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Rahmati F, Sethi D, Shu W, Asgari Lajayer B, Mosaferi M, Thomson A, Price GW. Advances in microbial exoenzymes bioengineering for improvement of bioplastics degradation. CHEMOSPHERE 2024; 355:141749. [PMID: 38521099 DOI: 10.1016/j.chemosphere.2024.141749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 03/06/2024] [Accepted: 03/16/2024] [Indexed: 03/25/2024]
Abstract
Plastic pollution has become a major global concern, posing numerous challenges for the environment and wildlife. Most conventional ways of plastics degradation are inefficient and cause great damage to ecosystems. The development of biodegradable plastics offers a promising solution for waste management. These plastics are designed to break down under various conditions, opening up new possibilities to mitigate the negative impact of traditional plastics. Microbes, including bacteria and fungi, play a crucial role in the degradation of bioplastics by producing and secreting extracellular enzymes, such as cutinase, lipases, and proteases. However, these microbial enzymes are sensitive to extreme environmental conditions, such as temperature and acidity, affecting their functions and stability. To address these challenges, scientists have employed protein engineering and immobilization techniques to enhance enzyme stability and predict protein structures. Strategies such as improving enzyme and substrate interaction, increasing enzyme thermostability, reinforcing the bonding between the active site of the enzyme and substrate, and refining enzyme activity are being utilized to boost enzyme immobilization and functionality. Recently, bioengineering through gene cloning and expression in potential microorganisms, has revolutionized the biodegradation of bioplastics. This review aimed to discuss the most recent protein engineering strategies for modifying bioplastic-degrading enzymes in terms of stability and functionality, including enzyme thermostability enhancement, reinforcing the substrate binding to the enzyme active site, refining with other enzymes, and improvement of enzyme surface and substrate action. Additionally, discovered bioplastic-degrading exoenzymes by metagenomics techniques were emphasized.
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Affiliation(s)
- Farzad Rahmati
- Department of Microbiology, Faculty of Science, Qom Branch, Islamic Azad University (IAU), Qom 37185364, Iran
| | - Debadatta Sethi
- Sugarcane Research Station, Odisha University of Agriculture and Technology, Nayagarh, India
| | - Weixi Shu
- Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada
| | | | - Mohammad Mosaferi
- Health and Environment Research Center, Tabriz Health Services Management Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Allan Thomson
- Perennia Food and Agriculture Corporation., 173 Dr. Bernie MacDonald Dr., Bible Hill, Truro, NS, B6L 2H5, Canada
| | - G W Price
- Faculty of Agriculture, Dalhousie University, Truro, NS, B2N 5E3, Canada.
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2
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Zhang Y, Zhang W, Ma G, Nian B, Hu Y. Octadecyl and sulfonyl modification of diatomite synergistically improved the immobilization efficiency of lipase and its application in the synthesis of pine sterol esters. Biotechnol J 2024; 19:e2300615. [PMID: 38472086 DOI: 10.1002/biot.202300615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/19/2024] [Accepted: 01/22/2024] [Indexed: 03/14/2024]
Abstract
Phytosterols usually have to be esterified to various phytosterol esters to avoid their disadvantages of unsatisfactory solubility and low bioavailability. The enzymatic synthesis of phytosterol esters in a solvent-free system has advantages in terms of environmental friendliness, sustainability, and selectivity. However, the limitation of the low stability and recyclability of the lipase in the solvent-free system, which often requires a relatively high temperature to induce the viscosity, also increased the industrial production cost. In this context, a low-cost material, namely diatomite, was employed as the support in the immobilization of Candida rugosa lipase (CRL) due to its multiple modification sites. The Fe3 O4 was also then introduced to this system for quick and simple separation via the magnetic field. Moreover, to further enhance the immobilization efficiency of diatomite, a modification strategy which involved the octadecyl and sulfonyl group for regulating the hydrophobicity and interaction between the support and lipase was successfully developed. The optimization of the ratio of the modifiers suggested that the -SO3 H/C18 (1:1.5) performed best with an enzyme loading and enzyme activity of 84.8 mg·g-1 and 54 U·g-1 , respectively. Compared with free CRL, the thermal and storage stability of CRL@OSMD was significantly improved, which lays the foundation for the catalytic synthesis of phytosterol esters in solvent-free systems. Fortunately, a yield of 95.0% was achieved after optimizing the reaction conditions, and a yield of 70.0% can still be maintained after six cycles.
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Affiliation(s)
- Yifei Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, China
| | - Wei Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, China
| | - Guangzheng Ma
- State Key Laboratory of Materials-Oriented Chemical Engineering, School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, China
| | - Binbin Nian
- State Key Laboratory of Materials-Oriented Chemical Engineering, School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, China
| | - Yi Hu
- State Key Laboratory of Materials-Oriented Chemical Engineering, School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, China
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3
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Tournier V, Duquesne S, Guillamot F, Cramail H, Taton D, Marty A, André I. Enzymes' Power for Plastics Degradation. Chem Rev 2023; 123:5612-5701. [PMID: 36916764 DOI: 10.1021/acs.chemrev.2c00644] [Citation(s) in RCA: 56] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Plastics are everywhere in our modern way of living, and their production keeps increasing every year, causing major environmental concerns. Nowadays, the end-of-life management involves accumulation in landfills, incineration, and recycling to a lower extent. This ecological threat to the environment is inspiring alternative bio-based solutions for plastic waste treatment and recycling toward a circular economy. Over the past decade, considerable efforts have been made to degrade commodity plastics using biocatalytic approaches. Here, we provide a comprehensive review on the recent advances in enzyme-based biocatalysis and in the design of related biocatalytic processes to recycle or upcycle commodity plastics, including polyesters, polyamides, polyurethanes, and polyolefins. We also discuss scope and limitations, challenges, and opportunities of this field of research. An important message from this review is that polymer-assimilating enzymes are very likely part of the solution to reaching a circular plastic economy.
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Affiliation(s)
- Vincent Tournier
- Carbios, Parc Cataroux-Bâtiment B80, 8 rue de la Grolière, 63100 Clermont-Ferrand, France
| | - Sophie Duquesne
- Toulouse Biotechnology Institute, TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France, 135, avenue de Rangueil, F-31077 Toulouse Cedex 04, France
| | - Frédérique Guillamot
- Carbios, Parc Cataroux-Bâtiment B80, 8 rue de la Grolière, 63100 Clermont-Ferrand, France
| | - Henri Cramail
- Université Bordeaux, CNRS, Bordeaux INP, LCPO, 16 Avenue Pey-Berland, 33600 Pessac, France
| | - Daniel Taton
- Université Bordeaux, CNRS, Bordeaux INP, LCPO, 16 Avenue Pey-Berland, 33600 Pessac, France
| | - Alain Marty
- Carbios, Parc Cataroux-Bâtiment B80, 8 rue de la Grolière, 63100 Clermont-Ferrand, France
| | - Isabelle André
- Toulouse Biotechnology Institute, TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France, 135, avenue de Rangueil, F-31077 Toulouse Cedex 04, France
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4
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Shehata M, Ünlü A, Iglesias-Fernández J, Osuna S, Sezerman OU, Timucin E. Brave new surfactant world revisited by thermoalkalophilic lipases: computational insights into the role of SDS as a substrate analog. Phys Chem Chem Phys 2023; 25:2234-2247. [PMID: 36594810 DOI: 10.1039/d2cp05093e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Non-ionic surfactants were shown to stabilize the active conformation of thermoalkalophilic lipases by mimicking the lipid substrate while the catalytic interactions formed by anionic surfactants have not been well characterized. In this study, we combined μs-scale molecular dynamics (MD) simulations and lipase activity assays to analyze the effect of ionic surfactant, sodium dodecyl sulfate (SDS), on the structure and activity of thermoalkalophilic lipases. Both the open and closed lipase conformations that differ in geometry were recruited to the MD analysis to provide a broader understanding of the molecular effect of SDS on the lipase structure. Simulations at 298 K showed the potential of SDS for maintaining the active lipase through binding to the sn-1 acyl-chain binding pocket in the open conformation or transforming the closed conformation to an open-like state. Consistent with MD findings, experimental analysis showed increased lipase activity upon SDS incubation at ambient temperature. Notably, the lipase cores stayed intact throughout 2 μs regardless of an increase in the simulation temperature or SDS concentration. However, the surface structures were unfolded in the presence of SDS and at elevated temperature for both conformations. Simulations of the dimeric lipase were also carried out and showed reduced flexibility of the surface structures which were unfolded in the monomer, indicating the insulating role of dimer interactions against SDS. Taken together, this study provides insights into the possible substrate mimicry by the ionic surfactant SDS for the thermoalkalophilic lipases without temperature elevation, underscoring SDS's potential for interfacial activation at ambient temperatures.
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Affiliation(s)
- Mohamed Shehata
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem University, Istanbul 34752, Turkey.
| | - Aişe Ünlü
- Department of Chemistry, Gebze Technical University, Kocaeli, Turkey
| | | | - Sílvia Osuna
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Department de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, 17003 Girona, Spain.,ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - O Ugur Sezerman
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem University, Istanbul 34752, Turkey.
| | - Emel Timucin
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem University, Istanbul 34752, Turkey.
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Wang F, Yao Z, Zhang X, Han Z, Chu X, Ge X, Lu F, Liu Y. High-level production of xylose from agricultural wastes using GH11 endo-xylanase and GH43 β-xylosidase from Bacillus sp. Bioprocess Biosyst Eng 2022; 45:1705-1717. [PMID: 36063213 DOI: 10.1007/s00449-022-02778-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/23/2022] [Indexed: 11/24/2022]
Abstract
As a promising feedstock, alkali-extracted xylan from lignocellulosic biomass is desired for producing xylose, which can be used for renewable biofuels production. In this study, an efficient pathway has been established for low-cost and high-yield production of xylose by hydrolysis of alkali-extracted xylan from agricultural wastes using an endo-1,4-xylanase (XYLA) from Bacillus safensis TCCC 111022 and a β-xylosidase (XYLO) from B. pumilus TCCC 11573. The optimum activities of recombinant XYLA (rXYLA) and XYLO (rXYLO) were 60 ℃ and pH 8.0, and 30 ℃ and pH 7.0, respectively. They were stable over a broad pH range (pH 6.0-11.0 and 7.0-10.0). rXYLO showed a relatively high xylose tolerance up to 100 mM. Furthermore, the yield of xylose from wheat straw, rice straw, corn stover, corncob and sugarcane bagasse by rXYLA and rXYLO was 63.77%, 71.76%, 68.55%, 53.81%, and 58.58%, respectively. This study demonstrated a strategy to produce xylose from agricultural wastes by integrating alkali-extracted xylan and enzymatic hydrolysis.
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Affiliation(s)
- Fenghua Wang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, No.29, 13th Avenue, Tianjin Economic and Technological Development Area, Tianjin, 300457, People's Republic of China
| | - Zhiming Yao
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, No.29, 13th Avenue, Tianjin Economic and Technological Development Area, Tianjin, 300457, People's Republic of China
| | - Xue Zhang
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, No.29, 13th Avenue, Tianjin Economic and Technological Development Area, Tianjin, 300457, People's Republic of China
| | - Zhuoxuan Han
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, No.29, 13th Avenue, Tianjin Economic and Technological Development Area, Tianjin, 300457, People's Republic of China
| | - Xiuxiu Chu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, No.29, 13th Avenue, Tianjin Economic and Technological Development Area, Tianjin, 300457, People's Republic of China
| | - Xiuqi Ge
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, No.29, 13th Avenue, Tianjin Economic and Technological Development Area, Tianjin, 300457, People's Republic of China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, No.29, 13th Avenue, Tianjin Economic and Technological Development Area, Tianjin, 300457, People's Republic of China.
| | - Yihan Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, No.29, 13th Avenue, Tianjin Economic and Technological Development Area, Tianjin, 300457, People's Republic of China.
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6
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Carniel A, Waldow VDA, Castro AMD. A comprehensive and critical review on key elements to implement enzymatic PET depolymerization for recycling purposes. Biotechnol Adv 2021; 52:107811. [PMID: 34333090 DOI: 10.1016/j.biotechadv.2021.107811] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/15/2021] [Accepted: 07/26/2021] [Indexed: 11/25/2022]
Abstract
Plastics production and recycling chains must be refitted to a circular economy. Poly(ethylene terephthalate) (PET) is especially suitable for recycling because of its hydrolysable ester bonds and high environmental impact due to employment in single-use packaging, so that recycling processes utilizing enzymes are a promising biotechnological route to monomer recovery. However, enzymatic PET depolymerization still faces challenges to become a competitive route at an industrial level. In this review, PET characteristics as a substrate for enzymes are discussed, as well as the analytical methods used to evaluate the reaction progress. A comprehensive view on the biocatalysts used is discussed. Subsequently, different strategies pursued to improve enzymatic PET depolymerization are presented, including enzyme modification through mutagenesis, utilization of multiple enzymes, improvement of the interaction between enzymes and the hydrophobic surface of PET, and various reaction conditions (e.g., particle size, reaction medium, agitation, and additives). All scientific developments regarding these different aspects of PET depolymerization are crucial to offer a scalable and competitive technology. However, they must be integrated into global processes from upstream to downstream, discussed here at the final sections, which must be evaluated for their economic feasibility and life cycle assessment to check if PET recycling chains can be broadly incorporated into the future circular economy.
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Affiliation(s)
- Adriano Carniel
- School of Chemistry, Federal University of Rio de Janeiro (UFRJ) - Cidade Universitária, Rio de Janeiro, RJ CEP 21949-900, Brazil
| | - Vinicius de Abreu Waldow
- Petrobras Research, Development and Innovation Center (Cenpes), Av. Horácio Macedo, n° 950 - Cidade Universitária, Rio de Janeiro, RJ CEP 21941-915, Brazil
| | - Aline Machado de Castro
- Petrobras Research, Development and Innovation Center (Cenpes), Av. Horácio Macedo, n° 950 - Cidade Universitária, Rio de Janeiro, RJ CEP 21941-915, Brazil.
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7
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Li Y, Wei J, Yang H, Dai J, Ge X. Molecular dynamics investigation of the interaction between Colletotrichum capsici cutinase and berberine suggested a mechanism for reduced enzyme activity. PLoS One 2021; 16:e0247236. [PMID: 33606796 PMCID: PMC7894860 DOI: 10.1371/journal.pone.0247236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/03/2021] [Indexed: 11/19/2022] Open
Abstract
Berberine is a promising botanical pesticide against fungal plant pathogens. However, whether berberine inhibits the invasion of fungal pathogen across plant surface remains unclear. Here we demonstrated that the enzyme activities of purified cutinase from fungal pathogen Colletotrichum capsici were partially inhibited in presence of berberine toward different substrates. Molecular dynamics simulation results suggested the rigidity of cutinase was decreased with berberine added into the system. Interestingly, aggregations of berberine to the catalytic center of cutinase were observed, and stronger hydrophobic interactions were detected between key residue His 208 and berberine with concentrations of berberine increased. More importantly, this hydrophobic interaction conferred conformational change of the imidazole ring of His 208, which swung out of the catalytic center to an inactive mode. In summary, we provided the molecular mechanism of the effect of berberine on cutinase from C. capsici.
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Affiliation(s)
- Ying Li
- Beijing Key Laboratory of Biomass Waste Resource Utilization, College of Biochemical Engineering, Beijing Union University, Beijing, China
| | - Jinqing Wei
- Beijing Key Laboratory of Biomass Waste Resource Utilization, College of Biochemical Engineering, Beijing Union University, Beijing, China
| | - Huizhen Yang
- Beijing Key Laboratory of Biomass Waste Resource Utilization, College of Biochemical Engineering, Beijing Union University, Beijing, China
| | - Jing Dai
- Beijing Aerospace Petrochemical EC&EP Technology Co., Ltd, Beijing, China
| | - Xizhen Ge
- Beijing Key Laboratory of Biomass Waste Resource Utilization, College of Biochemical Engineering, Beijing Union University, Beijing, China
- * E-mail:
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8
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Oliva F, Flores-Canales JC, Pieraccini S, Morelli CF, Sironi M, Schiøtt B. Simulating Multiple Substrate-Binding Events by γ-Glutamyltransferase Using Accelerated Molecular Dynamics. J Phys Chem B 2020; 124:10104-10116. [PMID: 33112625 DOI: 10.1021/acs.jpcb.0c06907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
γ-Glutamyltransferase (GGT) is an enzyme that uses γ-glutamyl compounds as substrates and catalyzes their transfer to a water molecule or an acceptor substrate with varied physiological function in bacteria, plants, and animals. Crystal structures of GGT are known for different species and in different states of the chemical reaction; however, the structural dynamics of the substrate binding to the catalytic site of GGT are unknown. Here, we modeled Escherichia coli GGT's glutamine binding by using a swarm of accelerated molecular dynamics (aMD) simulations. Characterization of multiple binding events identified three structural binding motifs composed of polar residues in the binding pocket that govern glutamine binding into the active site. Simulated open and closed conformations of a lid-loop protecting the binding cavity suggest its role as a gating element by allowing or blocking substrates entry into the binding pocket. Partially open states of the lid-loop are accessible within thermal fluctuations, while the estimated free energy cost of a complete open state is 2.4 kcal/mol. Our results suggest that both specific electrostatic interactions and GGT conformational dynamics dictate the molecular recognition of substrate-GGT complexes.
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Affiliation(s)
- Francesco Oliva
- Dipartimento di Chimica, Università degli studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Jose C Flores-Canales
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus, Denmark
| | - Stefano Pieraccini
- Dipartimento di Chimica, Università degli studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Carlo F Morelli
- Dipartimento di Chimica, Università degli studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Maurizio Sironi
- Dipartimento di Chimica, Università degli studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Birgit Schiøtt
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus, Denmark
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Monica P, Kapoor M. Alkali-stable GH11 endo-β-1,4 xylanase (XynB) from Bacillus subtilis strain CAM 21: application in hydrolysis of agro-industrial wastes, fruit/vegetable peels and weeds. Prep Biochem Biotechnol 2020; 51:475-487. [PMID: 33043796 DOI: 10.1080/10826068.2020.1830416] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
GH11 endo-xylanases, due to their inherent structural and biochemical properties, are the key to efficient bioconversion of lignocellulosic biomass into value-added products. A GH11 endo-xylanase (XynB) from Bacillus subtilis strain CAM 21 was cloned, over-expressed and purified (Mw∼24 kDa) using Ni-NTA affinity chromatography. XynB showed optimum activity at pH 7.0 and 50°C and was stable (>88%) in a broad range of pH (4-11). The apparent Km, Kcat and Kcat/Km of XynB were 2.9 mg/ml, 1961.2/sec, and 675.62 ml/mg/sec, respectively using birchwood xylan as substrate. XynB was a classical endo-xylanase as it hydrolyzed birchwood xylan to xylo-oligosaccharides and not xylose. Kinetic stability of XynB at 45-53°C was between 43-182 min. Secondary structure analysis of XynB using far-UV CD spectroscopy revealed presence of 51.85% β strands and 2.64% α helix and was consistent with the homology modeling studies. XynB hydrolyzed the xylan extracted from agro-industrial wastes and fruit/vegetable peels by releasing up to 670 mg/g of reducing sugars. The xylan extracted from weeds (Ageratum conyzoides, Achyranthes aspera and Tridax procumbens) had characteristic signatures of hemicelluloses and after XynB hydrolysis showed cracks, peeling and release of up to 135.2 mg/g reducing sugars.
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Affiliation(s)
- P Monica
- Department of Protein Chemistry and Technology, CSIR-Central Food Technological Research Institute, Mysuru, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR - Human Resource Development Centre (CSIR-HRDC) Campus, Ghaziabad, India
| | - Mukesh Kapoor
- Department of Protein Chemistry and Technology, CSIR-Central Food Technological Research Institute, Mysuru, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR - Human Resource Development Centre (CSIR-HRDC) Campus, Ghaziabad, India
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10
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Alfaro-Chávez AL, Liu JW, Stevenson BJ, Goldman A, Ollis DL. Evolving a lipase for hydrolysis of natural triglycerides along with enhanced tolerance towards a protease and surfactants. Protein Eng Des Sel 2019; 32:129-143. [PMID: 31504920 DOI: 10.1093/protein/gzz023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 06/30/2019] [Accepted: 07/04/2019] [Indexed: 11/15/2022] Open
Abstract
In the accompanying paper, we described evolving a lipase to the point where variants were soluble, stable and capable of degrading C8 TAG and C8 esters. These variants were tested for their ability to survive in an environment that might be encountered in a washing machine. Unfortunately, they were inactivated both by treatment with a protease used in laundry detergents and by very low concentrations of sodium dodecyl sulfate (SDS). In addition, all the variants had very low levels of activity with triglycerides with long aliphatic chains and with naturally occurring oils, like olive oil. Directed evolution was used to select variants with enhanced properties. In the first 10 rounds of evolution, the primary screen was selected for variants capable of hydrolyzing olive oil whereas the secondary screen was selected for enhanced tolerance towards a protease and SDS. In the final six rounds of evolution, the primary and secondary screens identified variants that retained activity after treatment with SDS. Sixteen cycles of evolution gave variants with greatly enhanced lipolytic activity on substrates that had both long (C16 and C18) as well as short (C3 and C8) chains. We found variants that were stable for more than 3 hours in protease concentrations that rapidly degrade the wild-type enzyme. Enhanced tolerance towards SDS was found in variants that could break down naturally occurring lipid and resist protease attack. The amino acid changes that gave enhanced properties were concentrated in the cap domain responsible for substrate binding.
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Affiliation(s)
- Ana L Alfaro-Chávez
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Jian-Wei Liu
- CSIRO Land and Water, Black Mountain, Canberra, ACT 2601, Australia
| | - Bradley J Stevenson
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Adrian Goldman
- School of Biomedical Sciences, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.,Molecular and Integrative Biosciences Program, University of Helsinki, Helsinki FIN-0018, Finland
| | - David L Ollis
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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11
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Wahab HA, Amaro RE, Cournia Z. A Celebration of Women in Computational Chemistry. J Chem Inf Model 2019; 59:1683-1692. [DOI: 10.1021/acs.jcim.9b00368] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | - Rommie E. Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, 3234 Urey Hall, #0340, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Zoe Cournia
- Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece
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