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Ng YK, Ikeno S, Kadhim Almansoori AK, Muhammad I, Abdul Rahim R. Characterization of Sphingobacterium sp. Ab3 Lipase and Its Coexpression with LEA Peptides. Microbiol Spectr 2022; 10:e0142221. [PMID: 36314920 PMCID: PMC9769720 DOI: 10.1128/spectrum.01422-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 09/23/2022] [Indexed: 12/24/2022] Open
Abstract
Sphingobacterium sp. is a yellowish Gram-negative bacterium that is usually characterized by high concentrations of sphingophospholipids as lipid components. As microbial enzymes have been in high demand in industrial fields in the past few decades, this study hopes to provide significant information on lipase activities of Sphingobacterium sp., since limited studies have been conducted on the Sphingobacterium sp. lipase. A microbe from one collected Artic soil sample, ARC4, was identified as psychrotolerant Sphingobacterium sp., and it could grow in temperatures ranging from 0°C to 24°C. The expression of Sphingobacterium sp. lipase was successfully performed through an efficient approach of utilizing mutated group 3 late embryogenesis abundant (G3LEA) proteins developed from Polypedilum vanderplanki. Purified enzyme was characterized using a few parameters, such as temperature, pH, metal ion cofactors, organic solvents, and detergents. The expressed enzyme is reported to be cold adapted and has the capability to work efficiently under neutral pH (pH 5.0 to 7.0), cofactors like Na+ ion, and the water-like solvent methanol. Addition of nonionic detergents greatly enhanced the activity of purified enzyme. IMPORTANCE The mechanism of action of LEA proteins has remained unknown to many; in this study we reveal their presence and improved protein expression due to the molecular shielding effect reported by others. This paper should be regarded as a useful example of using such proteins to influence an existing expression system to produce difficult-to-express proteins.
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Affiliation(s)
- You Kiat Ng
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Shinya Ikeno
- Department of Biological Functions and Engineering, Graduate School of Life Science and System Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
| | | | - Ibrahim Muhammad
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
- Department of Science Lab. Technology, Ramat Polytechnic Maiduguri, Maiduguri, Nigeria
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Esakkiraj P, Bharathi C, Ayyanna R, Jha N, Panigrahi A, Karthe P, Arul V. Functional and molecular characterization of a cold-active lipase from Psychrobacter celer PU3 with potential a*ntibiofilm property. Int J Biol Macromol 2022; 211:741-753. [PMID: 35504418 DOI: 10.1016/j.ijbiomac.2022.04.174] [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: 01/07/2022] [Revised: 04/07/2022] [Accepted: 04/24/2022] [Indexed: 11/05/2022]
Abstract
The lipase gene from Psychrobacter celer PU3 was cloned into pET-28a(+) expression vector and overexpressed in E. coli BL21 (DE3) pLysS cells. The purified Psychrobacter celer lipase (PCL) was characterized as an alkaline active enzyme and has a molecular mass of around 30 kDa. The PCL was active even at a low temperature and the optimum range was observed between 10 and 40 °C temperatures. MALDI-TOF and phylogenetic analysis ensued that Psychrobacter celer PU3 lipase (PCL) was closely related to P. aureginosa lipase (PAL). MD simulation results suggests that temperature change did not affect overall structure of PCL, but it may alter temperature- dependent PCL structural changes. R1 (129-135 AA) and R2 (187-191 AA) regions could be important for temperature-dependent PCL function as they fluctuate much at 35 °C temperature. PMSF completely inhibited PCL lipase activity and it demonstrates the presence of serine residues in the active site of PCL. PCL is moderately halophilic and most of the tested organic solvents found to be inhibiting the lipase activity except the solvents ethanol and methanol. PCL activity was increased with surfactants (SDS and CTAB) and bleaching agents (hydrogen peroxide). The effect of different metal ions on PCL resulted that only mercuric chloride was found as the enhancer of the lipase activity. Antibiofilm property of PCL was evaluated against pathogenic Vibrio parahaemolyticus isolated from the diseased shrimp and MIC value was 500 U. PCL significantly altered the morphology and biofilm density of V. parahaemolyticus and the same was observed through scanning electron microscope (SEM) and confocal laser scanning microscope (CLSM) imaging. RT-PCR analysis revealed that the mRNA expression level of biofilm, colony morphology and major toxin-related (aphA, luxS, opaR, tolC, toxR) genes of V. parahaemolyticus were significantly downregulated with PCL treatment.
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Affiliation(s)
- Palanichamy Esakkiraj
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry 605014, India; Crustacean Culture Division, ICAR-Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, R. A. Puram, Chennai 600 028, India
| | - Christian Bharathi
- CAS in Crystallography and Biophysics, University of Madras, Chennai 600025, India
| | - Repally Ayyanna
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Natwar Jha
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Akshaya Panigrahi
- Crustacean Culture Division, ICAR-Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, R. A. Puram, Chennai 600 028, India
| | - Ponnuraj Karthe
- CAS in Crystallography and Biophysics, University of Madras, Chennai 600025, India
| | - Venkatesan Arul
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Puducherry 605014, India.
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Engineering of Thermal Stability in a Cold-Active Oligo-1,6-Glucosidase from Exiguobacterium sibiricum with Unusual Amino Acid Content. Biomolecules 2021; 11:biom11081229. [PMID: 34439895 PMCID: PMC8392543 DOI: 10.3390/biom11081229] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/02/2021] [Accepted: 08/12/2021] [Indexed: 11/30/2022] Open
Abstract
A gene coding for a novel putative amylase, oligo-1,6-glucosidase from a psychrotrophic bacterium Exiguobacterium sibiricum from Siberian permafrost soil was cloned and expressed in Escherichia coli. The amino acid sequence of the predicted protein EsOgl and its 3D model displayed several features characteristic for the cold-active enzymes while possessing an unusually high number of proline residues in the loops—a typical feature of thermophilic enzymes. The activity of the purified recombinant protein was tested with p-nitrophenyl α-D-glucopyranoside as a substrate. The enzyme displayed a plateau-shaped temperature-activity profile with the optimum at 25 °C and a pronounced activity at low temperatures (50% of maximum activity at 5 °C). To improve the thermal stability at temperatures above 40 °C, we have introduced proline residues into four positions of EsOgl by site-directed mutagenesis according to “the proline rule”. Two of the mutants, S130P and A109P demonstrated a three- and two-fold increased half-life at 45 °C. Moreover, S130P mutation led to a 60% increase in the catalytic rate constant. Combining the mutations resulted in a further increase in stability transforming the temperature-activity profile to a typical mesophilic pattern. In the most thermostable variant A109P/S130P/E176P, the half-life at 45 °C was increased from 11 min (wild-type) to 129 min.
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Characterization of Two Unique Cold-Active Lipases Derived from a Novel Deep-Sea Cold Seep Bacterium. Microorganisms 2021; 9:microorganisms9040802. [PMID: 33920298 PMCID: PMC8069351 DOI: 10.3390/microorganisms9040802] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 03/30/2021] [Accepted: 04/09/2021] [Indexed: 11/29/2022] Open
Abstract
The deep ocean microbiota has unexplored potential to provide enzymes with unique characteristics. In order to obtain cold-active lipases, bacterial strains isolated from the sediment of the deep-sea cold seep were screened, and a novel strain gcc21 exhibited a high lipase catalytic activity, even at the low temperature of 4 °C. The strain gcc21 was identified and proposed to represent a new species of Pseudomonas according to its physiological, biochemical, and genomic characteristics; it was named Pseudomonas marinensis. Two novel encoding genes for cold-active lipases (Lipase 1 and Lipase 2) were identified in the genome of strain gcc21. Genes encoding Lipase 1 and Lipase 2 were respectively cloned and overexpressed in E. coli cells, and corresponding lipases were further purified and characterized. Both Lipase 1 and Lipase 2 showed an optimal catalytic temperature at 4 °C, which is much lower than those of most reported cold-active lipases, but the activity and stability of Lipase 2 were much higher than those of Lipase 1 under different tested pHs and temperatures. In addition, Lipase 2 was more stable than Lipase 1 when treated with different metal ions, detergents, potential inhibitors, and organic solvents. In a combination of mutation and activity assays, catalytic triads of Ser, Asp, and His in Lipase 1 and Lipase 2 were demonstrated to be essential for maintaining enzyme activity. Phylogenetic analysis showed that both Lipase 1 and Lipase 2 belonged to lipase family III. Overall, our results indicate that deep-sea cold seep is a rich source for novel bacterial species that produce potentially unique cold-active enzymes.
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Cold Active Lipases: Biocatalytic Tools for Greener Technology. Appl Biochem Biotechnol 2021; 193:2245-2266. [PMID: 33544363 DOI: 10.1007/s12010-021-03516-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/27/2021] [Indexed: 02/06/2023]
Abstract
Lipases are enzymes that catalyze the ester bond hydrolysis in triglycerides with the release of fatty acids, mono- and diglycerides, and glycerol. The microbial lipases account for $400 million market size in 2017 and it is expected to reach $590 million by 2023. Many biotechnological processes are expedited at high temperatures and hence much research is dealt with thermostable enzymes. Cold active lipases are now gaining importance in the detergent, synthesis of chiral intermediates and frail/fragile compounds, and food and pharmaceutical industries. In addition, they consume less energy since they are active at low temperatures. These cold active lipases have not been commercially exploited so far compared to mesophilic and thermophilc lipases. Cold active lipases are distributed in microbes found at low temperatures. Only a few microbes were studied for the production of these enzymes. These cold-adapted enzymes show increased flexibility of their structures in response to freezing effect of the cold habitats. This review presents an update on cold-active lipases from microbial sources along with some structural features justifying high enzyme activity at low temperature. In addition, recent achievements on their use in various industries will also be discussed.
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Boyko KM, Kryukova MV, Petrovskaya LE, Kryukova EA, Nikolaeva AY, Korzhenevsky DA, Lomakina GY, Novototskaya-Vlasova KA, Rivkina EM, Dolgikh DA, Kirpichnikov MP, Popov VO. Structural and Biochemical Characterization of a Cold-Active PMGL3 Esterase with Unusual Oligomeric Structure. Biomolecules 2021; 11:biom11010057. [PMID: 33466452 PMCID: PMC7824956 DOI: 10.3390/biom11010057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/30/2020] [Accepted: 01/03/2021] [Indexed: 11/23/2022] Open
Abstract
The gene coding for a novel cold-active esterase PMGL3 was previously obtained from a Siberian permafrost metagenomic DNA library and expressed in Escherichia coli. We elucidated the 3D structure of the enzyme which belongs to the hormone-sensitive lipase (HSL) family. Similar to other bacterial HSLs, PMGL3 shares a canonical α/β hydrolase fold and is presumably a dimer in solution but, in addition to the dimer, it forms a tetrameric structure in a crystal and upon prolonged incubation at 4 °C. Detailed analysis demonstrated that the crystal tetramer of PMGL3 has a unique architecture compared to other known tetramers of the bacterial HSLs. To study the role of the specific residues comprising the tetramerization interface of PMGL3, several mutant variants were constructed. Size exclusion chromatography (SEC) analysis of D7N, E47Q, and K67A mutants demonstrated that they still contained a portion of tetrameric form after heat treatment, although its amount was significantly lower in D7N and K67A compared to the wild type. Moreover, the D7N and K67A mutants demonstrated a 40 and 60% increase in the half-life at 40 °C in comparison with the wild type protein. Km values of these mutants were similar to that of the wt PMGL3. However, the catalytic constants of the E47Q and K67A mutants were reduced by ~40%.
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Affiliation(s)
- Konstantin M. Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia;
- Correspondence: (K.M.B.); (L.E.P.)
| | - Mariya V. Kryukova
- Kurchatov Complex of NBICS-Technologies, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia; (M.V.K.); (A.Y.N.); (D.A.K.)
| | - Lada E. Petrovskaya
- Department of Bioengineering, Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (E.A.K.); (D.A.D.); (M.P.K.)
- Correspondence: (K.M.B.); (L.E.P.)
| | - Elena A. Kryukova
- Department of Bioengineering, Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (E.A.K.); (D.A.D.); (M.P.K.)
| | - Alena Y. Nikolaeva
- Kurchatov Complex of NBICS-Technologies, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia; (M.V.K.); (A.Y.N.); (D.A.K.)
| | - Dmitry A. Korzhenevsky
- Kurchatov Complex of NBICS-Technologies, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia; (M.V.K.); (A.Y.N.); (D.A.K.)
| | - Galina Yu. Lomakina
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia;
- Department of Fundamental Sciences, Bauman Moscow State Technical University, 105005 Moscow, Russia
| | - Ksenia A. Novototskaya-Vlasova
- Laboratory of Soil Cryology, Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, 142290 Pushchino, Russia; (K.A.N.-V.); (E.M.R.)
| | - Elizaveta M. Rivkina
- Laboratory of Soil Cryology, Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, 142290 Pushchino, Russia; (K.A.N.-V.); (E.M.R.)
| | - Dmitry A. Dolgikh
- Department of Bioengineering, Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (E.A.K.); (D.A.D.); (M.P.K.)
- Department of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Mikhail P. Kirpichnikov
- Department of Bioengineering, Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (E.A.K.); (D.A.D.); (M.P.K.)
- Department of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Vladimir O. Popov
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia;
- Kurchatov Complex of NBICS-Technologies, National Research Centre “Kurchatov Institute”, 123182 Moscow, Russia; (M.V.K.); (A.Y.N.); (D.A.K.)
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7
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Kryukova MV, Petrovskaya LE, Novototskaya-Vlasova KA, Kryukova EA, Yakimov SA, Nikolaeva AY, Boyko KM, Dolgikh DA, Kirpichnikov MP. Effect of Cysteine Residue Substitution in the GCSAG Motif of the PMGL2 Esterase Active Site on the Enzyme Properties. BIOCHEMISTRY (MOSCOW) 2021; 85:709-716. [PMID: 32586234 DOI: 10.1134/s0006297920060085] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The gene coding for PMGL2 esterase, which belongs to the family of mammalian hormone-sensitive lipases (HSLs), was discovered by screening a metagenomic DNA library from a permafrost soil. The active site of PMGL2 contains conserved GXSXG motif which includes Cys173 residue next to the catalytic Ser174. In order to clarify the functional role of the cysteine residue in the GCSAG motif, we constructed a number of PMGL2 mutants with Cys173 substitutions and studied their properties. The specific activity of the C173D mutant exceeded the specific activity of the wild-type enzyme (wtPMGL2) by 60%, while the C173T/C202S mutant displayed reduced catalytic activity. The activity of the C173D mutant with p-nitrophenyl octanoate was 15% higher, while the activity of the C173T/C202S mutant was 17% lower compared to wtPMGL2. The C173D mutant was also characterized by a high activity at low temperatures (20-35°C) and significant loss of thermal stability. The kcat value for this protein was 56% higher than for the wild-type enzyme. The catalytic constants of the C173S mutant were close to those of wtPMGL2; this enzyme also demonstrated the highest thermal stability among the studied mutants. The obtained results demonstrate that substitutions of amino acid residues adjacent to the catalytic serine residue in the GXSXG motif can have a significant effect on the properties of PMGL2 esterase.
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Affiliation(s)
- M V Kryukova
- Kurchatov NBICS-Technologies Complex, Kurchatov Institute National Research Centre, Moscow, 123182, Russia
| | - L E Petrovskaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - K A Novototskaya-Vlasova
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - E A Kryukova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - S A Yakimov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - A Y Nikolaeva
- Kurchatov NBICS-Technologies Complex, Kurchatov Institute National Research Centre, Moscow, 123182, Russia
| | - K M Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, 119071, Russia
| | - D A Dolgikh
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.,Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
| | - M P Kirpichnikov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.,Lomonosov Moscow State University, Faculty of Biology, Moscow, 119234, Russia
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Boyko KM, Kryukova MV, Petrovskaya LE, Nikolaeva AY, Korzhenevsky DA, Novototskaya-Vlasova KA, Rivkina EM, Dolgikh DA, Kirpichnikov MP, Popov VO. Crystal structure of PMGL2 esterase from the hormone-sensitive lipase family with GCSAG motif around the catalytic serine. PLoS One 2020; 15:e0226838. [PMID: 31990908 PMCID: PMC6986724 DOI: 10.1371/journal.pone.0226838] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 12/05/2019] [Indexed: 12/26/2022] Open
Abstract
Lipases comprise a large class of hydrolytic enzymes which catalyze the cleavage of the ester bonds in triacylglycerols and find numerous biotechnological applications. Previously, we have cloned the gene coding for a novel esterase PMGL2 from a Siberian permafrost metagenomic DNA library. We have determined the 3D structure of PMGL2 which belongs to the hormone-sensitive lipase (HSL) family and contains a new variant of the active site motif, GCSAG. Similar to many other HSLs, PMGL2 forms dimers in solution and in the crystal. Our results demonstrated that PMGL2 and structurally characterized members of the GTSAG motif subfamily possess a common dimerization interface that significantly differs from that of members of the GDSAG subfamily of known structure. Moreover, PMGL2 had a unique organization of the active site cavity with significantly different topology compared to the other lipolytic enzymes from the HSL family with known structure including the distinct orientation of the active site entrances within the dimer and about four times larger size of the active site cavity. To study the role of the cysteine residue in GCSAG motif of PMGL2, the catalytic properties and structure of its double C173T/C202S mutant were examined and found to be very similar to the wild type protein. The presence of the bound PEG molecule in the active site of the mutant form allowed for precise mapping of the amino acid residues forming the substrate cavity.
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Affiliation(s)
- Konstantin M. Boyko
- Department of Enzyme Engineering, Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Marya V. Kryukova
- Kurchatov Complex of NBICS-technologies, National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Lada E. Petrovskaya
- Department of Bioengineering, Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alena Y. Nikolaeva
- Kurchatov Complex of NBICS-technologies, National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Dmitry A. Korzhenevsky
- Kurchatov Complex of NBICS-technologies, National Research Centre "Kurchatov Institute", Moscow, Russia
| | - Ksenia A. Novototskaya-Vlasova
- Laboratory of Soil Cryology, Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Elizaveta M. Rivkina
- Laboratory of Soil Cryology, Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
| | - Dmitry A. Dolgikh
- Department of Bioengineering, Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Department of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail P. Kirpichnikov
- Department of Bioengineering, Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Department of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Vladimir O. Popov
- Department of Enzyme Engineering, Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- Kurchatov Complex of NBICS-technologies, National Research Centre "Kurchatov Institute", Moscow, Russia
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Zhang H, Xia Y, Zhou M, Zheng J, Wang Z, Zhang Y. Purification and characterization of a thermoalkaliphilic esterase from Bacillus cereus WZZ006 for enantioselective resolution of indoxacarb intermediate. Int J Biol Macromol 2019; 140:358-367. [PMID: 31430490 DOI: 10.1016/j.ijbiomac.2019.08.140] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/15/2019] [Accepted: 08/16/2019] [Indexed: 01/11/2023]
Abstract
An intracellular esterase (BCE) from Bacillus cereus WZZ006 was purified to homogeneity with an 89.5-fold purification, specific activity of 1.79 U/mg, and 26.7% recovery. The estimated molecular weight of BCE was 96 kDa which was analyzed by SDS-PAGE and MALDI-TOF-MS. Activity staining denotes that BCE has an unexplored new carboxyl esterase characteristic. BCE enzyme activity was maximum at pH 8.5 and also at 50 °C with pNP-caproate as a substrate. This indicates that the studied BCE as a thermoalkaliphilic esterase. The kinetic properties like Km, Vmax, kcat and kcat/Km value for BCE was found to be 0.98 mM, 0.03 mM/min, 69.47 min-1 and 70.89 mM-1 min-1, respectively. Synthesis of (S)-5-chloro-1-oxo-2,3-dihydro-2-hydroxy-1H-indole-2-carboxylic acid methyl ester ((S)-CODHCM) by BCE can be shortened to 3 h compared to 36 h with whole-cell catalysis. The e.e.s achieved was 93.83%, and conversion around 52.78% with E being 39.95. These features render BCE as a promising biocatalyst for the synthesis of a key chiral intermediate for indoxacarb.
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Affiliation(s)
- Hongyun Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
| | - Ying Xia
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
| | - Mingpeng Zhou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
| | - Jianyong Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
| | - Zhao Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China
| | - Yinjun Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
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Draft Genome Sequence of Microbacterium sp. Gd 4-13, Isolated from Gydanskiy Peninsula Permafrost Sediments of Marine Origin. Microbiol Resour Announc 2019; 8:8/40/e00889-19. [PMID: 31582456 PMCID: PMC6776773 DOI: 10.1128/mra.00889-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Here, we report the draft genome sequence of Microbacterium sp. strain Gd 4-13, isolated from late Pleistocene permafrost of marine origin located on the Gydanskiy Peninsula. Genome sequence analysis was performed to understand strain survivability mechanisms under permafrost conditions and to expand biotechnology applications. Here, we report the draft genome sequence of Microbacterium sp. strain Gd 4-13, isolated from late Pleistocene permafrost of marine origin located on the Gydanskiy Peninsula. Genome sequence analysis was performed to understand strain survivability mechanisms under permafrost conditions and to expand biotechnology applications.
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Li T, Zhang W, Hao J, Sun M, Lin SX. Cold-active extracellular lipase: Expression in Sf9 insect cells, purification, and catalysis. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2019; 21:e00295. [PMID: 30568889 PMCID: PMC6290134 DOI: 10.1016/j.btre.2018.e00295] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 11/26/2018] [Accepted: 11/26/2018] [Indexed: 11/19/2022]
Abstract
Cold-active lipases are gaining special attention nowadays as they are increasingly used in various industries such as fine chemical synthesis, food processing, and washer detergent. In the present study, an extracellular lipase gene from Yarrowia lipolytica (LIPY8) was cloned and expressed by baculovirus expression system. The recombinant lipase (LipY8p) was purified using chromatographic techniques, resulting in a purification factor of 25.7-fold with a specific activity of 1102.9U/mg toward olive oil. The apparent molecular mass of purified LipY8p was 40 kDa. The enzyme was most active at pH 7.5 and 17 °C. It exhibited maximum activity toward medium chain (C10) esters. The presence of transition metals such as Zn2+, Cu2+, and Ni2+ strongly inhibited the enzyme activity, which was enhanced by EDTA. The lipase activity was affected by detergents and was elevated by various organic solvents at 10% (v/v). These enzymatic properties make this lipase of considerable potential for biotechnological applications.
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Key Words
- Baculovirus expression system
- C12E8, octaethylene glycol monododecyl ether
- Cold-active
- DMF, Dimethylformamide
- Extracellular lipase
- PH, polyhedrin
- Purification
- RhB, rhodamine B
- RhB-OOe, RhB-olive oil
- Yarrowia lipolytica
- pNPA, p-nitro phenyl acetate
- pNPB, p-nitro phenyl butyrate
- pNPD, p-nitro phenyl decanoate
- pNPL, p-nitro phenyl dodecanoate
- pNPM, p-nitro phenyl myristate
- pNPP, p-nitro phenyl palmitate
- β-DDM, n-Dodecyl-β-d-Maltoside
- β-ME, β-mercaptoethanol
- β-OG, n-octyl-β-d-glucoside
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Affiliation(s)
- Tang Li
- Molecular Endocrinology and Nephrology, Axe CHU Research Center and Department of Molecular Medicine, Laval University, 2705 boulevard Laurier, Québec, G1V 4G2, Canada
| | - Wenfa Zhang
- Molecular Endocrinology and Nephrology, Axe CHU Research Center and Department of Molecular Medicine, Laval University, 2705 boulevard Laurier, Québec, G1V 4G2, Canada
| | - Jianhua Hao
- Laboratory of Sustainable Development of Polar Fishery, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao 266071, China
| | - Mi Sun
- Laboratory of Sustainable Development of Polar Fishery, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 106 Nanjing Road, Qingdao 266071, China
| | - Sheng-Xiang Lin
- Molecular Endocrinology and Nephrology, Axe CHU Research Center and Department of Molecular Medicine, Laval University, 2705 boulevard Laurier, Québec, G1V 4G2, Canada
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12
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Latip W, Raja Abd Rahman RNZ, Leow ATC, Mohd Shariff F, Kamarudin NHA, Mohamad Ali MS. The Effect of N-Terminal Domain Removal towards the Biochemical and Structural Features of a Thermotolerant Lipase from an Antarctic Pseudomonas sp. Strain AMS3. Int J Mol Sci 2018; 19:ijms19020560. [PMID: 29438291 PMCID: PMC5855782 DOI: 10.3390/ijms19020560] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 12/04/2017] [Accepted: 12/12/2017] [Indexed: 12/28/2022] Open
Abstract
Lipase plays an important role in industrial and biotechnological applications. Lipases have been subject to modification at the N and C terminals, allowing better understanding of lipase stability and the discovery of novel properties. A thermotolerant lipase has been isolated from Antarctic Pseudomonas sp. The purified Antarctic AMS3 lipase (native) was found to be stable across a broad range of temperatures and pH levels. The lipase has a partial Glutathione-S-transferase type C (GST-C) domain at the N-terminal not found in other lipases. To understand the influence of N-terminal GST-C domain on the biochemical and structural features of the native lipase, the deletion of the GST-C domain was carried out. The truncated protein was successfully expressed in E. coli BL21(DE3). The molecular weight of truncated AMS3 lipase was approximately ~45 kDa. The number of truncated AMS3 lipase purification folds was higher than native lipase. Various mono and divalent metal ions increased the activity of the AMS3 lipase. The truncated AMS3 lipase demonstrated a similarly broad temperature range, with the pH profile exhibiting higher activity under alkaline conditions. The purified lipase showed a substrate preference for a long carbon chain substrate. In addition, the enzyme activity in organic solvents was enhanced, especially for toluene, Dimethylsulfoxide (DMSO), chloroform and xylene. Molecular simulation revealed that the truncated lipase had increased structural compactness and rigidity as compared to native lipase. Removal of the N terminal GST-C generally improved the lipase biochemical characteristics. This enzyme may be utilized for industrial purposes.
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Affiliation(s)
- Wahhida Latip
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Center, Department of Microbiology, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
| | - Adam Thean Chor Leow
- Enzyme and Microbial Technology Research Center, Department of Cell and Molecular Biology, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
| | - Fairolniza Mohd Shariff
- Enzyme and Microbial Technology Research Center, Department of Microbiology, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
| | - Nor Hafizah Ahmad Kamarudin
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Center, Department of Biochemistry, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia.
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13
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Fusion with the cold-active esterase facilitates autotransporter-based surface display of the 10th human fibronectin domain in Escherichia coli. Extremophiles 2017; 22:141-150. [PMID: 29256084 DOI: 10.1007/s00792-017-0990-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 12/08/2017] [Indexed: 10/24/2022]
Abstract
Cell surface display is a popular approach for the construction of whole-cell biocatalysts, live vaccines, and screening of combinatorial libraries. To develop a novel surface display system for the popular scaffold protein 10th human fibronectin type III domain (10Fn3) in Escherichia coli cells, we have used an α-helical linker and a C-terminal translocator domain from previously characterized autotransporter from Psychrobacter cryohalolentis K5T. The level of 10Fn3 passenger exposure at the cell surface provided by the hybrid autotransporter Fn877 and its C-terminal variants was low. To improve it, the fusion proteins containing 10Fn3 and the native autotransporter passenger Est877 or the cold-active esterase EstPc in different orientations were constructed and expressed as passenger domains. Using the whole-cell ELISA and activity assays, we have demonstrated that N-terminal position of EstPc in the passenger significantly improves the efficiency of the surface display of 10Fn3 in E. coli cells.
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14
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Genome content, metabolic pathways and biotechnological potential of the psychrophilic Arctic bacterium Psychrobacter sp. DAB_AL43B, a source and a host of novel Psychrobacter-specific vectors. J Biotechnol 2017; 263:64-74. [PMID: 28919459 DOI: 10.1016/j.jbiotec.2017.09.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 09/10/2017] [Accepted: 09/14/2017] [Indexed: 01/06/2023]
Abstract
Psychrobacter sp. DAB_AL43B, isolated from ornithogenic soil collected on the Arctic island of Spitsbergen, is a newly sequenced psychrophilic strain susceptible to conjugation and electrotransformation. Its genome consists of a circular chromosome (3.3 Mb) and four plasmids (4.4-6.4kb). In silico genome mining and microarray-based phenotypic analysis were performed to describe the metabolic potential of this strain and identify possible biotechnological applications. Metabolic reconstruction indicated that DAB_AL43B prefers low-molecular-weight carboxylates and amino acids as carbon and energy sources. Genetic determinants of heavy-metal resistance, anthracene degradation and possible aerobic denitrification were also identified. Comparative analyses revealed a relatively close relationship between DAB_AL43B and other sequenced Psychrobacter species. In addition, the plasmids of this strain were used as the basis for the construction of Escherichia coli-Psychrobacter spp. shuttle vectors. Taken together, the results of this work suggest that DAB_AL43B is a promising candidate as a new model strain for studies on Psychrobacter spp.
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15
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Petrovskaya LE, Novototskaya-Vlasova KA, Gapizov SS, Spirina EV, Durdenko EV, Rivkina EM. New member of the hormone-sensitive lipase family from the permafrost microbial community. Bioengineered 2017; 8:420-423. [PMID: 27753534 PMCID: PMC5553336 DOI: 10.1080/21655979.2016.1230571] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 08/24/2016] [Accepted: 08/24/2016] [Indexed: 10/20/2022] Open
Abstract
Siberian permafrost is a unique environment inhabited with diverse groups of microorganisms. Among them, there are numerous producers of biotechnologically relevant enzymes including lipases and esterases. Recently, we have constructed a metagenomic library from a permafrost sample and identified in it several genes coding for potential lipolytic enzymes. In the current work, properties of the recombinant esterases obtained from this library are compared with the previously characterized lipase from Psychrobacter cryohalolentis and other representatives of the hormone-sensitive lipase family.
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Affiliation(s)
- Lada E. Petrovskaya
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | - Sultan Sh. Gapizov
- Shemyakin & Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- M. V. Lomonosov Moscow State University, Department of Biology, Moscow, Russia
| | - Elena V. Spirina
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino, Russia
| | - Ekaterina V. Durdenko
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino, Russia
| | - Elizaveta M. Rivkina
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Pushchino, Russia
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16
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Santiago M, Ramírez-Sarmiento CA, Zamora RA, Parra LP. Discovery, Molecular Mechanisms, and Industrial Applications of Cold-Active Enzymes. Front Microbiol 2016; 7:1408. [PMID: 27667987 PMCID: PMC5016527 DOI: 10.3389/fmicb.2016.01408] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 08/25/2016] [Indexed: 11/17/2022] Open
Abstract
Cold-active enzymes constitute an attractive resource for biotechnological applications. Their high catalytic activity at temperatures below 25°C makes them excellent biocatalysts that eliminate the need of heating processes hampering the quality, sustainability, and cost-effectiveness of industrial production. Here we provide a review of the isolation and characterization of novel cold-active enzymes from microorganisms inhabiting different environments, including a revision of the latest techniques that have been used for accomplishing these paramount tasks. We address the progress made in the overexpression and purification of cold-adapted enzymes, the evolutionary and molecular basis of their high activity at low temperatures and the experimental and computational techniques used for their identification, along with protein engineering endeavors based on these observations to improve some of the properties of cold-adapted enzymes to better suit specific applications. We finally focus on examples of the evaluation of their potential use as biocatalysts under conditions that reproduce the challenges imposed by the use of solvents and additives in industrial processes and of the successful use of cold-adapted enzymes in biotechnological and industrial applications.
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Affiliation(s)
- Margarita Santiago
- Department of Chemical Engineering and Biotechnology, Centre for Biochemical Engineering and Biotechnology, Universidad de ChileSantiago, Chile
| | - César A. Ramírez-Sarmiento
- Schools of Engineering, Medicine and Biological Sciences, Institute for Biological and Medical Engineering, Pontificia Universidad Católica de ChileSantiago, Chile
| | - Ricardo A. Zamora
- Departamento de Biología, Facultad de Ciencias, Universidad de ChileSantiago, Chile
| | - Loreto P. Parra
- Schools of Engineering, Medicine and Biological Sciences, Institute for Biological and Medical Engineering, Pontificia Universidad Católica de ChileSantiago, Chile
- Department of Chemical and Bioprocesses Engineering, School of Engineering, Pontificia Universidad Católica de ChileSantiago, Chile
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17
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Affiliation(s)
- M. Kavitha
- School of Biosciences and Technology, VIT University, Vellore, India
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18
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Petrovskaya LE, Novototskaya-Vlasova KA, Kryukova EA, Rivkina EM, Dolgikh DA, Kirpichnikov MP. Cell surface display of cold-active esterase EstPc with the use of a new autotransporter from Psychrobacter cryohalolentis K5(T). Extremophiles 2014; 19:161-70. [PMID: 25253411 DOI: 10.1007/s00792-014-0695-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 09/14/2014] [Indexed: 01/26/2023]
Abstract
We have cloned the gene coding for AT877-a new predicted member of the autotransporter protein family with an esterase passenger domain from permafrost bacterium Psychrobacter cryohalolentis K5(T). Expression of AT877 gene in Escherichia coli resulted in accumulation of the recombinant autotransporter in the outer membrane fraction and at the surface of the induced cells. AT877 displayed maximum hydrolytic activity toward medium-chain p-nitrophenyl esters (C8-C10) at 50 °C and was resistant to the presence of several metal ions, organic solvents and detergents. Previously, we have described a cold-active esterase EstPc from the same bacterium which possesses high activity at low temperatures and relatively high thermal stability. To construct a cell surface display system for EstPc, the hybrid autotransporter gene coding for EstPc with the α-helical linker and the translocator domain from AT877 was constructed and expressed in E. coli. According to the results of the cell fractionation studies and esterase activity measurements, the EstPc passenger was successfully displayed at the surface of the induced cells. It demonstrated a temperature optimum at 15-25 °C and a substrate preference toward p-nitrophenyl butyrate (C4). Obtained results provide a new example of the biotechnologically relevant enzyme from the permafrost microbial community with potential applications for the conversion of short- and medium-chain ester substrates and a basis for the construction of a new cell surface display platform.
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Affiliation(s)
- L E Petrovskaya
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russian Federation,
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19
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Goodarzi N, Karkhane AA, Mirlohi A, Tabandeh F, Torktas I, Aminzadeh S, Yakhchali B, Shamsara M, Ghafouri MAS. Protein Engineering of Bacillus thermocatenulatus Lipase via Deletion of the α5 Helix. Appl Biochem Biotechnol 2014; 174:339-51. [DOI: 10.1007/s12010-014-1063-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Accepted: 07/18/2014] [Indexed: 10/25/2022]
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20
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Novototskaya-Vlasova K, Petrovskaya L, Kryukova E, Rivkina E, Dolgikh D, Kirpichnikov M. Expression and chaperone-assisted refolding of a new cold-active lipase from Psychrobacter cryohalolentis K5(T). Protein Expr Purif 2013; 91:96-103. [PMID: 23891837 DOI: 10.1016/j.pep.2013.07.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 07/03/2013] [Accepted: 07/08/2013] [Indexed: 11/19/2022]
Abstract
We describe cloning and expression of genes coding for lipase Lip2Pc and lipase-specific foldase LifPc from a psychrotrophic microorganism Psychrobacter cryohalolentis K5(T) isolated from a Siberian cryopeg (the lense of overcooled brine within permafrost). Upon expression in Escherichiacoli Lip2Pc accumulated in inclusion bodies while chaperone was synthesized in a soluble form. An efficient protocol for solubilization and subsequent refolding of the recombinant lipase in the presence of the truncated chaperone was developed. Using this procedure Lip2Pc with specific activity of 6900U/mg was obtained. Contrary to published data on other lipase-chaperone complexes, refolded Lip2Pc was mostly recovered from the complex with chaperone by metal-affinity chromatography. Recombinant Lip2Pc displayed maximum lipolytic activity at 25°C and pH 8.0 with p-nitrophenyl palmitate (C16) as a substrate. Activity assays conducted at different temperatures revealed that the recombinant Lip2Pc is a cold-adapted lipase with ability to utilize substrates with long (C10-C16) hydrocarbon chains in the temperature range from +5 to +65°C. It demonstrated relatively high stability at temperatures above 60°C and in the presence of various metal ions or organic solvents (ethanol, methanol, etc.). Non-ionic detergents, such as Triton X-100 and Tween 20 decreased Lip2Pc activity and SDS completely inhibited it.
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Affiliation(s)
- Ksenia Novototskaya-Vlasova
- Institute of Physicochemical and Biological Problems in Soil Science, Russian Academy of Sciences, Institutskaya str., 2, 142290 Pushchino, Moscow Region, Russian Federation.
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