1
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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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2
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Hwang DH, Lee ME, Cho BH, Oh JW, You SK, Ko YJ, Hyeon JE, Han SO. Enhanced biodegradation of waste poly(ethylene terephthalate) using a reinforced plastic degrading enzyme complex. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 842:156890. [PMID: 35753492 DOI: 10.1016/j.scitotenv.2022.156890] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/28/2022] [Accepted: 06/18/2022] [Indexed: 06/15/2023]
Abstract
Poly(ethylene terephthalate) (PET) is synthesized via a rich ester bond between terephthalate (TPA) and ethylene glycol (EG). Because of this, PET degradation takes a long time and PET accumulates in the environment. Many studies have been conducted to improve PET degrading enzyme to increase the efficiency of PET depolymerization. However, enzymatic PET decomposition is still restricted, making upcycling and recycling difficult. Here, we report a novel PET degrading complex composed of Ideonella sakaiensis PETase and Candida antarctica lipase B (CALB) that improves degradability, binding ability and enzyme stability. The reaction mechanism of chimeric PETase (cPETase) and chimeric CALB (cCALB) was confirmed by PET and bis (2-hydroxyethyl terephthalate) (BHET). cPETase generated BHET and mono (2-hydroxyethyl terephthalate (MHET) and cCALB produced terephthalate (TPA). Carbohydrate binding module 3 (CBM3) in the scaffolding protein greatly improved PET film binding affinity. Finally, the final enzyme complex demonstrated a 6.5-fold and 8.0-fold increase in the efficiency of hydrolysis from PET with either high crystalline or waste to TPA than single enzymes, respectively. This complex could effectively break down waste PET while maintaining enzyme stability and would be applied for biological upcycling of TPA.
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Affiliation(s)
- Dong-Hyeok Hwang
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Myeong-Eun Lee
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Byeong-Hyeon Cho
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Jun Won Oh
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Seung Kyou You
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Young Jin Ko
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Jeong Eun Hyeon
- Department of Food Science and Biotechnology, College of Knowledge-Based Services Engineering, Sungshin Women's University, Seoul 01133, Republic of Korea; Department of Next Generation Applied Sciences, The Graduate School of Sungshin University, Seoul 01133, Republic of Korea
| | - Sung Ok Han
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea.
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3
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Ma'ruf IF, Widhiastuty MP, Suharti, Moeis MR, Akhmaloka. Effect of mutation at oxyanion hole residu (H110F) on activity of Lk4 lipase. ACTA ACUST UNITED AC 2021; 29:e00590. [PMID: 33532247 PMCID: PMC7823203 DOI: 10.1016/j.btre.2021.e00590] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 12/15/2020] [Accepted: 01/01/2021] [Indexed: 11/28/2022]
Abstract
Mutant of lipase at oxyanion hole (H110 F) was constructed. The gene was highly expressed in Eschericia coli BL21 (DE3) and the recombinant protein was purified using Ni-NTA affinity chromatography. The activity of mutant enzyme was significantly increased compared to that the wild type. Further comparison showed that both of the enzymes exhibited same optimum pH and temperature, and showed highest lipolytic activity on pNP-decanoate (C10). The wild type appeared lost of activity on C14 and C16 substrates meanwhile the mutant still showed activity up to 20 %. In the presence of non polar organic solvent such as n-hexane, the wild type became inactive enzyme meanwhile the mutant still remained 50 % of its activity. The results suggested that mutation at oxyanion hole (H110 F) caused enzyme-substrate interaction change resulting on elevation of activity, better activity toward longer carbon chain substrate and improving the activity in the present of non polar organic solvent.
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Affiliation(s)
- Ilma Fauziah Ma'ruf
- Biochemistry Research Group, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Indonesia.,Genetic and Molecular Biotechnology Research Group, School of Life Sciences and Technology, Institut Teknologi Bandung, Indonesia
| | - Made Puspasari Widhiastuty
- Biochemistry Research Group, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Indonesia
| | - Suharti
- Biochemistry Research Group, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Indonesia.,Department of Chemistry, Faculty of Science and Computer, Universitas Pertamina, Indonesia
| | - Maelita Ramdani Moeis
- Genetic and Molecular Biotechnology Research Group, School of Life Sciences and Technology, Institut Teknologi Bandung, Indonesia
| | - Akhmaloka
- Biochemistry Research Group, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Indonesia.,Department of Chemistry, Faculty of Science and Computer, Universitas Pertamina, Indonesia
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4
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Rhizopus oryzae Lipase, a Promising Industrial Enzyme: Biochemical Characteristics, Production and Biocatalytic Applications. Catalysts 2020. [DOI: 10.3390/catal10111277] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Lipases are biocatalysts with a significant potential to enable a shift from current pollutant manufacturing processes to environmentally sustainable approaches. The main reason of this prospect is their catalytic versatility as they carry out several industrially relevant reactions as hydrolysis of fats in water/lipid interface and synthesis reactions in solvent-free or non-aqueous media such as transesterification, interesterification and esterification. Because of the outstanding traits of Rhizopus oryzae lipase (ROL), 1,3-specificity, high enantioselectivity and stability in organic media, its application in energy, food and pharmaceutical industrial sector has been widely studied. Significant advances have been made in the biochemical characterisation of ROL particularly in how its activity and stability are affected by the presence of its prosequence. In addition, native and heterologous production of ROL, the latter in cell factories like Escherichia coli, Saccharomyces cerevisiae and Komagataella phaffii (Pichia pastoris), have been thoroughly described. Therefore, in this review, we summarise the current knowledge about R. oryzae lipase (i) biochemical characteristics, (ii) production strategies and (iii) potential industrial applications.
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5
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Johnson AN, Barlow DE, Kelly AL, Varaljay VA, Crookes‐Goodson WJ, Biffinger JC. Current progress towards understanding the biodegradation of synthetic condensation polymers with active hydrolases. POLYM INT 2020. [DOI: 10.1002/pi.6131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
| | - Daniel E Barlow
- Chemistry Division Naval Research Laboratory Washington, DC USA
| | | | - Vanessa A Varaljay
- Soft Matter Materials Branch, Materials and Manufacturing Directorate Air Force Research Laboratory Wright‐Patterson Air Force Base OH USA
| | - Wendy J Crookes‐Goodson
- Soft Matter Materials Branch, Materials and Manufacturing Directorate Air Force Research Laboratory Wright‐Patterson Air Force Base OH USA
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6
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Cui H, Stadtmüller THJ, Jiang Q, Jaeger K, Schwaneberg U, Davari MD. How to Engineer Organic Solvent Resistant Enzymes: Insights from Combined Molecular Dynamics and Directed Evolution Study. ChemCatChem 2020. [DOI: 10.1002/cctc.202000422] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Haiyang Cui
- Lehrstuhl für Biotechnologie RWTH Aachen University Worringerweg 3 52074 Aachen Germany
| | - Tom H. J. Stadtmüller
- Lehrstuhl für Biotechnologie RWTH Aachen University Worringerweg 3 52074 Aachen Germany
| | - Qianjia Jiang
- Lehrstuhl für Biotechnologie RWTH Aachen University Worringerweg 3 52074 Aachen Germany
| | - Karl‐Erich Jaeger
- Institute of Molecular Enzyme Technology Heinrich Heine University Düsseldorf and Research Center Jülich Wilhelm Johnen Strasse 52426 Jülich Germany
| | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie RWTH Aachen University Worringerweg 3 52074 Aachen Germany
- DWI-Leibniz Institute for Interactive Materials Forckenbeckstraße 50 52074 Aachen Germany
| | - Mehdi D. Davari
- Lehrstuhl für Biotechnologie RWTH Aachen University Worringerweg 3 52074 Aachen Germany
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7
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Dulcey CE, López de Los Santos Y, Létourneau M, Déziel E, Doucet N. Semi-rational evolution of the 3-(3-hydroxyalkanoyloxy)alkanoate (HAA) synthase RhlA to improve rhamnolipid production in Pseudomonas aeruginosa and Burkholderia glumae. FEBS J 2019; 286:4036-4059. [PMID: 31177633 DOI: 10.1111/febs.14954] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 04/12/2019] [Accepted: 06/06/2019] [Indexed: 12/15/2022]
Abstract
The 3-(3-hydroxyalkanoyloxy)alkanoate (HAA) synthase RhlA is an essential enzyme involved in the biosynthesis of HAAs in Pseudomonas and Burkholderia species. RhlA modulates the aliphatic chain length in rhamnolipids, conferring distinct physicochemical properties to these biosurfactants exhibiting promising industrial and pharmaceutical value. A detailed molecular understanding of substrate specificity and catalytic performance in RhlA could offer protein engineering tools to develop designer variants involved in the synthesis of novel rhamnolipid mixtures for tailored eco-friendly products. However, current directed evolution progress remains limited due to the absence of high-throughput screening methodologies and lack of an experimentally resolved RhlA structure. In the present work, we used comparative modeling and chimeric-based approaches to perform a comprehensive semi-rational mutagenesis of RhlA from Pseudomonas aeruginosa. Our extensive RhlA mutational variants and chimeric hybrids between the Pseudomonas and Burkholderia homologs illustrate selective modulation of rhamnolipid alkyl chain length in both Pseudomonas aeruginosa and Burkholderia glumae. Our results also demonstrate the implication of a putative cap-domain motif that covers the catalytic site of the enzyme and provides substrate specificity to RhlA. This semi-rational mutant-based survey reveals promising 'hot-spots' for the modulation of RL congener patterns and potential control of enzyme activity, in addition to uncovering residue positions that modulate substrate selectivity between the Pseudomonas and Burkholderia functional homologs. DATABASE: Model data are available in the PMDB database under the accession number PM0081867.
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Affiliation(s)
- Carlos Eduardo Dulcey
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Laval, Canada
| | - Yossef López de Los Santos
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Laval, Canada
| | - Myriam Létourneau
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Laval, Canada
| | - Eric Déziel
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Laval, Canada
| | - Nicolas Doucet
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, Laval, Canada.,PROTEO, the Québec Network for Research on Protein Function, Engineering, and Applications, Université Laval, Canada
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8
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Yu S, Shen H, Cheng Y, Zhu Y, Li X, Mu W. Structural and Functional Basis of Difructose Anhydride III Hydrolase, Which Sequentially Converts Inulin Using the Same Catalytic Residue. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02424] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shuhuai Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Hui Shen
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yuanyuan Cheng
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Yingying Zhu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Xu Li
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
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9
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Padkina MV, Sambuk EV. Prospects for the Application of Yeast Display in Biotechnology and Cell Biology (Review). APPL BIOCHEM MICRO+ 2018. [DOI: 10.1134/s0003683818040105] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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10
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Abstract
Cell surface display of proteins/peptides has been established based on mechanisms of localizing proteins to the cell surface. In contrast to conventional intracellular and extracellular (secretion) expression systems, this method, generally called an arming technology, is particularly effective when using yeasts as a host, because the control of protein folding that is often required for the preparation of proteins can be natural. This technology can be employed for basic and applied research purposes. In this review, I describe various strategies for the construction of engineered yeasts and provide an outline of the diverse applications of this technology to industrial processes such as the production of biofuels and chemicals, as well as bioremediation and health-related processes. Furthermore, this technology is suitable for novel protein engineering and directed evolution through high-throughput screening, because proteins/peptides displayed on the cell surface can be directly analyzed using intact cells without concentration and purification. Functional proteins/peptides with improved or novel functions can be created using this beneficial, powerful, and promising technique.
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Affiliation(s)
- Mitsuyoshi Ueda
- a Division of Applied Life Sciences, Graduate School of Agriculture , Kyoto University , Sakyo-ku , Japan
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11
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Generation of a Functionally Distinct Rhizopus oryzae Lipase through Protein Folding Memory. PLoS One 2015; 10:e0124545. [PMID: 25970342 PMCID: PMC4430139 DOI: 10.1371/journal.pone.0124545] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 03/05/2015] [Indexed: 11/29/2022] Open
Abstract
Rhizopus oryzae lipase (ROL) has a propeptide at its N-terminus that functions as an intramolecular chaperone and facilitates the folding of mature ROL (mROL). In this study, we successfully generated a functionally distinct imprinted mROL (mROLimp) through protein folding memory using a mutated propeptide. The mutated propeptide left its structural memory on mROL and produced mROLimp that exhibited different substrate specificities compared with mROLWT (prepared from the wild type propeptide), although the amino acid sequences of both mROLs were the same. mROLimp showed a preference for substrates with medium chain-length acyl groups and, noticeably, recognized a peptidase-specific substrate. In addition, ROLimp was more stable than mROLWT. These results strongly suggest that proteins with identical amino acid sequences can fold into different conformations and that mutations in intramolecular chaperones can dynamically induce changes in enzymatic activity.
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12
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Miura N, Kuroda K, Ueda M. Enzyme Evolution by Yeast Cell Surface Engineering. Methods Mol Biol 2015; 1319:217-232. [PMID: 26060078 DOI: 10.1007/978-1-4939-2748-7_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Artificial evolution of proteins with the aim of acquiring novel or improved functionality is important for practical applications of the proteins. We have developed yeast cell surface engineering methods (or arming technology) for evolving enzymes. Here, we have described yeast cell surface engineering coupled with in vivo homologous recombination and library screening as a method for the artificial evolution of enzymes such as firefly luciferases. Using this method, novel luciferases with improved substrate specificity and substrate reactivity were engineered.
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Affiliation(s)
- Natsuko Miura
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan
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13
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Engineering of Yarrowia lipolytica lipase Lip8p by circular permutation to alter substrate and temperature characteristics. ACTA ACUST UNITED AC 2014; 41:757-62. [DOI: 10.1007/s10295-014-1428-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 02/25/2014] [Indexed: 10/25/2022]
Abstract
Abstract
Applications of lipases are mainly based on their catalytic efficiency and substrate specificity. In this study, circular permutation (CP), an unconventional protein engineering technique, was employed to acquire active mutants of Yarrowia lipolytica lipase Lip8p. A total of 21 mutant lipases exhibited significant shifts in substrate specificity. Cp128, the most active enzyme mutant, showed higher catalytic activity (14.5-fold) and higher affinity (4.6-fold) (decreased K m) to p-nitrophenyl-myristate (pNP-C14) than wild type (WT). Based on the three-dimensional (3D) structure model of the Lip8p, we found that most of the functional mutation occurred in the surface-exposed loop region in close proximity to the lid domain (S112–F122), which implies the steric effect of the lid on lipase activity and substrate specificity. The temperature properties of Cp128 were also investigated. In contrast to the optimal temperature of 45 °C for the WT enzyme, Cp128 exhibited the maximal activity at 37 °C. But it is noteworthy that there is no change in thermostability.
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14
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Kuroda K, Ueda M. Arming Technology in Yeast-Novel Strategy for Whole-cell Biocatalyst and Protein Engineering. Biomolecules 2013; 3:632-50. [PMID: 24970185 PMCID: PMC4030959 DOI: 10.3390/biom3030632] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 08/28/2013] [Accepted: 09/02/2013] [Indexed: 11/30/2022] Open
Abstract
Cell surface display of proteins/peptides, in contrast to the conventional intracellular expression, has many attractive features. This arming technology is especially effective when yeasts are used as a host, because eukaryotic modifications that are often required for functional use can be added to the surface-displayed proteins/peptides. A part of various cell wall or plasma membrane proteins can be genetically fused to the proteins/peptides of interest to be displayed. This technology, leading to the generation of so-called "arming technology", can be employed for basic and applied research purposes. In this article, we describe various strategies for the construction of arming yeasts, and outline the diverse applications of this technology to industrial processes such as biofuel and chemical productions, pollutant removal, and health-related processes, including oral vaccines. In addition, arming technology is suitable for protein engineering and directed evolution through high-throughput screening that is made possible by the feature that proteins/peptides displayed on cell surface can be directly analyzed using intact cells without concentration and purification. Actually, novel proteins/peptides with improved or developed functions have been created, and development of diagnostic/therapeutic antibodies are likely to benefit from this powerful approach.
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Affiliation(s)
- Kouichi Kuroda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
| | - Mitsuyoshi Ueda
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
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15
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Zhu SS, Li M, Yu X, Xu Y. Role of Met93 and Thr96 in the lid hinge region of Rhizopus chinensis lipase. Appl Biochem Biotechnol 2013; 170:436-47. [PMID: 23546870 DOI: 10.1007/s12010-013-0209-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Accepted: 03/18/2013] [Indexed: 10/27/2022]
Abstract
We engineered Rhizopus chinensis lipase to study its critical amino acid role in catalytic properties. Based on the amino acid sequence and three-dimensional model of the lipase, residues located in its lid hinge region (Met93 and Thr96) were replaced with corresponding amino acid residues (Ile93 and Asn96) found in the lid hinge region of Rhizopus oryzae lipase. The substitutions in the lid hinge region affected not only substrate specificity but also the thermostability of the lipase. Both lipases preferred p-nitrophenyl laurate and glyceryl trilaurate (C12). However, the variant S4-3O showed a slight decline in activity toward long-chain fatty acid (C16-C18). When enzymes activities decreased by half, the temperature of the variant (45 °C) was 22 °C lower than the parent (67 °C), probably substantially destabilized the structure of the lid region. The interfacial kinetic analysis of S4-3O suggested that the lower catalytic efficiency was due to a higher K m* value. According to the lipase structure investigated, Ile93Met played a role of narrowing the size of the hydrophobic patch, which affected the substrate binding affinity, and Asn96Thr destabilized the structure of the lipase by disrupting the H-bond interaction in the lid region.
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Affiliation(s)
- Shan-Shan Zhu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China
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16
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Nagayama M, Maeda H, Kuroda K, Ueda M. Mutated Intramolecular Chaperones Generate High-Activity Isomers of Mature Enzymes. Biochemistry 2012; 51:3547-53. [DOI: 10.1021/bi3001159] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mitsuru Nagayama
- Division
of Applied Life Sciences, Graduate School
of Agriculture, Kyoto University, Kitashirakawa,
Sakyo-ku, Kyoto 606-8502, Japan
| | - Haruko Maeda
- Division
of Applied Life Sciences, Graduate School
of Agriculture, Kyoto University, Kitashirakawa,
Sakyo-ku, Kyoto 606-8502, Japan
| | - Kouichi Kuroda
- Division
of Applied Life Sciences, Graduate School
of Agriculture, Kyoto University, Kitashirakawa,
Sakyo-ku, Kyoto 606-8502, Japan
| | - Mitsuyoshi Ueda
- Division
of Applied Life Sciences, Graduate School
of Agriculture, Kyoto University, Kitashirakawa,
Sakyo-ku, Kyoto 606-8502, Japan
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17
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Gera N, Hussain M, Rao BM. Protein selection using yeast surface display. Methods 2012; 60:15-26. [PMID: 22465794 DOI: 10.1016/j.ymeth.2012.03.014] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 03/09/2012] [Indexed: 12/16/2022] Open
Abstract
Binding proteins are typically isolated from combinatorial libraries of scaffold proteins using one of the many library screening tools available, such as phage display, yeast surface display or mRNA display. A key principle underlying these screening technologies is the establishment of a link between each unique mutant protein and its corresponding genetic code. The mutant proteins binding a desired target species are separated and subsequently identified using the genetic code. In this review, we largely focus on the use of yeast surface display for the isolation of binding proteins from combinatorial libraries. In yeast surface display, the yeast cell links the mutant protein to its coding DNA. Each yeast cell expresses the mutant proteins as fusions to a yeast cell wall protein; the yeast cell also carries plasmid DNA that codes for the mutant protein. Over the years, the yeast surface display platform has emerged as a powerful tool for protein engineering, and has been used in a variety of applications including affinity maturation, epitope mapping and biophysical characterization of proteins. Here we present a broad overview of the yeast surface display system and its applications, and compare it with other contemporary screening platforms. Further, we present detailed protocols for the use of yeast surface display to isolate de novo binding proteins from combinatorial libraries, and subsequent biophysical characterization of binders. These protocols can also be easily modified for affinity maturation of the isolated de novo binders.
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Affiliation(s)
- Nimish Gera
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
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Hong Lim K, Hwang I, Park S. Biotin-assisted folding of streptavidin on the yeast surface. Biotechnol Prog 2011; 28:276-83. [DOI: 10.1002/btpr.721] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Revised: 07/31/2011] [Indexed: 01/28/2023]
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Kourist R, Brundiek H, Bornscheuer UT. Protein engineering and discovery of lipases. EUR J LIPID SCI TECH 2010. [DOI: 10.1002/ejlt.200900143] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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SHIBASAKI S, MAEDA H, UEDA M. Molecular Display Technology Using Yeast-Arming Technology-. ANAL SCI 2009; 25:41-9. [DOI: 10.2116/analsci.25.41] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Seiji SHIBASAKI
- Laboratory of Bioanalytical Chemistry, Department of Pharmacy, School of Pharmacy, Hyogo University of Health Sciences
| | - Hatsuo MAEDA
- Laboratory of Bioanalytical Chemistry, Department of Pharmacy, School of Pharmacy, Hyogo University of Health Sciences
| | - Mitsuyoshi UEDA
- Laboratory of Biomacromolecular Chemistry, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University
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Boersma YL, Pijning T, Bosma MS, van der Sloot AM, Godinho LF, Dröge MJ, Winter RT, van Pouderoyen G, Dijkstra BW, Quax WJ. Loop Grafting of Bacillus subtilis Lipase A: Inversion of Enantioselectivity. ACTA ACUST UNITED AC 2008; 15:782-9. [DOI: 10.1016/j.chembiol.2008.06.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2008] [Revised: 05/06/2008] [Accepted: 06/06/2008] [Indexed: 11/26/2022]
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Kadonosono T, Kato-Murai M, Ueda M. Alteration of substrate specificity of rat neurolysin from matrix metalloproteinase-2/9-type to -3-type specificity by comprehensive mutation. Protein Eng Des Sel 2008; 21:507-13. [DOI: 10.1093/protein/gzn026] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Lipovšek D, Antipov E, Armstrong KA, Olsen MJ, Klibanov AM, Tidor B, Wittrup KD. Selection of Horseradish Peroxidase Variants with Enhanced Enantioselectivity by Yeast Surface Display. ACTA ACUST UNITED AC 2007; 14:1176-85. [DOI: 10.1016/j.chembiol.2007.09.008] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2007] [Revised: 08/28/2007] [Accepted: 09/18/2007] [Indexed: 11/26/2022]
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24
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Gai SA, Wittrup KD. Yeast surface display for protein engineering and characterization. Curr Opin Struct Biol 2007; 17:467-73. [PMID: 17870469 PMCID: PMC4038029 DOI: 10.1016/j.sbi.2007.08.012] [Citation(s) in RCA: 269] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2007] [Revised: 08/03/2007] [Accepted: 08/19/2007] [Indexed: 11/23/2022]
Abstract
Yeast surface display is being employed to engineer desirable properties into proteins for a broad variety of applications. Labeling with soluble ligands enables rapid and quantitative analysis of yeast-displayed libraries by flow cytometry, while cell-surface selections allow screening of libraries with insoluble or even as-yet-uncharacterized binding targets. In parallel, the utilization of yeast surface display for protein characterization, including in particular the mapping of functional epitopes mediating protein–protein interactions, represents a significant recent advance.
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Affiliation(s)
- S Annie Gai
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room E19-563, Cambridge, MA 02139, USA
| | - K Dane Wittrup
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room E19-563, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room E19-563, Cambridge, MA 02139, USA
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Kadonosono T, Kato M, Ueda M. Substrate specificity of rat brain neurolysin disclosed by molecular display system and putative substrates in rat tissues. Appl Microbiol Biotechnol 2007; 75:1353-60. [PMID: 17401561 DOI: 10.1007/s00253-007-0943-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2007] [Revised: 03/05/2007] [Accepted: 03/07/2007] [Indexed: 11/24/2022]
Abstract
To search for the substrates, other than neurotensin, of rat brain neurolysin, a novel method of determining peptidase activity was developed using a yeast molecular display system. This is a useful and convenient method of handling homogenously pure proteins to evaluate the properties of neurolysin. The neurolysin gene was ligated to the C-terminal half of the alpha-agglutinin gene with a FLAG tag sequence and a yeast cell-surface molecular displaying plasmid was constructed. Display of neurolysin with correct folding and appropriate activity was verified by immunofluorescence staining and activity measurement of a bradykinin-related peptide. The cleavage sites of peptides were determined by high-performance liquid chromatography (HPLC) and matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The results showed the amino acid preferences of hydrophobic, aromatic, and basic residues, which were the same as those of soluble neurolysin. Moreover, this method clearly showed the presence of two recognition motifs in neurolysin. By using these motifs, novel substrate candidates of neurolysin in rat tissues were screened, and several bioactive peptides that regulate feeding were found. We also discussed the ubiquitous distribution of neurolysin in rat tissues and the functions of substrate candidate peptides.
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Affiliation(s)
- Tetsuya Kadonosono
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto 606-8502, Japan
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Kato M, Fuchimoto J, Tanino T, Kondo A, Fukuda H, Ueda M. Preparation of a whole-cell biocatalyst of mutated Candida antarctica lipase B (mCALB) by a yeast molecular display system and its practical properties. Appl Microbiol Biotechnol 2007; 75:549-55. [PMID: 17262207 DOI: 10.1007/s00253-006-0835-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2006] [Revised: 12/25/2006] [Accepted: 12/28/2006] [Indexed: 10/23/2022]
Abstract
To prepare a whole-cell biocatalyst of a stable lipase at a low price, mutated Candida antarctica lipase B (mCALB) constructed on the basis of the primary sequences of CALBs from C. antarctica CBS 6678 strain and from C. antarctica LF 058 strain was displayed on a yeast cell surface by alpha-agglutinin as the anchor protein for easy handling and stability of the enzyme. When mCALB was displayed on the yeast cell surface, it showed a preference for short chain fatty acids, an advantage for producing flavors; although when Rhizopus oryzae lipase (ROL) was displayed, the substrate specificity was for middle chain lengths. When the thermal stability of mCALB on the cell surface was compared with that of ROL on a cell surface, T (1/2), the temperature required to give a residual activity of 50% for heat treatment of 30 min, was 60 degrees C for mCALB and 44 degrees C for ROL indicating that mCALB displayed on cell surface has a higher thermal stability. Furthermore, the activity of the displayed mCALB against p-nitrophenyl butyrate was 25-fold higher than that of soluble CALB, as reported previously. These findings suggest that mCALB-displaying yeast is more practical for industrial use as the whole-cell biocatalyst.
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Affiliation(s)
- Michiko Kato
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan.
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