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Ding JW, Kua GKB, Lim SC, Ng KH, Yang KL. Expression of a Recombinant Cholesterol Esterase from Mustela putorius furo in Pichia pastoris and Its Applicability for γ-Oryzanol Hydrolysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:21702-21710. [PMID: 39298915 DOI: 10.1021/acs.jafc.4c05238] [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: 09/22/2024]
Abstract
Ferulic acid (FA) exhibits antioxidant and anti-inflammatory properties, making it valuable for numerous industrial applications. Traditionally, FA is produced by the alkaline hydrolysis of γ-oryzanol, which is typically associated with wastewater generation. Recently, an increasing demand of natural FA necessitates its green production via enzymatic hydrolysis of γ-oryzanol, a mixture comprising triterpene alcohol ferulates and phytosteryl ferulates. Thus far, γ-oryzanol can be hydrolyzed by only four commercial cholesterol esterases with low yields. Herein, we report a recombinant cholesterol esterase from Mustela putorius furo (MPFCE) for the enzymatic hydrolysis of γ-oryzanol. The enzyme yielded 25.5% FA, which is the highest reported through enzymatic means thus far. The hydrolysis profile revealed that the enhanced yield primarily resulted from the near-complete hydrolysis of phytosteryl ferulates, together with slight hydrolysis of triterpene alcohol ferulates. MPFCE serves as a potential candidate for the enzymatic production of FA through targeted hydrolysis of γ-oryzanol.
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Affiliation(s)
- Jia Wen Ding
- Wilmar Innovation Centre, Wilmar International Limited, 28 Biopolis Road, Singapore 138568, Singapore
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore
| | - Glen Kai Bin Kua
- Wilmar Innovation Centre, Wilmar International Limited, 28 Biopolis Road, Singapore 138568, Singapore
| | - Siew Choo Lim
- Wilmar Innovation Centre, Wilmar International Limited, 28 Biopolis Road, Singapore 138568, Singapore
| | - Kian Hong Ng
- Wilmar Innovation Centre, Wilmar International Limited, 28 Biopolis Road, Singapore 138568, Singapore
| | - Kun-Lin Yang
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore 117585, Singapore
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Wang Y, Wang Z, Yu H, Teng H, Wu J, Xu J, Yang L. Enhancing the Thermostability and Catalytic Activity of the Lipase from Rhizopus oryzae via Introducing N-Glycosylation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:14912-14921. [PMID: 38913033 DOI: 10.1021/acs.jafc.4c02623] [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: 06/25/2024]
Abstract
Lipase from Rhizopus oryzae (ROL) exhibits remarkable sn-1,3 stereoselectivity and catalytic activity, but its poor thermostability limits its applications in the production of 1,3-dioleoyl-2-palmitoyl glycerol (OPO, a high-quality substitute for human milk fat). In this work, a semirational method was proposed to engineer the thermostability and catalytic activity of 4M (ROL mutant in our previous study). First, a computer-aided design is performed using 4M as a template, and N-glycosylation mutants are then recombinantly expressed and screened in Pichia pastoris, the optimal mutant N227 exhibited a half-life of 298.8 h at 45 °C, which is 7.23-folds longer than that of 4M. Its catalytic activity also reached 1043.80 ± 61.98 U/mg, representing a 29.2% increase compared to 4M (808.02 ± 47.02 U/mg). Molecular dynamics simulations of N227 suggested that the introduction of glycan enhanced the protein rigidity, while the strong hydrogen bonds formed between the glycan and the protein stabilized the lipase structure, thereby improving its thermostability. The acidolysis reaction between oleic acid (OA) and glycerol tripalmitate (PPP) was successfully carried out using immobilized N227, achieving a molar conversion rate of 90.2% for PPP. This engineering strategy guides the modification of lipases, while the glycomutants obtained in this study have potential applications in the biosynthesis of OPO.
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Affiliation(s)
- Yong Wang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, No. 38 Zhe-da Road, Hangzhou, Zhejiang 310027, China
| | - Ziyuan Wang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, No. 38 Zhe-da Road, Hangzhou, Zhejiang 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, No. 733 Jianshe 3rd Road, Xiaoshan District, Hangzhou, Zhejiang 311200, China
| | - Huifen Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, No. 38 Zhe-da Road, Hangzhou, Zhejiang 310027, China
| | - Haidong Teng
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, No. 38 Zhe-da Road, Hangzhou, Zhejiang 310027, China
| | - Jianping Wu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, No. 38 Zhe-da Road, Hangzhou, Zhejiang 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, No. 733 Jianshe 3rd Road, Xiaoshan District, Hangzhou, Zhejiang 311200, China
| | - Jiaqi Xu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, No. 38 Zhe-da Road, Hangzhou, Zhejiang 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, No. 733 Jianshe 3rd Road, Xiaoshan District, Hangzhou, Zhejiang 311200, China
| | - Lirong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, No. 38 Zhe-da Road, Hangzhou, Zhejiang 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, No. 733 Jianshe 3rd Road, Xiaoshan District, Hangzhou, Zhejiang 311200, China
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Tütüncü HE, Durmuş N, Sürmeli Y. Unraveling the potential of uninvestigated thermoalkaliphilic lipases by molecular docking and molecular dynamic simulation: an in silico characterization study. 3 Biotech 2024; 14:179. [PMID: 38882640 PMCID: PMC11176153 DOI: 10.1007/s13205-024-04023-5] [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: 11/17/2023] [Accepted: 05/29/2024] [Indexed: 06/18/2024] Open
Abstract
Thermoalkaliphilic lipase enzymes are mostly favored for use in the detergent industry. While there has been considerable research on Geobacillus lipases, a significant portion of these enzymes remains unexplored or undocumented in the scientific literature. This work performed in silico phylogeny, sequence alignment, structural and enzyme-substrate interaction analyses of the five thermoalkaliphilic lipases belonging to different Geobacillus species (Geobacillus stearothermophilus lipase = GsLip, Geobacillus sp. B4113_201601 lipase = Gb4Lip, Geobacillus kaustophilus HTA426 lipase = GkLip, Geobacillus sp. SP22 lipase = GspLip, Geobacillus sp. NTU 03 lipase = GntLip). For this purpose, unreviewed enzyme sequences of five Geobacillus thermoalkaliphilic lipases were analyzed at sequence and phylogeny levels. 3D homology enzyme models were built, validated, and investigated by different bioinformatics tools. The ligand interactions screening using seven para-nitrophenyl (pNP) esters and enzyme-ligand interactions were analyzed on Gb4Lip:pNP-C12 and BTL2:pNP-C12 by MD simulation. Biophysicochemical characteristic analysis showed that Gb4Lip had a theoretical T m value of above 65 ºC, and a higher aliphatic index indicating greater thermal stability. Sequence alignment showed a hydrophilic threonine in the α6 helix of Gb4Lip, indicating high enzymatic activity. A normalized temperature factor B (B'-factor) analysis showed that the lid domains of five lipases significantly possessed lower B'-factor values, compared to G. thermocatenulatus lipase 2 (BTL2), indicating that they had higher rigidity. Molecular docking results indicated that the five lipases had the highest binding affinity toward pNP-C12. The RMSF investigation revealed that the thermostability of Gb4Lip is influenced by specific molecular elements: D202-S203 within the αB region of the lid domain, and E274-Q275 within the b3 strand, as well as W278 in the b3-b4 loop, and H282 in the b4 strand of the Ca2+-binding region. MD simulation analysis showed that catalytic residue S114 and at least one oxyanion hole residue (F17 and/or Q114) in Gb4Lip frequently formed hydrogen bonds with the pNP-C12 ligand at 343 K and 348 K throughout the simulation process, indicating that Gb4Lip might catalyze relatively long-chain ligand pNP-C12 with high performance. In conclusion, Gb4Lip might be a more suitable candidate as the detergent additive. In addition, this investigation can offer valuable perspectives on Family I.5 lipases such as Gb4Lip for future exploration in the field of protein engineering. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-04023-5.
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Affiliation(s)
- Havva Esra Tütüncü
- Department of Nutrition and Dietetics, Malatya Turgut Özal University, 44210 Malatya, Turkey
| | - Naciye Durmuş
- Department of Molecular Biology and Genetics, İstanbul Technical University, 34485 Istanbul, Turkey
| | - Yusuf Sürmeli
- Department of Agricultural Biotechnology, Tekirdağ Namık Kemal University, 59030 Tekirdağ, Turkey
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Vardar-Yel N, Tütüncü HE, Sürmeli Y. Lipases for targeted industrial applications, focusing on the development of biotechnologically significant aspects: A comprehensive review of recent trends in protein engineering. Int J Biol Macromol 2024; 273:132853. [PMID: 38838897 DOI: 10.1016/j.ijbiomac.2024.132853] [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: 04/15/2024] [Revised: 05/26/2024] [Accepted: 05/31/2024] [Indexed: 06/07/2024]
Abstract
Lipases are remarkable biocatalysts, adept at catalyzing the breakdown of diverse compounds into glycerol, fatty acids, and mono- and di-glycerides via hydrolysis. Beyond this, they facilitate esterification, transesterification, alcoholysis, acidolysis, and more, making them versatile in industrial applications. In industrial processes, lipases that exhibit high stability are favored as they can withstand harsh conditions. However, most native lipases are unable to endure adverse conditions, making them unsuitable for industrial use. Protein engineering proves to be a potent technology in the development of lipases that can function effectively under challenging conditions and fulfill criteria for various industrial processes. This review concentrated on new trends in protein engineering to enhance the diversity of lipase genes and employed in silico methods for predicting and comprehensively analyzing target mutations in lipases. Additionally, key molecular factors associated with industrial characteristics of lipases, including thermostability, solvent tolerance, catalytic activity, and substrate preference have been elucidated. The present review delved into how industrial traits can be enhanced through directed evolution (epPCR, gene shuffling), rational design (FRESCO, ASR), combined engineering strategies (i.e. CAST, ISM, and FRISM) as protein engineering methodologies in contexts of biodiesel production, food processing, and applications of detergent, pharmaceutics, and plastic degradation.
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Affiliation(s)
- Nurcan Vardar-Yel
- Department of Medical Laboratory Techniques, Altınbaş University, 34145 İstanbul, Turkey
| | - Havva Esra Tütüncü
- Department of Nutrition and Dietetics, Malatya Turgut Özal University, 44210 Malatya, Turkey
| | - Yusuf Sürmeli
- Department of Agricultural Biotechnology, Tekirdağ Namık Kemal University, 59030 Tekirdağ, Turkey.
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Bell EL, Rosetto G, Ingraham MA, Ramirez KJ, Lincoln C, Clarke RW, Gado JE, Lilly JL, Kucharzyk KH, Erickson E, Beckham GT. Natural diversity screening, assay development, and characterization of nylon-6 enzymatic depolymerization. Nat Commun 2024; 15:1217. [PMID: 38336849 PMCID: PMC10858056 DOI: 10.1038/s41467-024-45523-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
Successes in biocatalytic polyester recycling have raised the possibility of deconstructing alternative polymers enzymatically, with polyamide (PA) being a logical target due to the array of amide-cleaving enzymes present in nature. Here, we screen 40 potential natural and engineered nylon-hydrolyzing enzymes (nylonases), using mass spectrometry to quantify eight compounds resulting from enzymatic nylon-6 (PA6) hydrolysis. Comparative time-course reactions incubated at 40-70 °C showcase enzyme-dependent variations in product distributions and extent of PA6 film depolymerization, with significant nylon deconstruction activity appearing rare. The most active nylonase, a NylCK variant we rationally thermostabilized (an N-terminal nucleophile (Ntn) hydrolase, NylCK-TS, Tm = 87.4 °C, 16.4 °C higher than the wild-type), hydrolyzes 0.67 wt% of a PA6 film. Reactions fail to restart after fresh enzyme addition, indicating that substrate-based limitations, such as restricted enzyme access to hydrolysable bonds, prohibit more extensive deconstruction. Overall, this study expands our understanding of nylonase activity distribution, indicates that Ntn hydrolases may have the greatest potential for further development, and identifies key targets for progressing PA6 enzymatic depolymerization, including improving enzyme activity, product selectivity, and enhancing polymer accessibility.
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Affiliation(s)
- Elizabeth L Bell
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
- BOTTLE Consortium, Golden, CO, 80401, USA
| | - Gloria Rosetto
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Morgan A Ingraham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
- BOTTLE Consortium, Golden, CO, 80401, USA
| | - Kelsey J Ramirez
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
- BOTTLE Consortium, Golden, CO, 80401, USA
| | - Clarissa Lincoln
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
- BOTTLE Consortium, Golden, CO, 80401, USA
| | - Ryan W Clarke
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
- BOTTLE Consortium, Golden, CO, 80401, USA
| | - Japheth E Gado
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
- BOTTLE Consortium, Golden, CO, 80401, USA
| | - Jacob L Lilly
- Battelle Memorial Institute, Columbus, OH, 43201, USA
| | | | - Erika Erickson
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
- BOTTLE Consortium, Golden, CO, 80401, USA
| | - Gregg T Beckham
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.
- BOTTLE Consortium, Golden, CO, 80401, USA.
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Guan A, Hou Y, Yang R, Qin J. Enzyme engineering for functional lipids synthesis: recent advance and perspective. BIORESOUR BIOPROCESS 2024; 11:1. [PMID: 38647956 PMCID: PMC10992173 DOI: 10.1186/s40643-023-00723-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/24/2023] [Indexed: 04/25/2024] Open
Abstract
Functional lipids, primarily derived through the modification of natural lipids by various processes, are widely acknowledged for their potential to impart health benefits. In contrast to chemical methods for lipid modification, enzymatic catalysis offers distinct advantages, including high selectivity, mild operating conditions, and reduced byproduct formation. Nevertheless, enzymes face challenges in industrial applications, such as low activity, stability, and undesired selectivity. To address these challenges, protein engineering techniques have been implemented to enhance enzyme performance in functional lipid synthesis. This article aims to review recent advances in protein engineering, encompassing approaches from directed evolution to rational design, with the goal of improving the properties of lipid-modifying enzymes. Furthermore, the article explores the future prospects and challenges associated with enzyme-catalyzed functional lipid synthesis.
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Affiliation(s)
- Ailin Guan
- College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, China
| | - Yue Hou
- College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, China
| | - Run Yang
- College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, China
| | - Jiufu Qin
- College of Biomass Science and Engineering, Sichuan University, Chengdu, 610065, China.
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Kua GKB, Nguyen GKT, Li Z. Enzyme Engineering for High-Yielding Amide Formation: Lipase-Catalyzed Synthesis of N-Acyl Glycines in Aqueous Media. Angew Chem Int Ed Engl 2023; 62:e202217878. [PMID: 36748100 DOI: 10.1002/anie.202217878] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/08/2023]
Abstract
Amide syntheses remain a key challenging green chemistry reaction. For instance, green synthesis of N-acyl glycines as biosurfactants and therapeutics is highly desirable to replace chemical pathways using toxic phosgene. Herein, we report a novel concept for enzymatic amidation in an aqueous system via glycerol activation of fatty acids and theirsubsequent aminolysis with glycine to synthesize N-acyl glycines. We then engineer an enzyme (proRML) by reshaping its catalytic pocket to enhance its aminolysis activity and catalytic efficiency by 103-fold and 465-fold, respectively. The evolved proRML (D156S/L258K/L267N/S83D/L58K/R86K/W88V) catalyzed the amidation of a fatty acid with glycine to give N-lauroylglycine with high yield (80 %). It accepts a broad range of medium- to long-chain fatty acids (C8 -C18 ), giving high yields of N-decanoyl-, N-myristoyl-, and N-oleoylglycine. The developed amidation concept may be general, and the engineered enzyme is useful for the green synthesis of N-acyl glycines.
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Affiliation(s)
- Glen Kai Bin Kua
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, Singapore, 117585, Singapore
- Wilmar International Limited, 28 Biopolis, Singapore, 138568, Singapore
| | | | - Zhi Li
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, Singapore, 117585, Singapore
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