1
|
Raczyńska A, Góra A, André I. An overview on polyurethane-degrading enzymes. Biotechnol Adv 2024; 77:108439. [PMID: 39241969 DOI: 10.1016/j.biotechadv.2024.108439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 08/26/2024] [Accepted: 09/02/2024] [Indexed: 09/09/2024]
Abstract
Polyurethanes (PUR) are durable synthetic polymers widely used in various industries, contributing significantly to global plastic consumption. PUR pose unique challenges in terms of degradability and recyclability, as they are characterised by intricate compositions and diverse formulations. Additives and proprietary structures used in commercial PUR formulations further complicate recycling efforts, making the effective management of PUR waste a daunting task. In this review, we delve into the complex challenge of enzymatic degradation of PUR, focusing on the structural and functional attributes of both enzymes and PUR. We also present documented native enzymes with reported efficacy in hydrolysing specific bonds within PUR, analysis of these enzyme structures, reaction mechanisms, substrate specificity, and binding site architecture. Furthermore, we propose essential features for the future redesign of enzymes to optimise PUR biodegradation efficiency. By outlining prospective research directions aimed at advancing the field of enzymatic biodegradation of PUR, we aim to contribute to the development of sustainable solutions for managing PUR waste and reducing environmental pollution.
Collapse
Affiliation(s)
- Agata Raczyńska
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, ul. Krzywoustego 8, 44-100 Gliwice, Poland; Toulouse Biotechnology Institute, TBI, Université de Toulouse, CNRS, INRAE, INSA, 135 avenue de Rangueil, F-31077 Toulouse Cedex, France; Faculty of Chemistry, Silesian University of Technology, ul. Strzody 9, 44-100 Gliwice, Poland
| | - Artur Góra
- Tunneling Group, Biotechnology Centre, Silesian University of Technology, ul. Krzywoustego 8, 44-100 Gliwice, Poland.
| | - Isabelle André
- Toulouse Biotechnology Institute, TBI, Université de Toulouse, CNRS, INRAE, INSA, 135 avenue de Rangueil, F-31077 Toulouse Cedex, France.
| |
Collapse
|
2
|
Kanprakobkit W, Wichai U, Bunyapraphatsara N, Kielar F. Isolation of Fatty Acids from the Enzymatic Hydrolysis of Capsaicinoids and Their Use in Enzymatic Acidolysis of Coconut Oil. J Oleo Sci 2023; 72:1097-1111. [PMID: 37989304 DOI: 10.5650/jos.ess23112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023] Open
Abstract
Herein we report the optimization of enzymatic hydrolysis of a mixture of capsaicinoids, capsaicin and dihydrocapsaicin obtained from chili peppers, and the utilization of the isolated fatty acids for the modification of coconut oil using enzyme catalyzed acidolysis. This work was carried out as the fatty acids that can be isolated from capsaicinoid hydrolysis have been shown to possess interesting biological properties. These biological properties could be better exploited by incorporating the fatty acids into a suitable delivery vehicle. The enzymatic hydrolysis of the mixture of capsaicin and dihydrocapsaicin was carried out using Novozym® 435 in phosphate buffer (pH 7.0) at 50℃. The enzyme catalyst could be reused in multiple cycles of the hydrolysis reaction. The desired 8-methyl-6-trans-nonenoic acid and 8-methylnonanoic acid were isolated from the hydrolysis reaction mixture using a simple extraction procedure with a 47.8% yield. This was carried out by first extracting the reaction mixture at pH 10 with ethyl acetate to remove any dissolved capsaicinoids and vanillyl amine side product. The fatty acids were isolated after adjustment of the pH of the reaction mixture to 5 and second extraction with ethyl acetate. The acidolysis of coconut oil with the obtained fatty acids was performed using Lipozyme® TL IM. The performance of the acidolysis reaction was evaluated using 1H-NMR spectroscopy and verified in selected cases using gas chromatography. The best performing conditions involved carrying out the acidolysis reaction at 60℃ with a 1.2 w/w ratio of the fatty acids to coconut oil and 10% enzyme loading for 72 h. This resulted in the incorporation of 26.61% and 9.86% of 8-methyl-6-trans-nonenoic acid and 8-methylnonanoic acid, respectively, into the modified coconut oil product. This product can act as a potential delivery vehicle for these interesting compounds.
Collapse
Affiliation(s)
- Winranath Kanprakobkit
- Department of Chemistry and Center of Excellence in Biomaterials, Faculty of Science, Naresuan University
| | - Uthai Wichai
- Department of Chemistry and Center of Excellence in Biomaterials, Faculty of Science, Naresuan University
| | | | - Filip Kielar
- Department of Chemistry and Center of Excellence in Biomaterials, Faculty of Science, Naresuan University
| |
Collapse
|
3
|
Thermostable lipases and their dynamics of improved enzymatic properties. Appl Microbiol Biotechnol 2021; 105:7069-7094. [PMID: 34487207 DOI: 10.1007/s00253-021-11520-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/29/2021] [Accepted: 07/31/2021] [Indexed: 10/20/2022]
Abstract
Thermal stability is one of the most desirable characteristics in the search for novel lipases. The search for thermophilic microorganisms for synthesising functional enzyme biocatalysts with the ability to withstand high temperature, and capacity to maintain their native state in extreme conditions opens up new opportunities for their biotechnological applications. Thermophilic organisms are one of the most favoured organisms, whose distinctive characteristics are extremely related to their cellular constituent particularly biologically active proteins. Modifications on the enzyme structure are critical in optimizing the stability of enzyme to thermophilic conditions. Thermostable lipases are one of the most favourable enzymes used in food industries, pharmaceutical field, and actively been studied as potential biocatalyst in biodiesel production and other biotechnology application. Particularly, there is a trade-off between the use of enzymes in high concentration of organic solvents and product generation. Enhancement of the enzyme stability needs to be achieved for them to maintain their enzymatic activity regardless the environment. Various approaches on protein modification applied since decades ago conveyed a better understanding on how to improve the enzymatic properties in thermophilic bacteria. In fact, preliminary approach using advanced computational analysis is practically conducted before any modification is being performed experimentally. Apart from that, isolation of novel extremozymes from various microorganisms are offering great frontier in explaining the crucial native interaction within the molecules which could help in protein engineering. In this review, the thermostability prospect of lipases and the utility of protein engineering insights into achieving functional industrial usefulness at their high temperature habitat are highlighted. Similarly, the underlying thermodynamic and structural basis that defines the forces that stabilize these thermostable lipase is discussed. KEY POINTS: • The dynamics of lipases contributes to their non-covalent interactions and structural stability. • Thermostability can be enhanced by well-established genetic tools for improved kinetic efficiency. • Molecular dynamics greatly provides structure-function insights on thermodynamics of lipase.
Collapse
|
4
|
Structure-Based Engineering of Amidase from Pantoea sp. for Efficient 2-Chloronicotinic Acid Biosynthesis. Appl Environ Microbiol 2019; 85:AEM.02471-18. [PMID: 30578259 DOI: 10.1128/aem.02471-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 12/08/2018] [Indexed: 11/20/2022] Open
Abstract
2-Chloronicotinic acid is a key intermediate of pharmaceuticals and pesticides. Amidase-catalyzed hydrolysis provides a promising enzymatic method for 2-chloronicotinic acid production from 2-chloronicotinamide. However, biocatalytic hydrolysis of 2-chloronicotinamide is difficult due to the strong steric and electronic effect caused by 2-position chlorine substituent of the pyridine ring. In this study, an amidase from a Pantoea sp. (Pa-Ami) was designed and engineered to have improved catalytic properties. Single mutant G175A and double mutant G175A/A305T strains exhibited 3.2- and 3.7-fold improvements in their specific activity for 2-chloronicotinamide, and the catalytic efficiency was significantly increased, with k cat/Km values 3.1 and 10.0 times higher than that of the wild type, respectively. Structure-function analysis revealed that the distance between Oγ of Ser177 (involved in the catalytic triad) and the carbonyl carbon of 2-chloronicotinamide was shortened in the G175A mutant, making the nucleophilic attack on the Oγ of Ser177 easier by virtue of proper orientation. In addition, the A305T mutation contributed to a suitable tunnel formation to facilitate the substrate entry and product release, resulting in improved catalytic efficiency. With the G175A/A305T double mutant as a biocatalyst, a maximum of 1,220 mM 2-chloronicotinic acid was produced with a 94% conversion, and the space-time yield reached as high as 575 gproduct liter-1 day-1 These results provide not only a novel robust biocatalyst for the production of 2-chloronicotinic acid but also new insights into amidase structure-function relationships.IMPORTANCE In recent years, the demand for 2-chloronicotinic acid has been greatly increased. To date, several chemical methods have been used for the synthesis of 2-chloronicotinic acid, but all include tedious steps and/or drastic reaction conditions, resulting in both economic and environmental issues. It is requisite to develop an efficient and green synthesis route. We recently screened Pa-Ami and demonstrated its potential for synthesis of 2-chloronicotinic acid from 2-chloronicotinamide. However, chlorine substitution on the pyridine ring of nicotinamide significantly affected the activity of Pa-Ami. Especially for 2-chloronicotinamide, the enzyme activity and catalytic efficiency were relatively low. In this study, based on structure-function analysis, we succeeded in engineering the amidase by structure-guided saturation mutagenesis. The engineered Pa-Ami exhibited quite high catalytic activity toward 2-chloronicotinamide and could serve as a promising biocatalyst for the biosynthesis of 2-chloronicotinic acid.
Collapse
|
5
|
Li YM, Gao JQ, Pei XZ, Du C, Fan C, Yuan WJ, Bai FW. Production of L-alanyl-L-glutamine by immobilized Pichia pastoris GS115 expressing α-amino acid ester acyltransferase. Microb Cell Fact 2019; 18:27. [PMID: 30711013 PMCID: PMC6359838 DOI: 10.1186/s12934-019-1077-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 01/29/2019] [Indexed: 11/10/2022] Open
Abstract
Background l-Alanyl-l-glutamine (Ala-Gln) represents the great application potential in clinic due to the unique physicochemical properties. A new approach was developed to synthesize Ala-Gln by recombinant Escherichia coli OPA, which could overcome the disadvantages of traditional chemical synthesis. Although satisfactory results had been obtained with recombinant E. coli OPA, endotoxin and the use of multiple antibiotics along with toxic inducer brought the potential biosafety hazard for the clinical application of Ala-Gln. Results In this study, the safer host Pichia pastoris was applied as an alternative to E. coli. A recombinant P. pastoris (named GPA) with the original gene of α-amino acid ester acyltransferase (SsAet) from Sphingobacterium siyangensis SY1, was constructed to produce Ala-Gln. To improve the expression efficiency of SsAet in P. pastoris, codon optimization was conducted to obtain the strain GPAp. Here, we report that Ala-Gln production by GPAp was approximately 2.5-fold more than that of GPA. The optimal induction conditions (cultivated for 3 days at 26 °C with a daily 1.5% of methanol supplement), the optimum reaction conditions (28 °C and pH 8.5), and the suitable substrate conditions (AlaOMe/Gln = 1.5/1) were also achieved for GPAp. Although most of the metal ions had no effects, the catalytic activity of GPAp showed a slight decrease in the presence of Fe3+ and an obvious increase when cysteine or PMSF were added. Under the optimum conditions, the Ala-Gln generation by GPAp realized the maximum molar yield of 63.5% and the catalytic activity of GPAp by agar embedding maintained extremely stable after 10 cycles. Conclusions Characterized by economy, efficiency and practicability, production of Ala-Gln by recycling immobilized GPAp (whole-cell biocatalyst) is represents a green and promising way in industrial. Electronic supplementary material The online version of this article (10.1186/s12934-019-1077-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yi-Min Li
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Jiao-Qi Gao
- Division of Biotechnology, Dalian Institute of Chemical Physics, Dalian, 116023, China
| | - Xu-Ze Pei
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Cong Du
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Chao Fan
- Research and Development Center, Dalian Innobio Corporation Limited, Dalian, 116600, China
| | - Wen-Jie Yuan
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China.
| | - Feng-Wu Bai
- School of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai, 200240, China
| |
Collapse
|
6
|
Tonin F, Arends IWCE. Latest development in the synthesis of ursodeoxycholic acid (UDCA): a critical review. Beilstein J Org Chem 2018; 14:470-483. [PMID: 29520309 PMCID: PMC5827811 DOI: 10.3762/bjoc.14.33] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 02/05/2018] [Indexed: 12/13/2022] Open
Abstract
Ursodeoxycholic acid (UDCA) is a pharmaceutical ingredient widely used in clinics. As bile acid it solubilizes cholesterol gallstones and improves the liver function in case of cholestatic diseases. UDCA can be obtained from cholic acid (CA), which is the most abundant and least expensive bile acid available. The now available chemical routes for the obtainment of UDCA yield about 30% of final product. For these syntheses several protection and deprotection steps requiring toxic and dangerous reagents have to be performed, leading to the production of a series of waste products. In many cases the cholic acid itself first needs to be prepared from its taurinated and glycilated derivatives in the bile, thus adding to the complexity and multitude of steps involved of the synthetic process. For these reasons, several studies have been performed towards the development of microbial transformations or chemoenzymatic procedures for the synthesis of UDCA starting from CA or chenodeoxycholic acid (CDCA). This promising approach led several research groups to focus their attention on the development of biotransformations with non-pathogenic, easy-to-manage microorganisms, and their enzymes. In particular, the enzymatic reactions involved are selective hydrolysis, epimerization of the hydroxy functions (by oxidation and subsequent reduction) and the specific hydroxylation and dehydroxylation of suitable positions in the steroid rings. In this minireview, we critically analyze the state of the art of the production of UDCA by several chemical, chemoenzymatic and enzymatic routes reported, highlighting the bottlenecks of each production step. Particular attention is placed on the precursors availability as well as the substrate loading in the process. Potential new routes and recent developments are discussed, in particular on the employment of flow-reactors. The latter technology allows to develop processes with shorter reaction times and lower costs for the chemical and enzymatic reactions involved.
Collapse
Affiliation(s)
- Fabio Tonin
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Isabel W C E Arends
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| |
Collapse
|
7
|
Li Y, Yuan W, Gao J, Fan C, Wu W, Bai F. Production of l-alanyl-l-glutamine by recycling E. coli expressing α-amino acid ester acyltransferase. BIORESOURCE TECHNOLOGY 2017; 245:1603-1609. [PMID: 28624247 DOI: 10.1016/j.biortech.2017.06.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 06/01/2017] [Accepted: 06/03/2017] [Indexed: 05/22/2023]
Abstract
In this study, the optimum induction and reaction conditions, and fermentation process of producing Ala-Gln by E. coli Origami 2 overexpressing α-amino acid ester acyltransferase (OPA) were investigated. Besides, the Ala-Gln synthesis by OPA achieved the maximum molar yield of 94.7% and productivity of 1.89g/L/min due to the extremely high enzyme activity. On this basis, repeated-cycle batch fermentation to produce Ala-Gln indicated that OPA could maintain high Ala-Gln yields and enzyme stabilities after several cell recycling. Consequently, the cost-efficient and environmentally friendly approach for Ala-Gln production by recycling OPA makes a great contribution to further industrial-scale applications.
Collapse
Affiliation(s)
- Yimin Li
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China
| | - Wenjie Yuan
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China.
| | - Jiaoqi Gao
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China
| | - Chao Fan
- Dalian Innobio Biological Co., LTD, Dalian 116600, China
| | - Wenzhong Wu
- Dalian Innobio Biological Co., LTD, Dalian 116600, China
| | - Fengwu Bai
- School of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai 200240, China
| |
Collapse
|
8
|
Syal P, Verma VV, Gupta R. Targeted mutations and MD simulations of a methanol-stable lipase YLIP9 from Yarrowia lipolytica MSR80 to develop a biodiesel enzyme. Int J Biol Macromol 2017; 104:78-88. [DOI: 10.1016/j.ijbiomac.2017.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 05/31/2017] [Accepted: 06/01/2017] [Indexed: 11/17/2022]
|
9
|
Hendil-Forssell P, Martinelle M, Syrén PO. Exploring water as building bricks in enzyme engineering. Chem Commun (Camb) 2015; 51:17221-4. [DOI: 10.1039/c5cc07162c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A de novo designed water pattern is used to achieve a 34-fold accelerated promiscuous enzyme catalysis by efficient transition state stabilization.
Collapse
Affiliation(s)
- Peter Hendil-Forssell
- KTH Royal Institute of Technology
- Division of Industrial Biotechnology
- AlbaNova University Centre
- 106 91 Stockholm
- Sweden
| | - Mats Martinelle
- KTH Royal Institute of Technology
- Division of Industrial Biotechnology
- AlbaNova University Centre
- 106 91 Stockholm
- Sweden
| | - Per-Olof Syrén
- KTH Royal Institute of Technology
- Division of Proteomics & Nanobiotechnology
- Science for Life Laboratory
- 171 21 Stockholm
- Sweden
| |
Collapse
|
10
|
Ferrario V, Ebert C, Svendsen A, Besenmatter W, Gardossi L. An integrated platform for automatic design and screening of virtual mutants based on 3D-QSAR analysis. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2013.12.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
11
|
Hackenschmidt S, Moldenhauer EJ, Behrens GA, Gand M, Pavlidis IV, Bornscheuer UT. Enhancement of Promiscuous Amidase Activity of a Bacillus subtilis
Esterase by Formation of a π-π Network. ChemCatChem 2013. [DOI: 10.1002/cctc.201300837] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
12
|
Hediger MR, De Vico L, Rannes JB, Jäckel C, Besenmatter W, Svendsen A, Jensen JH. In silico screening of 393 mutants facilitates enzyme engineering of amidase activity in CalB. PeerJ 2013; 1:e145. [PMID: 24010022 PMCID: PMC3757469 DOI: 10.7717/peerj.145] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 08/06/2013] [Indexed: 11/25/2022] Open
Abstract
Our previously presented method for high throughput computational screening of mutant activity (Hediger et al., 2012) is benchmarked against experimentally measured amidase activity for 22 mutants of Candida antarctica lipase B (CalB). Using an appropriate cutoff criterion for the computed barriers, the qualitative activity of 15 out of 22 mutants is correctly predicted. The method identifies four of the six most active mutants with ≥3-fold wild type activity and seven out of the eight least active mutants with ≤0.5-fold wild type activity. The method is further used to screen all sterically possible (386) double-, triple- and quadruple-mutants constructed from the most active single mutants. Based on the benchmark test at least 20 new promising mutants are identified.
Collapse
Affiliation(s)
- Martin R Hediger
- Department of Chemistry, University of Copenhagen , Copenhagen , Denmark
| | | | | | | | | | | | | |
Collapse
|
13
|
Hediger MR, Steinmann C, De Vico L, Jensen JH. A computational method for the systematic screening of reaction barriers in enzymes: searching for Bacillus circulans xylanase mutants with greater activity towards a synthetic substrate. PeerJ 2013; 1:e111. [PMID: 23904990 PMCID: PMC3728886 DOI: 10.7717/peerj.111] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 07/03/2013] [Indexed: 12/04/2022] Open
Abstract
We present a semi-empirical (PM6-based) computational method for systematically estimating the effect of all possible single mutants, within a certain radius of the active site, on the barrier height of an enzymatic reaction. The intent of this method is not a quantitative prediction of the barrier heights, but rather to identify promising mutants for further computational or experimental study. The method is applied to identify promising single and double mutants of Bacillus circulans xylanase (BCX) with increased hydrolytic activity for the artificial substrate ortho-nitrophenyl β-xylobioside (ONPX2). The estimated reaction barrier for wild-type (WT) BCX is 18.5 kcal/mol, which is in good agreement with the experimental activation free energy value of 17.0 kcal/mol extracted from the observed k cat using transition state theory (Joshi et al., 2001). The PM6 reaction profiles for eight single point mutations are recomputed using FMO-MP2/PCM/6-31G(d) single points. PM6 predicts an increase in barrier height for all eight mutants while FMO predicts an increase for six of the eight mutants. Both methods predict that the largest change in barrier occurs for N35F, where PM6 and FMO predict a 9.0 and 15.8 kcal/mol increase, respectively. We thus conclude that PM6 is sufficiently accurate to identify promising mutants for further study. We prepared a set of all theoretically possible (342) single mutants in which every amino acid of the active site (except for the catalytically active residues E78 and E172) was mutated to every other amino acid. Based on results from the single mutants we construct a set of 111 double mutants consisting of all possible pairs of single mutants with the lowest barrier for a particular position and compute their reaction profile. None of the mutants have, to our knowledge, been prepared experimentally and therefore present experimentally testable predictions.
Collapse
Affiliation(s)
- Martin R. Hediger
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Casper Steinmann
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Luca De Vico
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Jan H. Jensen
- Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
14
|
Yang G, De Santi C, de Pascale D, Pucciarelli S, Pucciarelli S, Miceli C. Characterization of the first eukaryotic cold-adapted patatin-like phospholipase from the psychrophilic Euplotes focardii: Identification of putative determinants of thermal-adaptation by comparison with the homologous protein from the mesophilic Euplotes crassus. Biochimie 2013; 95:1795-806. [PMID: 23796575 DOI: 10.1016/j.biochi.2013.06.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 06/13/2013] [Indexed: 11/28/2022]
Abstract
The ciliated protozoon Euplotes focardii, originally isolated from the coastal seawaters of Terra Nova Bay in Antarctica, shows a strictly psychrophilic phenotype, including optimal survival and multiplication rates at 4-5 °C. This characteristic makes E. focardii an ideal model species for identifying the molecular bases of cold adaptation in psychrophilic organisms, as well as a suitable source of novel cold-active enzymes for industrial applications. In the current study, we characterized the patatin-like phospholipase from E. focardii (EfPLP), and its enzymatic activity was compared to that of the homologous protein from the mesophilic congeneric species Euplotes crassus (EcPLP). Both EfPLP and EcPLP have consensus motifs conserved in other patatin-like phospholipases. By analyzing both esterase and phospholipase A2 activity, we determined the thermostability and the optimal pH, temperature dependence and substrates of these enzymes. We demonstrated that EfPLP shows the characteristics of a psychrophilic phospholipase. Furthermore, we analyzed the enzymatic activity of three engineered versions of the EfPLP, in which unique residues of EfPLP, Gly80, Ala201 and Val204, were substituted through site-directed mutagenesis with residues found in the E. crassus homolog (Glu, Pro and Ile, respectively). Additionally, three corresponding mutants of EcPLP were also generated and characterized. These analyses showed that the substitution of amino acids with rigid and bulky charged/hydrophobic side chain in the psychrophilic EfPLP confers enzymatic properties similar to those of the mesophilic patatin-like phospholipase, and vice versa. This is the first report on the isolation and characterization of a cold-adapted patatin-like phospholipase from eukaryotes. The results reported in this paper support the idea that enzyme thermal-adaptation is based mainly on some amino acid residues that influence the structural flexibility of polypeptides and that EfPLP is an attractive biocatalyst for industrial processes at low temperatures.
Collapse
Affiliation(s)
- Guang Yang
- School of Biosciences and Biotechnology, University of Camerino, Italy
| | | | | | | | | | | |
Collapse
|
15
|
Syrén PO. The solution of nitrogen inversion in amidases. FEBS J 2013; 280:3069-83. [DOI: 10.1111/febs.12241] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 03/06/2013] [Accepted: 03/08/2013] [Indexed: 01/06/2023]
Affiliation(s)
- Per-Olof Syrén
- Institute of Technical Biochemistry; University of Stuttgart; Germany
| |
Collapse
|
16
|
Syrén PO, Le Joubioux F, Ben Henda Y, Maugard T, Hult K, Graber M. Proton Shuttle Mechanism in the Transition State of Lipase-Catalyzed N-Acylation of Amino Alcohols. ChemCatChem 2013. [DOI: 10.1002/cctc.201200751] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
17
|
Jung S, Kim J, Park S. Rational design for enhancing promiscuous activity of Candida antarctica lipase B: a clue for the molecular basis of dissimilar activities between lipase and serine-protease. RSC Adv 2013. [DOI: 10.1039/c2ra23333a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
18
|
Suplatov DA, Besenmatter W, Svedas VK, Svendsen A. Bioinformatic analysis of α/β-hydrolase fold enzymes reveals subfamily-specific positions responsible for discrimination of amidase and lipase activities. Protein Eng Des Sel 2012; 25:689-97. [PMID: 23043134 DOI: 10.1093/protein/gzs068] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Superfamily of alpha-beta hydrolases is one of the largest groups of structurally related enzymes with diverse catalytic functions. Bioinformatic analysis was used to study how lipase and amidase catalytic activities are implemented into the same structural framework. Subfamily-specific positions--conserved within lipases and peptidases but different between them--that were supposed to be responsible for functional discrimination have been identified. Mutations at subfamily-specific positions were used to introduce amidase activity into Candida antarctica lipase B (CALB). Molecular modeling was implemented to evaluate influence of selected residues on binding and catalytic conversion of amide substrate by corresponding library of mutants. In silico screening was applied to select reactive enzyme-substrate complexes that satisfy knowledge-based criteria of amidase catalytic activity. Selected CALB variants with substitutions at subfamily-specific positions Gly39, Thr103, Trp104, and Leu278 were produced and showed significant improvement of experimentally measured amidase activity. Based on these results, we suggest that value of subfamily-specific positions should be further explored in order to develop a systematic tool to study structure-function relationship in enzymes and to use this information for rational enzyme engineering.
Collapse
Affiliation(s)
- D A Suplatov
- Faculty of Bioengineering and Bioinformatics and Belozersky Institute of Physicochemical Biology, Lomonosov Moscow State University, Lenin Hills 1/73, Moscow 119991, Russia
| | | | | | | |
Collapse
|
19
|
Wang B, Liu Y, Zhang D, Feng Y, Li J. Efficient kinetic resolution of amino acids catalyzed by lipase AS ‘Amano’ via cleavage of an amide bond. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.tetasy.2012.08.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
20
|
Syrén PO, Hendil-Forssell P, Aumailley L, Besenmatter W, Gounine F, Svendsen A, Martinelle M, Hult K. Esterases with an introduced amidase-like hydrogen bond in the transition state have increased amidase specificity. Chembiochem 2012; 13:645-8. [PMID: 22378481 DOI: 10.1002/cbic.201100779] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Indexed: 11/08/2022]
Affiliation(s)
- Per-Olof Syrén
- Department of Biochemistry, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91 Stockholm, Sweden
| | | | | | | | | | | | | | | |
Collapse
|
21
|
Martini VP, Glogauer A, Iulek J, Souza EM, Pedrosa FO, Krieger N. Crystallization and preliminary crystallographic analysis of LipC12, a true lipase isolated through a metagenomics approach. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:175-177. [PMID: 22297992 PMCID: PMC3274396 DOI: 10.1107/s1744309111051323] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Accepted: 11/29/2011] [Indexed: 05/31/2023]
Abstract
LipC12, a true lipase from family I.1 of bacterial lipases which was previously isolated through a metagenomics approach, contains 293 amino acids. Among lipases of known three-dimensional structure, it has a sequence identity of 47% to the lipase from Pseudomonas aeruginosa PAO1. Recombinant N-terminally His(6)-tagged LipC12 protein was expressed in Escherichia coli, purified in a homogenous form and crystallized in several conditions, with the best crystals being obtained using 2.0 M sodium formate and 0.1 M bis-tris propane pH 7.0. X-ray diffraction data were collected to 2.70 Å resolution. The crystals belonged to the tetragonal space group P4(1)22, with unit-cell parameters a = b = 58.62, c = 192.60 Å.
Collapse
Affiliation(s)
- V. P. Martini
- Department of Chemistry, Federal University of Paraná, Curitiba-PR, Brazil
| | - A. Glogauer
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba-PR, Brazil
| | - J. Iulek
- Department of Chemistry, State University of Ponta Grossa, Ponta Grossa-PR, Brazil
| | - E. M. Souza
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba-PR, Brazil
| | - F. O. Pedrosa
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba-PR, Brazil
| | - N. Krieger
- Department of Chemistry, Federal University of Paraná, Curitiba-PR, Brazil
| |
Collapse
|
22
|
Torres LL, Schließmann A, Schmidt M, Silva-Martin N, Hermoso JA, Berenguer J, Bornscheuer UT, Hidalgo A. Promiscuous enantioselective (−)-γ-lactamase activity in the Pseudomonas fluorescens esterase I. Org Biomol Chem 2012; 10:3388-92. [DOI: 10.1039/c2ob06887g] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
23
|
Gene cloning and characterization of α-amino acid ester acyl transferase in Empedobacter brevis ATCC14234 and Sphingobacterium siyangensis AJ2458. Biosci Biotechnol Biochem 2011; 75:2087-92. [PMID: 22056425 DOI: 10.1271/bbb.110181] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The gene encoding α-amino acid ester acyl transferase (AET), the enzyme that catalyzes the peptide-forming reaction from amino acid methyl esters and amino acids, was cloned from Empedobacter brevis ATCC14234 and Sphingobacterium siyangensis AJ2458 and expressed in Escherichia coli. This is the first report on the aet gene. It encodes a polypeptide composed of 616 (ATCC14234) and 619 (AJ2458) amino acids residues. The V(max) values of these recombinant enzymes during the catalysis of L-alanyl-L-glutamine formation from L-alanine methylester and L-glutamine were 1,010 U/mg (ATCC14234) and 1,154 U/mg (AJ2458). An amino acid sequence similarity search revealed 35% (ATCC14234) and 36% (AJ2458) identity with an α-amino acid ester hydrolase from Acetobacter pasteurianus, which contains an active-site serine in the consensus serine enzyme motif, GxSYxG. In the deduced amino acid sequences of AET from both bacteria, the GxSYxG motif was conserved, suggesting that AET is a serine enzyme.
Collapse
|
24
|
Assessing directed evolution methods for the generation of biosynthetic enzymes with potential in drug biosynthesis. Future Med Chem 2011; 3:809-19. [PMID: 21644826 DOI: 10.4155/fmc.11.48] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
To address the synthesis of increasingly structurally diverse small-molecule drugs, methods for the generation of efficient and selective biological catalysts are becoming increasingly important. 'Directed evolution' is an umbrella term referring to a variety of methods for improving or altering the function of enzymes using a nature-inspired twofold strategy of mutagenesis followed by selection. This article provides an objective assessment of the effectiveness of directed evolution campaigns in generating enzymes with improved catalytic parameters for new substrates from the last decade, excluding studies that aimed to select for only improved physical properties and those that lack kinetic characterization. An analysis of the trends of methodologies and their success rates from 81 qualifying examples in the literature reveals the average fold improvement for k (cat) (or V (max)), K (m) and k (cat)/K (m) to be 366-, 12- and 2548-fold, respectively, whereas the median fold improvements are 5.4, 3 and 15.6. Further analysis by enzyme class, library-generation methodology and screening methodology explores relationships between successful campaigns and the methodologies employed.
Collapse
|
25
|
Modulating the synthetase activity of penicillin G acylase in organic media by addition of N-methylimidazole: Using vinyl acetate as activated acyl donor. J Biotechnol 2011; 153:111-5. [DOI: 10.1016/j.jbiotec.2011.03.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2010] [Revised: 02/22/2011] [Accepted: 03/10/2011] [Indexed: 11/18/2022]
|
26
|
Syrén PO, Hult K. Amidases Have a Hydrogen Bond that Facilitates Nitrogen Inversion, but Esterases Have Not. ChemCatChem 2011. [DOI: 10.1002/cctc.201000448] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
27
|
Busto E, Gotor-Fernández V, Gotor V. Hydrolases: catalytically promiscuous enzymes for non-conventional reactions in organic synthesis. Chem Soc Rev 2010; 39:4504-23. [DOI: 10.1039/c003811c] [Citation(s) in RCA: 246] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
28
|
Liljeblad A, Kallio P, Vainio M, Niemi J, Kanerva LT. Formation and hydrolysis of amide bonds by lipase A from Candida antarctica; exceptional features. Org Biomol Chem 2010; 8:886-95. [PMID: 20135048 DOI: 10.1039/b920939p] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Arto Liljeblad
- Institute of Biomedicine, Pharmacology, Drug Development and Therapeutics/Laboratory of Synthetic Drug Chemistry and Department of Chemistry, University of Turku, Lemminkäisenkatu 5 C, FIN-20520, Turku, Finland.
| | | | | | | | | |
Collapse
|
29
|
Vieites JM, Ghazi A, Beloqui A, Polaina J, Andreu JM, Golyshina OV, Nechitaylo TY, Waliczek A, Yakimov MM, Golyshin PN, Ferrer M. Inter-conversion of catalytic abilities in a bifunctional carboxyl/feruloyl-esterase from earthworm gut metagenome. Microb Biotechnol 2009; 3:48-58. [PMID: 21255305 PMCID: PMC3815946 DOI: 10.1111/j.1751-7915.2009.00135.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Carboxyl esterases (CE) exhibit various reaction specificities despite of their overall structural similarity. In present study we have exploited functional metagenomics, saturation mutagenesis and experimental protein evolution to explore residues that have a significant role in substrate discrimination. We used an enzyme, designated 3A6, derived from the earthworm gut metagenome that exhibits CE and feruloyl esterase (FAE) activities with p‐nitrophenyl and cinnamate esters, respectively, with a [(kcat/Km)]CE/[(kcat/Km)]FAE factor of 17. Modelling‐guided saturation mutagenesis at specific hotspots (Lys281, Asp282, Asn316 and Lys317) situated close to the catalytic core (Ser143/Asp273/His305) and a deletion of a 34‐AA–long peptide fragment yielded mutants with the highest CE activity, while cinnamate ester bond hydrolysis was effectively abolished. Although, single to triple mutants with both improved activities (up to 180‐fold in kcat/Km values) and enzymes with inverted specificity ((kcat/Km)CE/(kcat/Km)FAE ratio of ∼0.4) were identified, no CE inactive variant was found. Screening of a large error‐prone PCR‐generated library yielded by far less mutants for substrate discrimination. We also found that no significant changes in CE activation energy occurs after any mutation (7.3 to −5.6 J mol−1), whereas a direct correlation between loss/gain of FAE function and activation energies (from 33.05 to −13.7 J mol−1) was found. Results suggest that the FAE activity in 3A6 may have evolved via introduction of a limited number of ‘hot spot’ mutations in a common CE ancestor, which may retain the original hydrolytic activity due to lower restrictive energy barriers but conveys a dynamic energetically favourable switch of a second hydrolytic reaction.
Collapse
Affiliation(s)
- José María Vieites
- CSIC, Institute of Catalysis, 28049 Madrid, Spain. CSIC, Instituto de Agroquímica y Tecnología de Alimentos, 46980 Valencia, Spain
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Bershtein S, Tawfik DS. Advances in laboratory evolution of enzymes. Curr Opin Chem Biol 2008; 12:151-8. [PMID: 18284924 DOI: 10.1016/j.cbpa.2008.01.027] [Citation(s) in RCA: 193] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2007] [Revised: 01/17/2008] [Accepted: 01/24/2008] [Indexed: 11/19/2022]
Abstract
We address recent developments in the area of laboratory, or directed evolution, with a focus on enzymes and on new methodologies of generic potential. We survey three main areas: (i) library making techniques, including the application of computational and rational methods for library design; (ii) screening and selection techniques, including recent applications of enzyme screening by FACS (fluorescence activated cell sorter); (iii) new approaches for performing directed evolution, and in particular, the application of 'neutral drifts' (libraries generated by rounds of mutation and selection for the enzyme's original function) and of consensus mutations to generate highly evolvable starting points for directed evolution.
Collapse
Affiliation(s)
- Shimon Bershtein
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | | |
Collapse
|