pursued sustainable technology for carbon neutrality. However, low CO2 activation with formate dehydrogenase (FDH) remains a major challenge for further upcycling due to the poor CO2 affinity, reduction activity and stability of currently used FDHs. Here, we present two recombined mutants, ΔFDHPa48 and ΔFDHPa4814, which exhibit high CO2 reduction activity and antioxidative activity. Compared to FDHPa, the reduction activity of ΔFDHPa48 was increased up to 743 % and the yield in the reduction of CO2 to methanol was increased by 3.16-fold. Molecular dynamics identified that increasing the width of the substrate pocket of ΔFDHPa48 could improve the enzyme reduction activity. Meanwhile, the enhanced rigidity of C-terminal residues effectively protected the active center. These results fundamentally advanced our understanding of the CO2 activation process and efficient FDH for enzymatic CO2 activation and conversion.
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Affiliation(s)
- Yaju Xue
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China; School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiuling Ji
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China; Langfang Technological Centre of Green Industry, Hebei 065001, China
| | - Zhuang Li
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China; School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fuqiang Ma
- Medical Enzyme Engineering Center, CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Jiangsu 215163, China
| | - Jingjie Jiang
- Medical Enzyme Engineering Center, CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Jiangsu 215163, China
| | - Yuhong Huang
- Beijing Key Laboratory of Ionic Liquids Clean Process, CAS Key Laboratory of Green Process and Engineering, State Key Laboratory of Multiphase Complex Systems, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, China; Langfang Technological Centre of Green Industry, Hebei 065001, China.
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8
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Wang LY, Tang H, Zhao JQ, Wang MN, Xue YP, Zheng YG. Correlation Analysis of Key Residue Sites between Computational-Aided Design Thermostability d-Amino Acid Oxidase and Ancestral Enzymes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:20177-20186. [PMID: 38064545 DOI: 10.1021/acs.jafc.3c06865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
The d-amino acid oxidase (DAAO) from Rhodotorula taiwanensis has proven to have great potential for applications due to its excellent catalytic kinetic parameters. However, its poor thermal stability has limited its performance in biocatalysis. Herein, starting from the variant SHVG of RtwDAAO, this study employed a comprehensive computational design approach for protein stability engineering, resulting in positive substitutions at specific sites (A43S, T45M, C234L, E195Y). The generated variant combination, SHVG/SMLY, exhibited a significant synergistic effect, leading to an extension of the half-life and Tmapp. The ancestral sequence reconstruction revealed the conservation of the variant sites. The association of the variant sites with the highly stable ancestral enzyme was further explored. After determining the contribution of the variant sites to thermal stability, it was applied to other homologous sequences and validated. Molecular dynamics simulations indicated that the increased hydrophobicity of the variant SHVG/SMLY was a key factor for the increased stability, with strengthened intersubunit interactions playing an important role. In addition, the physical properties of the amino acids themselves were identified as crucial factors for thermal stability generality in homologous enzymes, which is important for the rapid acquisition of a series of stable enzymes.
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Affiliation(s)
- Liu-Yu Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, P. R. China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Heng Tang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, P. R. China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Jin-Qiao Zhao
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, P. R. China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Meng-Nan Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, P. R. China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Ya-Ping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, P. R. China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, P. R. China
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, P. R. China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, Hangzhou 310014, P. R. China
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9
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Chi H, Jiang Q, Feng Y, Zhang G, Wang Y, Zhu P, Lu Z, Lu F. Thermal Stability Enhancement of L-Asparaginase from Corynebacterium glutamicum Based on a Semi-Rational Design and Its Effect on Acrylamide Mitigation Capacity in Biscuits. Foods 2023; 12:4364. [PMID: 38231880 DOI: 10.3390/foods12234364] [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: 09/29/2023] [Revised: 10/19/2023] [Accepted: 11/29/2023] [Indexed: 01/19/2024] Open
Abstract
Acrylamide is present in thermally processed foods, and it possesses toxic and carcinogenic properties. L-asparaginases could effectively regulate the formation of acrylamide at the source. However, current L-asparaginases have drawbacks such as poor thermal stability, low catalytic activity, and poor substrate specificity, thereby restricting their utility in the food industry. To address this issue, this study employed consensus design to predict the crucial residues influencing the thermal stability of Corynebacterium glutamicum L-asparaginase (CgASNase). Subsequently, a combination of site-point saturating mutation and combinatorial mutation techniques was applied to generate the double-mutant enzyme L42T/S213N. Remarkably, L42T/S213N displayed significantly enhanced thermal stability without a substantial impact on its enzymatic activity. Notably, its half-life at 40 °C reached an impressive 13.29 ± 0.91 min, surpassing that of CgASNase (3.24 ± 0.23 min). Moreover, the enhanced thermal stability of L42T/S213N can be attributed to an increased positive surface charge and a more symmetrical positive potential, as revealed by three-dimensional structural simulations and structure comparison analyses. To assess the impact of L42T/S213N on acrylamide removal in biscuits, the optimal treatment conditions for acrylamide removal were determined through a combination of one-way and orthogonal tests, with an enzyme dosage of 300 IU/kg flour, an enzyme reaction temperature of 40 °C, and an enzyme reaction time of 30 min. Under these conditions, compared to the control (464.74 ± 6.68 µg/kg), the acrylamide reduction in double-mutant-enzyme-treated biscuits was 85.31%, while the reduction in wild-type-treated biscuits was 68.78%. These results suggest that L42T/S213N is a promising candidate for industrial applications of L-asparaginase.
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Affiliation(s)
- Huibing Chi
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Qingwei Jiang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yiqian Feng
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Guizheng Zhang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Yilian Wang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Ping Zhu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Fengxia Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
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10
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Shafaghi M, Bahadori Z, Barzi SM, Afshari E, Madanchi H, Mousavi SF, Shabani AA. A new candidate epitope-based vaccine against PspA PhtD of Streptococcus pneumoniae: a computational experimental approach. Front Cell Infect Microbiol 2023; 13:1271143. [PMID: 38035337 PMCID: PMC10684780 DOI: 10.3389/fcimb.2023.1271143] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/26/2023] [Indexed: 12/02/2023] Open
Abstract
Introduction Pneumococcus is an important respiratory pathogen that is associated with high rates of death in newborn children and the elderly. Given the disadvantages of current polysaccharide-based vaccines, the most promising alternative for developing improved vaccines may be to use protein antigens with different roles in pneumococcus virulence. PspA and PhtD, highly immunogenic surface proteins expressed by almost all pneumococcal strains, are capable of eliciting protective immunity against lethal infections. Methods In this study using immunoinformatics approaches, we constructed one fusion construct (called PAD) by fusing the immunodominant regions of PspA from families 1 & 2 (PA) to the immunodominant regions of PhtD (PD). The objective of this project was to test the immunogenicity of the fusion protein PAD and to compare its protective activity against S. pneumoniae infection with PA or PD alone and a combination of PA and PD. The prediction of physicochemical properties, antigenicity, allergenicity, toxicity, and 3D-structure of the constructs, as well as molecular docking with HLA receptor and immune simulation were performed using computational tools. Finally, mice were immunized and the serum levels of antibodies/cytokines and functionality of antibodies in vitro were evaluated after immunization. The mice survival rates and decrease of bacterial loads in the blood/spleen were examined following the challenge. Results The computational analyses indicated the proposed constructs could be antigenic, non-allergenic, non-toxic, soluble and able to elicit robust immune responses. The results of actual animal experiments revealed the candidate vaccines could induce the mice to produce high levels of antibodies and cytokines. The complement-mediated bactericidal activity of antibodies was confirmed and the antibodies provided favorable survival in immunized mice after bacterial challenge. In general, the experimental results verified the immunoinformatics studies. Conclusion For the first time this report presents novel peptide-based vaccine candidates consisting of immunodominant regions of PspA and PhtD antigens. The obtained findings confirmed that the fusion formulation could be relatively more efficient than the individual and combination formulations. The results propose that the fusion protein alone could be used as a serotype-independent pneumococcal vaccine or as an effective partner protein for a conjugate polysaccharide vaccine.
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Affiliation(s)
- Mona Shafaghi
- Department of Medical Biotechnology, faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Zohreh Bahadori
- Department of Medical Biotechnology, faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | | | - Elnaz Afshari
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Hamid Madanchi
- Department of Medical Biotechnology, faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
- Drug Design and Bioinformatics Unit, Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | | | - Ali Akbar Shabani
- Department of Medical Biotechnology, faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
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11
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Li X, Chen B, Chen W, Pu Z, Qi X, Yang L, Wu J, Yu H. Customized multiple sequence alignment as an effective strategy to improve performance of Taq DNA polymerase. Appl Microbiol Biotechnol 2023; 107:6507-6525. [PMID: 37658164 DOI: 10.1007/s00253-023-12744-5] [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: 04/13/2023] [Revised: 08/06/2023] [Accepted: 08/24/2023] [Indexed: 09/03/2023]
Abstract
Engineering Taq DNA polymerase (TaqPol) for improved activity, stability and sensitivity was critical for its wide applications. Multiple sequence alignment (MSA) has been widely used in engineering enzymes for improved properties. Here, we first designed TaqPol mutations based on MSA of 2756 sequences from both thermophilic and non-thermophilic organisms. Two double mutations were generated including a variant H676F/R677G showing a decrease in both activity and stability, and a variant Y686R/E687K showing an improved activity, but a decreased stability. Mutations targeted on coevolutionary residues of Arg677 and Tyr686 were then applied to rescue stability or activity loss of the double mutants, which achieved a partial success. Sequence analysis revealed that the two mutations are abundant in non-thermophilic sequences but not in thermophilic homologues. Then, a small-scale MSA containing sequences from only thermophilic organisms was applied to predict 13 single variants and two of them, E507Q and E734N showed a simultaneous increase in both stability and activity, even in sensitivity. A customized MSA was hence more effective in engineering a thermophilic enzyme and could be used in engineering other enzymes. Molecular dynamics simulations revealed the impact of mutations on the protein dynamics and interactions between TaqPol and substrates. KEY POINTS: • The pool of sequence for alignment is critical to engineering Taq DNA polymerase. • The variants with low properties can be rescued by mutations in coevolving network. • Improving binding with DNA can improve DNA polymerase stability and activity.
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Affiliation(s)
- Xinjia Li
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Binbin Chen
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Wanyi Chen
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Zhongji Pu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Xin Qi
- Building No.4, Zhongguancun Dongsheng International Science Park, No. 1 North Yongtaizhuang Road, Haidian District, Beijing, 100192, China
| | - Lirong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Jianping Wu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Haoran Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China.
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China.
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12
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Ouyang B, Wang G, Zhang N, Zuo J, Huang Y, Zhao X. Recent Advances in β-Glucosidase Sequence and Structure Engineering: A Brief Review. Molecules 2023; 28:4990. [PMID: 37446652 DOI: 10.3390/molecules28134990] [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: 06/01/2023] [Revised: 06/21/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
β-glucosidases (BGLs) play a crucial role in the degradation of lignocellulosic biomass as well as in industrial applications such as pharmaceuticals, foods, and flavors. However, the application of BGLs has been largely hindered by issues such as low enzyme activity, product inhibition, low stability, etc. Many approaches have been developed to engineer BGLs to improve these enzymatic characteristics to facilitate industrial production. In this article, we review the recent advances in BGL engineering in the field, including the efforts from our laboratory. We summarize and discuss the BGL engineering studies according to the targeted functions as well as the specific strategies used for BGL engineering.
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Affiliation(s)
- Bei Ouyang
- College of Life Science, Jiangxi Normal University, Nanchang 330022, China
| | - Guoping Wang
- College of Life Science, Jiangxi Normal University, Nanchang 330022, China
| | - Nian Zhang
- College of Life Science, Jiangxi Normal University, Nanchang 330022, China
| | - Jiali Zuo
- School of Computer and Information Engineering, Jiangxi Normal University, Nanchang 330022, China
| | - Yunhong Huang
- College of Life Science, Jiangxi Normal University, Nanchang 330022, China
| | - Xihua Zhao
- College of Life Science, Jiangxi Normal University, Nanchang 330022, China
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13
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Wu H, Yi M, Wu X, Ding Y, Pu M, Wen L, Cheng Y, Zhang W, Mu W. Engineering the thermostability of d-lyxose isomerase from Caldanaerobius polysaccharolyticus via multiple computer-aided rational design for efficient synthesis of d-mannose. Synth Syst Biotechnol 2023; 8:323-330. [PMID: 37168606 PMCID: PMC10165151 DOI: 10.1016/j.synbio.2023.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/16/2023] [Accepted: 04/17/2023] [Indexed: 05/13/2023] Open
Abstract
d-Mannose is an attractive functional sugar that exhibits many physiological benefits on human health. The demand for low-calorie sugars and sweeteners in foods are increasingly available on the market. Some sugar isomerases, such as d-lyxose isomerase (d-LIase), can achieve an isomerization reaction between d-mannose and d-fructose. However, the weak thermostability of d-LIase limits its efficient conversion from d-fructose to d-mannose. Nonetheless, few studies are available that have investigated the molecular modification of d-LIase to improve its thermal stability. In this study, computer-aided tools including FireProt, PROSS, and Consensus Finder were employed to jointly design d-LIase mutants with improved thermostability for the first time. Finally, the obtained five-point mutant M5 (N21G/E78P/V58Y/C119Y/K170P) showed high thermal stability and catalytic activity. The half-life of M5 at 65 °C was 10.22 fold, and the catalytic efficiency towards 600 g/L of d-fructose was 2.6 times to that of the wild type enzyme, respectively. Molecular dynamics simulation and intramolecular forces analysis revealed a thermostability mechanism of highly rigidity conformation, newly formed hydrogen bonds and π-cation interaction between and within protein domains, and redistributed surface electrostatic charges for the mutant M5. This research provided a promising d-LIase mutant for the industrial production of d-mannose from d-fructose.
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Affiliation(s)
- Hao Wu
- School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha, 410114, China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Ming Yi
- School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha, 410114, China
| | - Xiaoyi Wu
- School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha, 410114, China
| | - Yating Ding
- School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha, 410114, China
| | - Minghui Pu
- School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha, 410114, China
| | - Li Wen
- School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha, 410114, China
| | - Yunhui Cheng
- School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha, 410114, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
- Corresponding author. State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, China.
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
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14
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Wang X, Dong T, Zhou Q, Tong L, Zheng J, Qin X, Wang X, Wang Y, Yao B, Huang H, Luo H. Improving the Activity and Stability of Serine Protease ThAPT3 by Alleviating Self-Cleavage and Its Application in Deproteinization of Shrimp Shells. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:7777-7790. [PMID: 37161941 DOI: 10.1021/acs.jafc.3c01618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The self-cleavage properties of proteases result in low activity and instability, which limit their industrial application. In this study, the serine protease ThAPT3 from Torrubiella hemipterigena was successfully expressed in Komagataella phaffii. We investigated the self-degradation mechanism of ThAPT3 and presented a rational strategy to alleviate self-cleavage. A major self-degradation site (Leu238-Met239) and a primary autolysis region were identified. The autolysis regions (loop18, α8-helix, and loop19) were redesigned and optimized using loop transplantation, energy calculations, surface cavity optimization, and loop anchoring. A triple-superposition mutant, ThAPT3-M9 (M239GKDGAVAAGLC250 → M239TLNRTTAANAC250/A251E/A254Q/R259L/A267E/S280N), was obtained. Compared to the wild type, the autolysis of M9 was significantly alleviated, and its half-life at 60 °C was increased approximately 39-fold (from 1.6 to 62.4 min). The optimal temperature and specific activity of M9 increased by 5 °C (from 60 to 65 °C) and 62% (4985 vs 3078 U/mg), respectively. M9 showed significant advantages in shrimp shell deproteinization.
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Affiliation(s)
- Xiao Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tao Dong
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Qiao Zhou
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- College of Animal Science and Technology, Northwest Agriculture and Forestry University, Yangling, Shaanxi 712100, China
| | - Lige Tong
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jie Zheng
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xing Qin
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaolu Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yaru Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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15
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Li S, Cao L, Yang X, Wu X, Xu S, Liu Y. Simultaneously optimizing multiple properties of β-glucosidase Bgl6 using combined (semi-)rational design strategies and investigation of the underlying mechanisms. BIORESOURCE TECHNOLOGY 2023; 374:128792. [PMID: 36842511 DOI: 10.1016/j.biortech.2023.128792] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
The performance of β-glucosidase during cellulose saccharification is determined by thermostability, activity and glucose tolerance. However, conflicts between them make it challenging to simultaneously optimize three properties. In this work, such a case was reported using Bgl6-M3 as a starting point. Firstly, four thermostability-enhancing mutations were obtained using computer-aided engineering strategies (mutant M7). Secondly, substrate binding pocket of M7 was reshaped, generating two mutations that increased activity but decreased glucose tolerance (mutant M9). Then a key region lining active site cavity was redesigned, resulting in three mutations that boosted glucose tolerance and activity. Finally, mutant M12 with simultaneously improved thermostability (half-life of 20-fold), activity (kcat/Km of 5.6-fold) and glucose tolerance (ΔIC50 of 200 mM) was obtained. Mechanisms for property improvement were elucidated by structural analysis and molecular dynamics simulations. Overall, the strategies used here and new insights into the underlying mechanisms may provide guidance for multi-property engineering of other enzymes.
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Affiliation(s)
- Shuifeng Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Lichuang Cao
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Xiangpeng Yang
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Xiangrui Wu
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Shujing Xu
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China
| | - Yuhuan Liu
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China.
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16
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Chi H, Zhu X, Shen J, Lu Z, Lu F, Lyu Y, Zhu P. Thermostability enhancement and insight of L-asparaginase from Mycobacterium sp. via consensus-guided engineering. Appl Microbiol Biotechnol 2023; 107:2321-2333. [PMID: 36843197 DOI: 10.1007/s00253-023-12443-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 02/06/2023] [Accepted: 02/13/2023] [Indexed: 02/28/2023]
Abstract
Acrylamide alleviation in food has represented as a critical issue due to its neurotoxic effect on human health. L-Asparaginase (ASNase, EC 3.5.1.1) is considered a potential additive for acrylamide alleviation in food. However, low thermal stability hinders the application of ASNase in thermal food processing. To obtain highly thermal stable ASNase for its industrial application, a consensus-guided approach combined with site-directed saturation mutation (SSM) was firstly reported to engineer the thermostability of Mycobacterium gordonae L-asparaginase (GmASNase). The key residues Gly97, Asn159, and Glu249 were identified for improving thermostability. The combinatorial triple mutant G97T/N159Y/E249Q (TYQ) displayed significantly superior thermostability with half-life values of 61.65 ± 8.69 min at 50 °C and 5.12 ± 1.66 min at 55 °C, whereas the wild-type was completely inactive at these conditions. Moreover, its Tm value increased by 8.59 °C from parent wild-type. Interestingly, TYQ still maintained excellent catalytic efficiency and specific activity. Further molecular dynamics and structure analysis revealed that the additional hydrogen bonds, increased hydrophobic interactions, and favorable electrostatic potential were essential for TYQ being in a more rigid state for thermostability enhancement. These results suggested that our strategy was an efficient engineering approach for improving fundamental properties of GmASNase and offering GmASNase as a potential agent for efficient acrylamide mitigation in food industry. KEY POINTS: • The thermostability of GmASNase was firstly improved by consensus-guided engineering. • The half-life and Tm value of triple mutant TYQ were significantly increased. • Insight on improved thermostability of TYQ was revealed by MD and structure analysis.
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Affiliation(s)
- Huibing Chi
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoyu Zhu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Juan Shen
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhaoxin Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fengxia Lu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yunbin Lyu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Ping Zhu
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China.
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17
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Chen Q, Xiao H, Li ZP, Pei XQ, Yang W, Liu Y, Wu ZL. Stereo-complementary epoxidation of 4-vinyl-2,3-dihydrobenzofuran using mutants of SeStyA with enhanced stability and enantioselectivity. MOLECULAR CATALYSIS 2023. [DOI: 10.1016/j.mcat.2023.113055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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18
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Lee JM, Park BS, Oh MK. Production of 2’-Fucosyllactose using ⍺1,2-fucosyltransferase from a GRAS bacterial strain. Enzyme Microb Technol 2023; 167:110232. [PMID: 37028251 DOI: 10.1016/j.enzmictec.2023.110232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/25/2023] [Accepted: 03/26/2023] [Indexed: 03/30/2023]
Abstract
2'-Fucosyllactose (2'-FL) is a major oligosaccharide found in human breast milk. It is produced from GDP-L-fucose and D-lactose by ⍺1,2-fucosyltransferase (⍺1,2-fucT), but the enzyme has been identified mostly in pathogens. In this study, an ⍺1,2-fucT was isolated from a Generally Recognized as Safe (GRAS) Bacillus megaterium strain. The enzyme was successfully expressed in metabolically-engineered Escherichia coli. Furthermore, replacement of non-conserved amino acid residues with conserved ones in the protein led to an increase in the rate of 2'-FL production. As a result, fed-batch fermentation of E. coli produced 30 g/L of 2'-FL from glucose and lactose. Thus, the overproduction of 2'-FL using a novel enzyme from a GRAS bacteria strain was successfully demonstrated.
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Affiliation(s)
- Jun-Min Lee
- Department of Chemical & Biological Engineering, Korea University, Seoul 136-763, South Korea
| | - Bu-Soo Park
- Department of Chemical & Biological Engineering, Korea University, Seoul 136-763, South Korea
| | - Min-Kyu Oh
- Department of Chemical & Biological Engineering, Korea University, Seoul 136-763, South Korea.
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Clifton BE, Kozome D, Laurino P. Efficient Exploration of Sequence Space by Sequence-Guided Protein Engineering and Design. Biochemistry 2023; 62:210-220. [PMID: 35245020 DOI: 10.1021/acs.biochem.1c00757] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The rapid growth of sequence databases over the past two decades means that protein engineers faced with optimizing a protein for any given task will often have immediate access to a vast number of related protein sequences. These sequences encode information about the evolutionary history of the protein and the underlying sequence requirements to produce folded, stable, and functional protein variants. Methods that can take advantage of this information are an increasingly important part of the protein engineering tool kit. In this Perspective, we discuss the utility of sequence data in protein engineering and design, focusing on recent advances in three main areas: the use of ancestral sequence reconstruction as an engineering tool to generate thermostable and multifunctional proteins, the use of sequence data to guide engineering of multipoint mutants by structure-based computational protein design, and the use of unlabeled sequence data for unsupervised and semisupervised machine learning, allowing the generation of diverse and functional protein sequences in unexplored regions of sequence space. Altogether, these methods enable the rapid exploration of sequence space within regions enriched with functional proteins and therefore have great potential for accelerating the engineering of stable, functional, and diverse proteins for industrial and biomedical applications.
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Affiliation(s)
- Ben E Clifton
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna, Okinawa 904-0495, Japan
| | - Dan Kozome
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna, Okinawa 904-0495, Japan
| | - Paola Laurino
- Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna, Okinawa 904-0495, Japan
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Wang X, Qin X, Tong L, Zheng J, Dong T, Wang X, Wang Y, Huang H, Yao B, Zhang H, Luo H. Improving the catalytic activity of a detergent-compatible serine protease by rational design. Microb Biotechnol 2023; 16:947-960. [PMID: 36636777 PMCID: PMC10128134 DOI: 10.1111/1751-7915.14218] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 12/30/2022] [Accepted: 01/02/2023] [Indexed: 01/14/2023] Open
Abstract
Serine proteases are among the most important biological additives in various industries such as detergents, leather, animal feed and food. A serine protease gene, Fgapt4, from Fusarium graminearum 2697 was identified, cloned and expressed in Pichia pastoris. The optimal pH and temperature of FgAPT4 were 8.5 and 40°C, respectively. The relative activity was >30% even at 10°C. It had a wide range of pH stability (4.0-12.0) and detergent compatibility. To improve the catalytic activity, a strategy combining molecular docking and evolutionary analysis was adopted. Twelve amino acid residue sites and three loops (A, B and C) were selected as potential hot spots that might play critical roles in the enzyme's functional properties. Twenty-eight mutants targeting changes in individual sites or loops were designed, and mutations with good performance were combined. The best mutant was FgAPT4-M3 (Q70N/D142S/A143S/loop C). The specific activity and catalytic efficiency of FgAPT4-M3 increased by 1.6 (1008.5 vs. 385.9 U/mg) and 2.2-fold (3565.1 vs. 1106.3/s/mM), respectively. Computational analyses showed that the greater flexibility of the substrate pocket may be responsible for the increased catalytic activity. In addition, its application in detergents indicated that FgAPT4-M3 has great potential in washing.
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Affiliation(s)
- Xiao Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xing Qin
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lige Tong
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jie Zheng
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tao Dong
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaolu Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuan Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huoqing Huang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bin Yao
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Honglian Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huiying Luo
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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21
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Genome-Based Multi-Antigenic Epitopes Vaccine Construct Designing against Staphylococcus hominis Using Reverse Vaccinology and Biophysical Approaches. Vaccines (Basel) 2022; 10:vaccines10101729. [PMID: 36298594 PMCID: PMC9611379 DOI: 10.3390/vaccines10101729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/11/2022] [Accepted: 10/14/2022] [Indexed: 11/07/2022] Open
Abstract
Staphylococcus hominis is a Gram-positive bacterium from the staphylococcus genus; it is also a member of coagulase-negative staphylococci because of its opportunistic nature and ability to cause life-threatening bloodstream infections in immunocompromised patients. Gram-positive and opportunistic bacteria have become a major concern for the medical community. It has also drawn the attention of scientists due to the evaluation of immune evasion tactics and the development of multidrug-resistant strains. This prompted the need to explore novel therapeutic approaches as an alternative to antibiotics. The current study aimed to develop a broad-spectrum, multi-epitope vaccine to control bacterial infections and reduce the burden on healthcare systems. A computational framework was designed to filter the immunogenic potent vaccine candidate. This framework consists of pan-genomics, subtractive proteomics, and immunoinformatics approaches to prioritize vaccine candidates. A total of 12,285 core proteins were obtained using a pan-genome analysis of all strains. The screening of the core proteins resulted in the selection of only two proteins for the next epitope prediction phase. Eleven B-cell derived T-cell epitopes were selected that met the criteria of different immunoinformatics approaches such as allergenicity, antigenicity, immunogenicity, and toxicity. A vaccine construct was formulated using EAAAK and GPGPG linkers and a cholera toxin B subunit. This formulated vaccine construct was further used for downward analysis. The vaccine was loop refined and improved for structure stability through disulfide engineering. For an efficient expression, the codons were optimized as per the usage pattern of the E coli (K12) expression system. The top three refined docked complexes of the vaccine that docked with the MHC-I, MHC-II, and TLR-4 receptors were selected, which proved the best binding potential of the vaccine with immune receptors; this was followed by molecular dynamic simulations. The results indicate the best intermolecular bonding between immune receptors and vaccine epitopes and that they are exposed to the host’s immune system. Finally, the binding energies were calculated to confirm the binding stability of the docked complexes. This work aimed to provide a manageable list of immunogenic and antigenic epitopes that could be used as potent vaccine candidates for experimental in vivo and in vitro studies.
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22
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Thermostability Improvement of L-Asparaginase from Acinetobacter soli via Consensus-Designed Cysteine Residue Substitution. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27196670. [PMID: 36235209 PMCID: PMC9572581 DOI: 10.3390/molecules27196670] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 09/30/2022] [Accepted: 10/05/2022] [Indexed: 11/05/2022]
Abstract
To extend the application range of L-asparaginase in food pre-processing, the thermostability improvement of the enzyme is essential. Herein, two non-conserved cysteine residues with easily oxidized free sulfhydryl groups, Cys8 and Cys283, of Acinetobacter soli L-asparaginase (AsA) were screened out via consensus design. After saturation mutagenesis and combinatorial mutation, the mutant C8Y/C283Q with highly improved thermostability was obtained with a half-life of 361.6 min at 40 °C, an over 34-fold increase compared with that of the wild-type. Its melting temperature (Tm) value reaches 62.3 °C, which is 7.1 °C higher than that of the wild-type. Molecular dynamics simulation and structure analysis revealed the formation of new hydrogen bonds of Gln283 and the aromatic interaction of Tyr8 formed with adjacent residues, resulting in enhanced thermostability. The improvement in the thermostability of L-asparaginase could efficiently enhance its effect on acrylamide inhibition; the contents of acrylamide in potato chips were efficiently reduced by 86.50% after a mutant C8Y/C283Q treatment, which was significantly higher than the 59.05% reduction after the AsA wild-type treatment. In addition, the investigation of the mechanism behind the enhanced thermostability of AsA could further direct the modification of L-asparaginases for expanding their clinical and industrial applications.
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23
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Thieker DF, Maguire JB, Kudlacek ST, Leaver‐Fay A, Lyskov S, Kuhlman B. Stabilizing proteins, simplified: A Rosetta-based webtool for predicting favorable mutations. Protein Sci 2022; 31:e4428. [PMID: 36173174 PMCID: PMC9490798 DOI: 10.1002/pro.4428] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 08/06/2022] [Accepted: 08/21/2022] [Indexed: 11/07/2022]
Abstract
Many proteins have low thermodynamic stability, which can lead to low expression yields and limit functionality in research, industrial and clinical settings. This article introduces two, web-based tools that use the high-resolution structure of a protein along with the Rosetta molecular modeling program to predict stabilizing mutations. The protocols were recently applied to three genetically and structurally distinct proteins and successfully predicted mutations that improved thermal stability and/or protein yield. In all three cases, combining the stabilizing mutations raised the protein unfolding temperatures by more than 20°C. The first protocol evaluates point mutations and can generate a site saturation mutagenesis heatmap. The second identifies mutation clusters around user-defined positions. Both applications only require a protein structure and are particularly valuable when a deep multiple sequence alignment is not available. These tools were created to simplify protein engineering and enable research that would otherwise be infeasible due to poor expression and stability of the native molecule.
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Affiliation(s)
- David F. Thieker
- Department of Biochemistry and BiophysicsUniversity of North Carolina School of MedicineChapel HillNorth CarolinaUSA
| | - Jack B. Maguire
- Department of Biochemistry and BiophysicsUniversity of North Carolina School of MedicineChapel HillNorth CarolinaUSA
| | - Stephan T. Kudlacek
- Department of Biochemistry and BiophysicsUniversity of North Carolina School of MedicineChapel HillNorth CarolinaUSA
| | - Andrew Leaver‐Fay
- Department of Biochemistry and BiophysicsUniversity of North Carolina School of MedicineChapel HillNorth CarolinaUSA
| | - Sergey Lyskov
- Department of Chemical and Biomolecular EngineeringJohns Hopkins UniversityBaltimoreMarylandUSA
| | - Brian Kuhlman
- Department of Biochemistry and BiophysicsUniversity of North Carolina School of MedicineChapel HillNorth CarolinaUSA
- Lineburger Comprehensive Cancer CenterUniversity of North Carolina at Chapel HillChapel HillNorth CarolinaUSA
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24
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Liu P, Guo J, Miao L, Liu H. Enhancing the secretion of a feruloyl esterase in Bacillus subtilis by signal peptide screening and rational design. Protein Expr Purif 2022; 200:106165. [PMID: 36038098 DOI: 10.1016/j.pep.2022.106165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/08/2022] [Accepted: 08/22/2022] [Indexed: 11/28/2022]
Abstract
Feruloyl esterase is a subclass of α/β hydrolase, which could release ferulic acid from biomass residues for use as an efficient additive in food or pharmaceutical industries. In the present study, a feruloyl esterase with broad substrate specificity was characterised and secreted by Bacillus subtilis WB600. After codon usage optimisation and signal peptide library screening, the secretion amount of feruloyl esterase was enhanced by up to 10.2-fold in comparison with the base strain. The site-specific amino acid substitutions that facilitate protein folding further improved the secretion by about 1.5-fold. The purified rationally designed enzyme exhibited maximal activity against methyl ferulate at pH 6.5 and 65 °C. In the solid-state fermentation, the genetically engineered B. subtilis released about 37% of the total alkali-extractable ferulic acid in maize bran. This study provides a promising candidate for ferulic acid production and demonstrates that the secretion of a heterologous enzyme from B. subtilis can be cumulatively improved by changes in protein sequence features.
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Affiliation(s)
- Pulin Liu
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Jingxiao Guo
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Lihong Miao
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China.
| | - Hanyan Liu
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023, China
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25
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Barreto HC, Abreu B, Gordo I. Fluctuating selection on bacterial iron regulation in the mammalian gut. Curr Biol 2022; 32:3261-3275.e4. [PMID: 35793678 DOI: 10.1016/j.cub.2022.06.017] [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: 01/14/2022] [Revised: 04/27/2022] [Accepted: 06/08/2022] [Indexed: 10/17/2022]
Abstract
Iron is critical in host-microbe interactions, and its availability is tightly regulated in the mammalian gut. Antibiotics and inflammation can perturb iron availability in the gut, which could alter host-microbe interactions. Here, we show that an adaptive allele of iscR, a major regulator of iron homeostasis of Escherichia coli, is under fluctuating selection in the mouse gut. In vivo competitions in immune-competent, immune-compromised, and germ-free mice reveal that the selective pressure on an iscR mutant E. coli is modulated by the presence of antibiotics, the microbiota, and the immune system. In vitro assays show that iron availability is an important mediator of the iscR allele fitness benefits or costs. We identify Lipocalin-2, a host's immune protein that prevents bacterial iron acquisition, as a major host mechanism underlying fluctuating selection of iscR. Our results provide a remarkable example of strong fluctuating selection acting on bacterial iron regulation in the mammalian gut.
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Affiliation(s)
- Hugo C Barreto
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal.
| | - Beatriz Abreu
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | - Isabel Gordo
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal.
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26
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Tian Y, Hou X, Ni D, Xu W, Guang C, Zhang W, Chen Q, Rao Y, Mu W. Structure-based interface engineering methodology in designing a thermostable amylose-forming transglucosylase. J Biol Chem 2022; 298:102074. [PMID: 35643316 PMCID: PMC9234714 DOI: 10.1016/j.jbc.2022.102074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 11/30/2022] Open
Abstract
Many drugs and prebiotics derive their activities from sugar substituents. Due to the prevalence and complexity of these biologically active compounds, enzymatic glycodiversification that facilitates easier access to these compounds can make profound contributions to the pharmaceutical, food, and feed industries. Amylosucrases (ASases) are attractive tools for glycodiversification because of their broad acceptor substrate specificity, but the lack of structural information and their poor thermostability limit their industrial applications. Herein, we reported the crystal structure of ASase from Calidithermus timidus, which displays a homotetrameric quaternary organization not previously observed for other ASases. We employed a workflow composed of five common strategies, including interface engineering, folding energy calculations, consensus sequence, hydrophobic effects enhancement, and B-factor analysis, to enhance the thermostability of C. timidus ASase. As a result, we obtained a quadruple-point mutant M31 ASase with a half-life at 65 °C increased from 22.91 h to 52.93 h, which could facilitate biosynthesis of glucans with a degree of polymerization of more than 20 using sucrose as a substrate at 50 °C. In conclusion, this study provides a structural basis for understanding the multifunctional biocatalyst ASase and presents a powerful methodology to effectively and systematically enhance protein thermostability.
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Affiliation(s)
- Yuqing Tian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Xiaodong Hou
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Dawei Ni
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Wei Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Cuie Guang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Qiuming Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yijian Rao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, Jiangsu, China.
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27
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Su C, Gong JS, Qin A, Li H, Li H, Qin J, Qian JY, Xu ZH, Shi JS. A combination of bioinformatics analysis and rational design strategies to enhance keratinase thermostability for efficient biodegradation of feathers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 818:151824. [PMID: 34808176 DOI: 10.1016/j.scitotenv.2021.151824] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 11/06/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
Keratinase has shown great significance and application potentials in the biodegradation and recycle of keratin waste due to its unique and efficient hydrolysis ability. However, the inherent instability of the enzyme limits its practical utilization. Herein, we obtained a thermostability-enhanced keratinase based on a combination of bioinformatics analysis and rational design strategies for the efficient biodegradation of feathers. A systematical in silico analysis combined with filtering of virtual libraries derived a smart library for experimental validation. Synergistic mutations around the highly flexible loop, the calcium binding site and the non-consensus amino acids generated a dominant mutant which increased the optimal temperature of keratinase from 40 °C to 60 °C, and the half-life at 60 °C was increased from 17.3 min to 66.1 min. The mutant could achieve more than 66% biodegradation of 50 g/L feathers to high-valued keratin product with a major molecular weight of 36 kDa. Collectively, this work provided a promising keratinase variant with enhanced thermostability for efficient conversion of keratin wastes to valuable products. It also generated a general strategy to facilitate enzyme thermostability design which is more targeted and predictable.
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Affiliation(s)
- Chang Su
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, PR China
| | - Jin-Song Gong
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, PR China.
| | - Anqi Qin
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, PR China
| | - Heng Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, PR China
| | - Hui Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, PR China
| | - Jiufu Qin
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China
| | - Jian-Ying Qian
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, PR China
| | - Zheng-Hong Xu
- National Engineering Laboratory for Cereal Fermentation Technology, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, PR China
| | - Jin-Song Shi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Pharmaceutical Sciences, Jiangnan University, Wuxi 214122, PR China.
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28
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Park BS, Choi YH, Kim MW, Park BG, Kim EJ, Kim JY, Kim JH, Kim BG. Enhancing biosynthesis of 2'-Fucosyllactose in Escherichia coli through engineering lactose operon for lactose transport and α -1,2-Fucosyltransferase for solubility. Biotechnol Bioeng 2022; 119:1264-1277. [PMID: 35099812 DOI: 10.1002/bit.28048] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 01/09/2022] [Accepted: 01/19/2022] [Indexed: 11/12/2022]
Abstract
2'-Fucosyllactose (2'-FL) is the most abundant oligosaccharide in human milk and one of the most actively studied human milk oligosaccharides (HMO). When 2'-FL is produced through biological production using a microorganism, like Escherichia coli, D-lactose is often externally fed as an acceptor substrate for fucosyltransferase (FT). When D-glucose is used as a carbon source for the cell growth and D-lactose is transported by lactose permease (LacY) in lac operon, D-lactose transport is under the control of catabolite repression (CR), limiting the supply of D-lactose for FT reaction in the cell, hence decreasing the production of 2'-FL. In this study, a remarkable increase of 2'-FL production was achieved by relieving the CR from the lac operon of the host E. coli BL21 and introducing adequate site-specific mutations into α-1,2-FT (FutC) for enhancement of catalytic activity and solubility. For the host engineering, the native lac promoter (Plac ) was substituted for tac promoter (Ptac ), so that the lac operon could be turned on, but not subjected to CR by high D-glucose concentration. Next, for protein engineering of FutC, family multiple sequence analysis for conserved amino acid sequences and protein-ligand substrate docking analysis led us to find several mutation sites, which could increase the solubility of FutC and its activity. As a result, a combination of four mutation sites (F40S/Q150H/C151R/Q239S) was identified as the best candidate, and the quadruple mutant of FutC enhanced 2'-FL titer by 2.4-fold. When the above-mentioned E. coli mutant host transformed with the quadruple mutant of futC was subjected to fed-batch culture, 40 g l-1 of 2'-FL titer was achieved with the productivity of 0.55 g l-1 h-1 and the specific 2'-FL yield of 1.0 g g-1 DCW. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Bum Seok Park
- School of Chemical and Biological Engineering, Seoul National University, Seoul, 08826, South Korea.,Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 08826, South Korea
| | - Yun Hee Choi
- Interdisciplinary Program for Biochemical Engineering and Biotechnology, Seoul National University, Seoul, 08826, South Korea.,Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 08826, South Korea
| | - Min Woo Kim
- Interdisciplinary Program for Biochemical Engineering and Biotechnology, Seoul National University, Seoul, 08826, South Korea.,Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 08826, South Korea
| | - Beom Gi Park
- School of Chemical and Biological Engineering, Seoul National University, Seoul, 08826, South Korea.,Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 08826, South Korea
| | - Eun-Jung Kim
- Bio-MAX/N-Bio Institute, Seoul National University, Seoul, 08826, South Korea
| | - Jin Young Kim
- Interdisciplinary Program for Biochemical Engineering and Biotechnology, Seoul National University, Seoul, 08826, South Korea.,Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 08826, South Korea
| | - Jung Hwa Kim
- School of Chemical and Biological Engineering, Seoul National University, Seoul, 08826, South Korea.,Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 08826, South Korea
| | - Byung-Gee Kim
- School of Chemical and Biological Engineering, Seoul National University, Seoul, 08826, South Korea.,Interdisciplinary Program for Biochemical Engineering and Biotechnology, Seoul National University, Seoul, 08826, South Korea.,Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 08826, South Korea.,Bio-MAX/N-Bio Institute, Seoul National University, Seoul, 08826, South Korea.,Institute for Sustainable Development (ISD), Seoul National University, Seoul, 08826, South Korea
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29
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Chiu N, Lee W, Liu PK, Levi SR, Wang HH, Chen N, Kang EYC, Seo GH, Lee H, Liu L, Wu WC, Tsai SH, Wang NK. A homozygous in-frame duplication within the LRRCT consensus sequence of CFAP410 causes cone-rod dystrophy, macular staphyloma and short stature. Ophthalmic Genet 2021; 43:378-384. [PMID: 34915818 DOI: 10.1080/13816810.2021.2010773] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Ciliopathies are a group of genetic dystrophies causing syndromic and non-syndromic retinal degeneration. We identified CFAP410 as the causative gene in a patient with childhood-onset retinal dystrophy without other systemic symptoms at the age of 20. This 20-year-old man presented with cone-rod dystrophy and CFAP410 homozygous in-frame duplication variants (c.340_351dup). His clinical features included early subnormal vision, posterior pole staphyloma, and short stature. Unlike the previously reported features of retinal ciliopathy, our patient showed no obvious retinal pigmentation and only a slight hyper-autofluorescent parafoveal ring at the 16-year follow up. This case report aims to characterize the clinical features in a patient with novel, homozygous and likely pathogenic in-frame duplication variants in the CFAP410 gene. Ultimately, this report will help contribute to the understanding of CFAP410-associated ciliopathies.
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Affiliation(s)
- Ning Chiu
- Department of Ophthalmology, Mackay Memorial Hospital, Taipei, Taiwan
| | - Winston Lee
- Department of Genetics and Development, Columbia University, New York, New York, USA.,Edward S. Harkness Eye Institute, Department of Ophthalmology, Columbia University Irving Medical Center, New York, New York, USA
| | - Pei-Kang Liu
- Edward S. Harkness Eye Institute, Department of Ophthalmology, Columbia University Irving Medical Center, New York, New York, USA.,Department of Ophthalmology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.,School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Sarah R Levi
- Edward S. Harkness Eye Institute, Department of Ophthalmology, Columbia University Irving Medical Center, New York, New York, USA
| | - Hung-Hsi Wang
- Edward S. Harkness Eye Institute, Department of Ophthalmology, Columbia University Irving Medical Center, New York, New York, USA
| | - Nelson Chen
- Edward S. Harkness Eye Institute, Department of Ophthalmology, Columbia University Irving Medical Center, New York, New York, USA
| | - Eugene Yu-Chuan Kang
- College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Go Hun Seo
- Division of Medical Genetics, 3billion Inc., Seoul, South Korea
| | - Hane Lee
- Division of Medical Genetics, 3billion Inc., Seoul, South Korea
| | - Laura Liu
- College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Wei-Chi Wu
- College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Ophthalmology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Shawn H Tsai
- Department of Ophthalmology, Mackay Memorial Hospital, Taipei, Taiwan.,Department of Optometry, Chung Shan Medical University, Taichung, Taiwan.,Department of Optometry, Mackay Junior College of Medicine, Nursing, and Management, Taipei, Taiwan
| | - Nan-Kai Wang
- Edward S. Harkness Eye Institute, Department of Ophthalmology, Columbia University Irving Medical Center, New York, New York, USA
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30
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Enhanced Thermostability of Pseudomonas nitroreducens Isoeugenol Monooxygenase by the Combinatorial Strategy of Surface Residue Replacement and Consensus Mutagenesis. Catalysts 2021. [DOI: 10.3390/catal11101199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Vanillin has many applications in industries. Isoeugenol monooxygenase (IEM) can catalyze the oxidation of isoeugenol to vanillin in the presence of oxygen under mild conditions. However, the low thermal stability of IEM limits its practical application in the biosynthesis of natural vanillin. Herein, two rational strategies were combined to improve the thermostability of IEM from Pseudomonas nitroreducens Jin1. Two variants (K83R and K95R) with better thermostability and one mutant (G398A) with higher activity were identified from twenty candidates based on the Surface Residue Replacement method. According to the Consensus Mutagenesis method, one mutant (I352R) with better thermostability and another mutant (L273F) with higher activity were also identified from nine candidates. After combinatorial mutation, a triple mutant K83R/K95R/L273F with the best thermostability and catalytic efficiency was generated. Compared with the wild-type IEM, the thermal inactivation half-lives (t1/2) of K83R/K95R/L273F at 25 °C, 30 °C, and 35 °C increased 2.9-fold, 11.9-fold, and 24.7-fold, respectively. Simultaneously, it also exhibited a 4.8-fold increase in kcat, leading to a 1.2-fold increase in catalytic efficiency (kcat/Km). When the whole cell of K83R/K95R/L273F was applied to the biotransformation of isoeugenol on preparative scale, the vanillin concentration reached 240.1 mM with space-time yield of 109.6 g/L/d, and vanillin was achieved in 77.6% isolated yield and >99% purity.
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Gargiulo S, Soumillion P. Directed evolution for enzyme development in biocatalysis. Curr Opin Chem Biol 2020; 61:107-113. [PMID: 33385931 DOI: 10.1016/j.cbpa.2020.11.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/25/2020] [Accepted: 11/29/2020] [Indexed: 02/07/2023]
Abstract
As an important sector of the chemical industry, biocatalysis requires the continuous development of enzymes with tailor-made activity, selectivity, stability, or tolerance to unnatural environments. This is now routinely achieved by directed evolution based on iterative cycles of genetic diversification and activity screening. Here, we highlight its recent developments. First, the design of "smarter" libraries by focused mutagenesis may be a crucial start-up for a fast and successful outcome. Then library assembly and expression are also key steps that benefits from modern molecular biology progresses. Finally, various strategies may be considered for library screening depending on the final objective: while low-throughput direct assays have been very successful in generating enzymes for important biocatalytic processes, even in bringing completely new chemistries to the enzyme world, ultrahigh-throughput screening methods are emerging as powerful approaches for engineering the next generation of industrial enzymes.
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Affiliation(s)
- Serena Gargiulo
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Place Croix du Sud 4-5, 1390 Louvain-la-Neuve, Belgium
| | - Patrice Soumillion
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Place Croix du Sud 4-5, 1390 Louvain-la-Neuve, Belgium.
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