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Rabbani G, Ahmad E, Ahmad A, Khan RH. Structural features, temperature adaptation and industrial applications of microbial lipases from psychrophilic, mesophilic and thermophilic origins. Int J Biol Macromol 2023; 225:822-839. [PMID: 36402388 DOI: 10.1016/j.ijbiomac.2022.11.146] [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: 06/10/2022] [Revised: 11/13/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022]
Abstract
Microbial lipases are very prominent biocatalysts because of their ability to catalyze a wide variety of reactions in aqueous and non-aqueous media. Here microbial lipases from different origins (psychrophiles, mesophiles, and thermophiles) have been reviewed. This review emphasizes an update of structural diversity in temperature adaptation and industrial applications, of psychrophilic, mesophilic, and thermophilic lipases. The microbial origins of lipases are logically dynamic, proficient, and also have an extensive range of industrial uses with the manufacturing of altered molecules. It is therefore of interest to understand the molecular mechanisms of adaptation to temperature in occurring lipases. However, lipases from extremophiles (psychrophiles, and thermophiles) are widely used to design biotransformation reactions with higher yields, fewer byproducts, or useful side products and have been predicted to catalyze those reactions also, which otherwise are not possible with the mesophilic lipases. Lipases as a multipurpose biological catalyst have given a favorable vision in meeting the needs of several industries such as biodiesel, foods, and drinks, leather, textile, detergents, pharmaceuticals, and medicals.
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Affiliation(s)
- Gulam Rabbani
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202 002, India; Department of Medical Biotechnology, Yeungnam University, 280 Daehak-ro, Gyeongsan, Gyeongbuk 38541, Republic of Korea.
| | - Ejaz Ahmad
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, United States of America
| | - Abrar Ahmad
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202 002, India.
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Li L, Lin X, Bao J, Xia H, Li F. Two Extracellular Poly(ε-caprolactone)-Degrading Enzymes From Pseudomonas hydrolytica sp. DSWY01T: Purification, Characterization, and Gene Analysis. Front Bioeng Biotechnol 2022; 10:835847. [PMID: 35372294 PMCID: PMC8971842 DOI: 10.3389/fbioe.2022.835847] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/02/2022] [Indexed: 11/17/2022] Open
Abstract
Poly(ε-caprolactone) (PCL) is an artificial polyester with commercially promising application. In this study, two novel PCL-degrading enzymes named PCLase I and PCLase II were purified to homogeneity from the culture supernatant of an effective polyester-degrading bacterium, Pseudomonas hydrolytica sp. DSWY01T. The molecular masses of PCLase I and PCLase II were determined to be 27.5 and 30.0 kDa, respectively. The optimum temperatures for the enzyme activities were 50 and 40°C, and the optimum pH values were 9.0 and 10.0, respectively. The two enzymes exhibited different physical and chemical properties, but both enzymes could degrade PCL substrates into monomers and oligomers. Weight loss detection and scanning electron microscopy revealed that PCLase I had more effective degradation ability than PCLase II. The genes of the two enzymes were cloned on the basis of the peptide fingerprint analysis results. The sequence analysis and substrate specificity analysis results showed that PCLase I and PCLase II were cutinase and lipase, respectively. Interface activation experiment also confirmed this conclusion. Structural analysis and modeling were further performed to obtain possible insights on the mechanism.
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Affiliation(s)
- Linying Li
- School of Life Sciences, Northeast Normal University, Changchun, China
- Engineering Research Center of Glycoconjugates, Ministry of Education, Changchun, China
| | - Xiumei Lin
- Changchun GeneScience Pharmaceutical Co., Ltd., Changchun, China
| | - Jianfeng Bao
- School of Life Sciences, Northeast Normal University, Changchun, China
| | - Hongmei Xia
- School of Life Sciences, Northeast Normal University, Changchun, China
- National Demonstration Center for Experimental Biology Education, Northeast Normal University, Changchun, China
| | - Fan Li
- School of Life Sciences, Northeast Normal University, Changchun, China
- Engineering Research Center of Glycoconjugates, Ministry of Education, Changchun, China
- *Correspondence: Fan Li,
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Ramos‐de‐la‐Peña AM, Aguilar O. High Pressure Processing of Lipase (
Thermomyces lanuginosus)
: Kinetics and Structure Assessment. EUR J LIPID SCI TECH 2019. [DOI: 10.1002/ejlt.201900289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ana Mayela Ramos‐de‐la‐Peña
- Tecnologico de Monterrey School of Engineering and Science, Av. Eugenio Garza Sada 2501 Sur Monterrey Nuevo Leon 64849 Mexico
| | - Oscar Aguilar
- Tecnologico de Monterrey School of Engineering and Science, Av. Eugenio Garza Sada 2501 Sur Monterrey Nuevo Leon 64849 Mexico
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Saravanan P, Dubey VK, Patra S. Emulating structural stability of Pseudomonas mendocina lipase: in silico mutagenesis and molecular dynamics studies. J Mol Model 2014; 20:2501. [DOI: 10.1007/s00894-014-2501-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 10/13/2014] [Indexed: 11/24/2022]
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Kold D, Dauter Z, Laustsen AK, Brzozowski AM, Turkenburg JP, Nielsen AD, Koldsø H, Petersen E, Schiøtt B, De Maria L, Wilson KS, Svendsen A, Wimmer R. Thermodynamic and structural investigation of the specific SDS binding of Humicola insolens cutinase. Protein Sci 2014; 23:1023-35. [PMID: 24832484 DOI: 10.1002/pro.2489] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 05/01/2014] [Accepted: 05/01/2014] [Indexed: 11/05/2022]
Abstract
The interaction of lipolytic enzymes with anionic surfactants is of great interest with respect to industrially produced detergents. Here, we report the interaction of cutinase from the thermophilic fungus Humicola insolens with the anionic surfactant SDS, and show the enzyme specifically binds a single SDS molecule under nondenaturing concentrations. Protein interaction with SDS was investigated by NMR, ITC and molecular dynamics simulations. The NMR resonances of the protein were assigned, with large stretches of the protein molecule not showing any detectable resonances. SDS is shown to specifically interact with the loops surrounding the catalytic triad with medium affinity (Ka ≈ 10(5) M(-1) ). The mode of binding is closely similar to that seen previously for binding of amphiphilic molecules and substrate analogues to cutinases, and hence SDS acts as a substrate mimic. In addition, the structure of the enzyme has been solved by X-ray crystallography in its apo form and after cocrystallization with diethyl p-nitrophenyl phosphate (DNPP) leading to a complex with monoethylphosphate (MEP) esterified to the catalytically active serine. The enzyme has the same fold as reported for other cutinases but, unexpectedly, esterification of the active site serine is accompanied by the ethylation of the active site histidine which flips out from its usual position in the triad.
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Affiliation(s)
- David Kold
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Sohngaardsholmsvej 49, DK-9000, Aalborg, Denmark
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Prabhakar PK, Rao KK, Balaji PV. The Cys78–Asn88 loop region of the Campylobacter jejuni CstII is essential for α2,3-sialyltransferase activity: analysis of the His85 mutants. ACTA ACUST UNITED AC 2014; 156:229-38. [DOI: 10.1093/jb/mvu033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Anobom CD, Pinheiro AS, De-Andrade RA, Aguieiras ECG, Andrade GC, Moura MV, Almeida RV, Freire DM. From structure to catalysis: recent developments in the biotechnological applications of lipases. BIOMED RESEARCH INTERNATIONAL 2014; 2014:684506. [PMID: 24783219 PMCID: PMC3982246 DOI: 10.1155/2014/684506] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Accepted: 02/17/2014] [Indexed: 12/23/2022]
Abstract
Microbial lipases are highly appreciated as biocatalysts due to their peculiar characteristics such as the ability to utilize a wide range of substrates, high activity and stability in organic solvents, and regio- and/or enantioselectivity. These enzymes are currently being applied in a variety of biotechnological processes, including detergent preparation, cosmetics and paper production, food processing, biodiesel and biopolymer synthesis, and the biocatalytic resolution of pharmaceutical derivatives, esters, and amino acids. However, in certain segments of industry, the use of lipases is still limited by their high cost. Thus, there is a great interest in obtaining low-cost, highly active, and stable lipases that can be applied in several different industrial branches. Currently, the design of specific enzymes for each type of process has been used as an important tool to address the limitations of natural enzymes. Nowadays, it is possible to "order" a "customized" enzyme that has ideal properties for the development of the desired bioprocess. This review aims to compile recent advances in the biotechnological application of lipases focusing on various methods of enzyme improvement, such as protein engineering (directed evolution and rational design), as well as the use of structural data for rational modification of lipases in order to create higher active and selective biocatalysts.
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Affiliation(s)
- Cristiane D. Anobom
- Departamento de Bioquímica, Universidade Federal do Rio de Janeiro, Avenida Athos da Silveira Ramos, 21941-909 Rio de Janeiro, RJ, Brazil
| | - Anderson S. Pinheiro
- Departamento de Bioquímica, Universidade Federal do Rio de Janeiro, Avenida Athos da Silveira Ramos, 21941-909 Rio de Janeiro, RJ, Brazil
| | - Rafael A. De-Andrade
- Departamento de Bioquímica, Universidade Federal do Rio de Janeiro, Avenida Athos da Silveira Ramos, 21941-909 Rio de Janeiro, RJ, Brazil
| | - Erika C. G. Aguieiras
- Departamento de Bioquímica, Universidade Federal do Rio de Janeiro, Avenida Athos da Silveira Ramos, 21941-909 Rio de Janeiro, RJ, Brazil
| | - Guilherme C. Andrade
- Departamento de Bioquímica, Universidade Federal do Rio de Janeiro, Avenida Athos da Silveira Ramos, 21941-909 Rio de Janeiro, RJ, Brazil
| | - Marcelo V. Moura
- Departamento de Bioquímica, Universidade Federal do Rio de Janeiro, Avenida Athos da Silveira Ramos, 21941-909 Rio de Janeiro, RJ, Brazil
| | - Rodrigo V. Almeida
- Departamento de Bioquímica, Universidade Federal do Rio de Janeiro, Avenida Athos da Silveira Ramos, 21941-909 Rio de Janeiro, RJ, Brazil
| | - Denise M. Freire
- Departamento de Bioquímica, Universidade Federal do Rio de Janeiro, Avenida Athos da Silveira Ramos, 21941-909 Rio de Janeiro, RJ, Brazil
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Improvement of thermostable aldehyde dehydrogenase by directed evolution for application in Synthetic Cascade Biomanufacturing. Enzyme Microb Technol 2013; 53:307-14. [PMID: 24034429 DOI: 10.1016/j.enzmictec.2013.07.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Revised: 07/06/2013] [Accepted: 07/08/2013] [Indexed: 11/22/2022]
Abstract
The aldehyde dehydrogenase from Thermoplasma acidophilum, which was previously implemented as a key enzyme in a synthetic cell-free reaction cascade for the production of alcohols, was optimized by directed evolution. Improvements have been made to enhance reaction velocity and solubility. Using a random approach followed by site-directed and saturation mutagenesis, three beneficial amino acid mutations were found after screening of ca. 20,000 variants. Mutation Y399C enhanced the protein solubility after recombinant expression in Escherichia coli 6-fold. Two further mutations, F34M and S405N, enhanced enzyme activity with the cofactor NAD(+) by a factor of eight. Impacts on enzyme stability and substrate specificity were negligible. Modeling of the enzyme structure did not reveal any direct interactions between the amino acid substitutions and residues of the active site or the enzyme's substrates. Thus, a directed evolution approach allowed for the generation of improved enzyme variants which were unlikely to be found by rational or semi-rational strategies.
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Côté A, Shareck F. Expression and characterization of a novel heterologous moderately thermostable lipase derived from metagenomics in Streptomyces lividans. J Ind Microbiol Biotechnol 2010; 37:883-91. [PMID: 20495942 DOI: 10.1007/s10295-010-0735-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Accepted: 04/28/2010] [Indexed: 10/19/2022]
Abstract
Seven lipolytic genes were isolated and sequenced from a metagenomic library that was constructed following biomass enrichment in a fed-batch bioreactor submitted to high temperature (50-70 degrees C) and alkaline pH (7-8.5). Among those sequences, lipIAF1-6 was chosen for further study and cloned in Streptomyces lividans 10-164. The G+C content within the sequence was 64.3%. The encoded protein, LipIAF1-6, was related to various putative lipases previously identified in different genome sequences. Homology of LipIAF-6 with the different lipases did not exceed 31%. The optimum pH (8.5) and temperature (60 degrees C) of the purified enzyme were in agreement with the enrichment conditions. Furthermore, the enzyme was thermostable for as long as 30 min at 70 degrees C. The maximum activity of the purified lipase was 4,287 IU/mg towards p-nitrophenyl (p-NP) butyrate (60 degrees C; pH 8.5). LipIAF1-6 does not seem to need the presence of metal ions for its activity. The enzyme was slightly inhibited by 10 mM CoCl2 (14%), HgCl2 (12%), and dithiothreitol (DTT) (15%). The serine protease inhibitor phenylmethylsulphonyl fluoride (PMSF) reduced activity by 39% and 71% when incubated at concentrations of 1 and 10 mM, respectively. Finally, LipIAF1-6 was stable in different organic solvents, and against several surfactants and oxidative agents commonly found in detergent formulations. These results are quite encouraging for further use of this enzyme in different industrial processes.
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Affiliation(s)
- Amélie Côté
- INRS-Institut Armand-Frappier, 531 boul. des Prairies, Laval, QC H7V1B7, Canada
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Ranaldi S, Belle V, Woudstra M, Bourgeas R, Guigliarelli B, Roche P, Vezin H, Carrière F, Fournel A. Amplitude of Pancreatic Lipase Lid Opening in Solution and Identification of Spin Label Conformational Subensembles by Combining Continuous Wave and Pulsed EPR Spectroscopy and Molecular Dynamics. Biochemistry 2010; 49:2140-9. [DOI: 10.1021/bi901918f] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sebastien Ranaldi
- CNRS Laboratoire de Bioénergétique et Ingénierie des Protéines, UPR 9036
| | - Valérie Belle
- CNRS Laboratoire de Bioénergétique et Ingénierie des Protéines, UPR 9036
| | - Mireille Woudstra
- CNRS Laboratoire de Bioénergétique et Ingénierie des Protéines, UPR 9036
| | - Raphael Bourgeas
- CNRS Laboratoire Interactions et Modulateurs de Réponses, FRE3083
| | - Bruno Guigliarelli
- CNRS Laboratoire de Bioénergétique et Ingénierie des Protéines, UPR 9036
| | - Philippe Roche
- CNRS Laboratoire Interactions et Modulateurs de Réponses, FRE3083
| | - Hervé Vezin
- CNRS Laboratoire de Chimie Organique et Macromoléculaire, UMR 8009, Villeneuve d'Ascq, France
| | - Fredéric Carrière
- CNRS Laboratoire d’Enzymologie Interfaciale et de Physiologie de la Lipolyse, UPR 9025
| | - André Fournel
- CNRS Laboratoire de Bioénergétique et Ingénierie des Protéines, UPR 9036
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Hiraga K, Soga I, Dansereau JT, Pereira B, Derbyshire V, Du Z, Wang C, Van Roey P, Belfort G, Belfort M. Selection and structure of hyperactive inteins: peripheral changes relayed to the catalytic center. J Mol Biol 2009; 393:1106-17. [PMID: 19744499 DOI: 10.1016/j.jmb.2009.08.074] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Revised: 08/27/2009] [Accepted: 08/31/2009] [Indexed: 02/05/2023]
Abstract
Inteins are phylogenetically diverse self-splicing proteins that are of great functional, evolutionary, biotechnological, and medical interest. To address the relationship between intein structure and function, particularly with respect to regulating the splicing reaction, and to groom inteins for application, we developed a phage display system to extend current in vivo selection for enhanced intein function to selection in vitro. We thereby isolated inteins that can function under excursions in temperature, pH, and denaturing environment. Remarkably, most mutations mapped to the surface of the intein, remote from the active site. We chose two mutants with enhanced splicing activity for crystallography, one of which was also subjected to NMR analysis. These studies define a "ripple effect", whereby mutations in peripheral non-catalytic residues can cause subtle allosteric changes in the active-site environment in a way that facilitates intein activity. Altered salt-bridge formation and chemical shift changes of the mutant inteins provide a molecular rationale for their phenotypes. These fundamental insights will advance the utility of inteins in chemical biology, biotechnology, and medicine.
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Affiliation(s)
- Kaori Hiraga
- Wadsworth Center, New York State Department of Health, 150 New Scotland Avenue, Albany, NY 12208, USA
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Kamerzell TJ, Russell Middaugh C. The Complex Inter-Relationships Between Protein Flexibility and Stability. J Pharm Sci 2008; 97:3494-517. [DOI: 10.1002/jps.21269] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Cavity-creating mutations in Pseudomonas aeruginosa azurin: effects on protein dynamics and stability. Biophys J 2008; 95:771-81. [PMID: 18424505 DOI: 10.1529/biophysj.107.128009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Changes in flexibility and structural stability of Pseudomonas aeruginosa azurin in response to cavity-creating mutations were probed by the phosphorescence emission of Trp-48, which was deeply buried in the compact hydrophobic core of the macromolecule, and by measurements of guanidinum hydrochloride unfolding, respectively. Replacement of the bulky side chains Phe-110, Phe-29, and Tyr-108 with the smaller Ala introduced cavities at different distances from the hydrophobic core. The phosphorescence lifetime (tau(0)) of Trp-48, buried inside the protein core, and the acrylamide quenching rate constant (k(q)) were used to monitor local and global flexibility changes induced by the introduction of the cavity. The results of this work demonstrate the following: 1), the effect on core flexibility of the insertion of cavities is not correlated readily to the distance of the cavity from the core; 2), the protein global flexibility results are related to the cavity distance from the packed core of the macromolecule; and 3), the increase in protein flexibility does not correspond necessarily to a comparable destabilizing effect of some mutations.
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