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Maltseva PY, Plotnitskaya NA, Krivoruchko AV, Beletskiy AV, Rakitin AL, Mardanov AV, Ivshina IB. Bioinformatics Analysis of the Genome of Rhodococcus rhodochrous IEGM 1362, an (-)-Isopulegol Biotransformer. Genes (Basel) 2024; 15:992. [PMID: 39202353 PMCID: PMC11354180 DOI: 10.3390/genes15080992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Revised: 07/20/2024] [Accepted: 07/26/2024] [Indexed: 09/03/2024] Open
Abstract
A genome of Rhodococcus rhodochrous IEGM 1362 was sequenced and annotated. This strain can transform monoterpene alcohol (-)-isopulegol with the formation of two novel pharmacologically promising metabolites. Nine genes encoding cytochrome P450, presumably involved in (-)-isopulegol transformation, were found in the genome of R. rhodochrous IEGM 1362. Primers and PCR conditions for their detection were selected. The obtained data can be used for the further investigation of genes encoding enzymes involved in monoterpene biotransformation.
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Affiliation(s)
- Polina Yu. Maltseva
- Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center of the Ural Branch of the Russian Academy of Sciences, 13 Golev Str., 614081 Perm, Russia; (P.Y.M.); (N.A.P.); (A.V.K.)
- Department of Microbiology and Immunology, Perm State University, 15 Bukirev Str., 614990 Perm, Russia
| | - Natalia A. Plotnitskaya
- Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center of the Ural Branch of the Russian Academy of Sciences, 13 Golev Str., 614081 Perm, Russia; (P.Y.M.); (N.A.P.); (A.V.K.)
- Department of Microbiology and Immunology, Perm State University, 15 Bukirev Str., 614990 Perm, Russia
| | - Anastasiia V. Krivoruchko
- Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center of the Ural Branch of the Russian Academy of Sciences, 13 Golev Str., 614081 Perm, Russia; (P.Y.M.); (N.A.P.); (A.V.K.)
- Department of Microbiology and Immunology, Perm State University, 15 Bukirev Str., 614990 Perm, Russia
| | - Aleksey V. Beletskiy
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 7-1 Prosp. 60-let Oktyabrya, 117312 Moscow, Russia; (A.V.B.); (A.L.R.); (A.V.M.)
| | - Andrey L. Rakitin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 7-1 Prosp. 60-let Oktyabrya, 117312 Moscow, Russia; (A.V.B.); (A.L.R.); (A.V.M.)
| | - Andrey V. Mardanov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 7-1 Prosp. 60-let Oktyabrya, 117312 Moscow, Russia; (A.V.B.); (A.L.R.); (A.V.M.)
| | - Irina B. Ivshina
- Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center of the Ural Branch of the Russian Academy of Sciences, 13 Golev Str., 614081 Perm, Russia; (P.Y.M.); (N.A.P.); (A.V.K.)
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, 7-1 Prosp. 60-let Oktyabrya, 117312 Moscow, Russia; (A.V.B.); (A.L.R.); (A.V.M.)
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Jeon YW, Song HM, Lee KY, Kim YA, Kim HK. Synthesis of Isoamyl Fatty Acid Ester, a Flavor Compound, by Immobilized Rhodococcus Cutinase. J Microbiol Biotechnol 2024; 34:1356-1364. [PMID: 38754998 PMCID: PMC11239401 DOI: 10.4014/jmb.2402.02033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 05/18/2024]
Abstract
Isoamyl fatty acid esters (IAFEs) are widely used as fruity flavor compounds in the food industry. In this study, various IAFEs were synthesized from isoamyl alcohol and various fatty acids using a cutinase enzyme (Rcut) derived from Rhodococcus bacteria. Rcut was immobilized on methacrylate divinylbenzene beads and used to synthesize isoamyl acetate, butyrate, hexanoate, octanoate, and decanoate. Among them, Rcut synthesized isoamyl butyrate (IAB) most efficiently. Docking model studies showed that butyric acid was the most suitable substrate in terms of binding energy and distance from the active site serine (Ser114) γ-oxygen. Up to 250 mM of IAB was synthesized by adjusting reaction conditions such as substrate concentration, reaction temperature, and reaction time. When the enzyme reaction was performed by reusing the immobilized enzyme, the enzyme activity was maintained at least six times. These results demonstrate that the immobilized Rcut enzyme can be used in the food industry to synthesize a variety of fruity flavor compounds, including IAB.
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Affiliation(s)
- Ye Won Jeon
- Division of Biotechnology, The Catholic University of Korea, Bucheon 14662, Republic of Korea
| | - Ha Min Song
- Division of Biotechnology, The Catholic University of Korea, Bucheon 14662, Republic of Korea
| | - Ka Yeong Lee
- Division of Biotechnology, The Catholic University of Korea, Bucheon 14662, Republic of Korea
| | - Yeong A Kim
- Division of Biotechnology, The Catholic University of Korea, Bucheon 14662, Republic of Korea
| | - Hyung Kwoun Kim
- Division of Biotechnology, The Catholic University of Korea, Bucheon 14662, Republic of Korea
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Romano A, Varriale S, Pezzella C, Totaro G, Andanson JM, Verney V, Sisti L. Natural deep eutectic solvents as thermostabilizer for Humicola insolens cutinase. N Biotechnol 2023:S1871-6784(23)00027-4. [PMID: 37257817 DOI: 10.1016/j.nbt.2023.05.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/07/2023] [Accepted: 05/27/2023] [Indexed: 06/02/2023]
Abstract
As a new generation of green solvents, deep eutectic solvents (DESs) are considered a promising alternative to current harsh organic solvents and find application in many chemical processing methods such as extraction and synthesis. DESs, normally formed by two or more components via various hydrogen bond interactions, offer high potential as medium for biocatalysis reactions where they can improve efficiency by enhancing substrate solubility and the activity and stability of the enzymes. In the current study, the stabilization of Humicola insolens cutinase (HiC) in natural deep eutectic solvents (NADESs) was assessed. The best hydrogen bond donor among sorbitol, xylitol, erythritol, glycerol and ethylene glycol, and the best acceptor among betaine, choline chloride, choline acetate, choline dihydrogen citrate and tetramethylammonium chloride, were selected, evaluating binding energies and molecular orientations through molecular docking simulations, and finally used to prepare NADES aqueous solutions. The effects of component ratio and NADES concentration on HiC thermostability at 90 °C were also investigated. The choline dihydrogen citrate:xylitol, in a 1:1 ratio with a 20wt% concentration, was selected as the best combination in stabilizing HiC, increasing its half-life three-fold.
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Affiliation(s)
- Angela Romano
- Department of Civil, Chemical Environmental and Materials Engineering, University of Bologna, via Terracini 28, 40131 Bologna Italy
| | | | - Cinzia Pezzella
- Biopox srl, Viale Maria Bakunin 12, 80125 Naples, Italy; Department of Chemical Sciences, University of Naples Federico II, via Cintia 4, 80126 Naples, Italy
| | - Grazia Totaro
- Department of Civil, Chemical Environmental and Materials Engineering, University of Bologna, via Terracini 28, 40131 Bologna Italy
| | - Jean-Michel Andanson
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, ICCF, F-63000 Clermont-Ferrand, France
| | - Vincent Verney
- Université Clermont Auvergne, Clermont Auvergne INP, CNRS, ICCF, F-63000 Clermont-Ferrand, France
| | - Laura Sisti
- Department of Civil, Chemical Environmental and Materials Engineering, University of Bologna, via Terracini 28, 40131 Bologna Italy
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Ivshina IB, Luchnikova NA, Maltseva PY, Ilyina IV, Volcho KP, Gatilov YV, Korchagina DV, Kostrikina NA, Sorokin VV, Mulyukin AL, Salakhutdinov NF. Biotransformation of (–)-Isopulegol by Rhodococcus rhodochrous. Pharmaceuticals (Basel) 2022; 15:ph15080964. [PMID: 36015112 PMCID: PMC9412403 DOI: 10.3390/ph15080964] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/29/2022] [Accepted: 08/01/2022] [Indexed: 11/16/2022] Open
Abstract
The ability of actinobacteria of the genus Rhodococcus to biotransform the monoterpenoid (–)-isopulegol has been established for the first time. R. rhodochrous strain IEGM 1362 was selected as a bacterium capable of metabolizing (–)-isopulegol to form new, previously unknown, 10-hydroxy (2) and 10-carboxy (3) derivatives, which may presumably have antitumor activity and act as respiratory stimulants and cancer prevention agents. In the experiments, optimal conditions were selected to provide the maximum target catalytic activity of rhodococci. Using up-to-date (TEM, AFM-CLSM, and EDX) and traditional (cell size, roughness, and zeta potential measurements) biophysical and microbiological methods, it was shown that (–)-isopulegol and halloysite nanotubes did not negatively affect the bacterial cells. The data obtained expand our knowledge of the biocatalytic potential of rhodococci and their possible involvement in the synthesis of pharmacologically active compounds from plant derivatives.
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Affiliation(s)
- Irina B. Ivshina
- Institute of Ecology and Genetics of Microorganisms of the Ural Branch of the Russian Academy of Sciences, Perm Federal Research Center of the Ural Branch of the Russian Academy of Sciences, 13 Golev Str., 614081 Perm, Russia;
- Department of Microbiology and Immunology, Perm State National Research University, 15 Bukirev Str., 614990 Perm, Russia;
- Correspondence: ; Tel.: +7-(342)-2808114; Fax: +7-(342)-2809211
| | - Natalia A. Luchnikova
- Institute of Ecology and Genetics of Microorganisms of the Ural Branch of the Russian Academy of Sciences, Perm Federal Research Center of the Ural Branch of the Russian Academy of Sciences, 13 Golev Str., 614081 Perm, Russia;
- Department of Microbiology and Immunology, Perm State National Research University, 15 Bukirev Str., 614990 Perm, Russia;
| | - Polina Yu. Maltseva
- Department of Microbiology and Immunology, Perm State National Research University, 15 Bukirev Str., 614990 Perm, Russia;
| | - Irina V. Ilyina
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry of the Siberian Branch of the Russian Academy of Sciences, 9 Lavrentiev Avenue, 630090 Novosibirsk, Russia; (I.V.I.); (K.P.V.); (Y.V.G.); (D.V.K.); (N.F.S.)
| | - Konstantin P. Volcho
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry of the Siberian Branch of the Russian Academy of Sciences, 9 Lavrentiev Avenue, 630090 Novosibirsk, Russia; (I.V.I.); (K.P.V.); (Y.V.G.); (D.V.K.); (N.F.S.)
| | - Yurii V. Gatilov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry of the Siberian Branch of the Russian Academy of Sciences, 9 Lavrentiev Avenue, 630090 Novosibirsk, Russia; (I.V.I.); (K.P.V.); (Y.V.G.); (D.V.K.); (N.F.S.)
| | - Dina V. Korchagina
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry of the Siberian Branch of the Russian Academy of Sciences, 9 Lavrentiev Avenue, 630090 Novosibirsk, Russia; (I.V.I.); (K.P.V.); (Y.V.G.); (D.V.K.); (N.F.S.)
| | - Nadezhda A. Kostrikina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 60 let Oktyabrya, 7, bld. 2, 117312 Moscow, Russia; (N.A.K.); (V.V.S.); (A.L.M.)
| | - Vladimir V. Sorokin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 60 let Oktyabrya, 7, bld. 2, 117312 Moscow, Russia; (N.A.K.); (V.V.S.); (A.L.M.)
| | - Andrey L. Mulyukin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, 60 let Oktyabrya, 7, bld. 2, 117312 Moscow, Russia; (N.A.K.); (V.V.S.); (A.L.M.)
| | - Nariman F. Salakhutdinov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry of the Siberian Branch of the Russian Academy of Sciences, 9 Lavrentiev Avenue, 630090 Novosibirsk, Russia; (I.V.I.); (K.P.V.); (Y.V.G.); (D.V.K.); (N.F.S.)
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Abstract
The use of biological enzyme catalysts could have huge ramifications for chemical industries. However, these enzymes are often inactive in nonbiological conditions, such as high temperatures, present in industrial settings. Here, we show that the enzyme PETase (polyethylene terephthalate [PET]), with potential application in plastic recycling, is stabilized at elevated temperature through complexation with random copolymers. We demonstrate this through simulations and experiments on different types of substrates. Our simulations also provide strategies for designing more enzymatically active complexes by altering polymer composition and enzyme charge distribution. Engineered and native enzymes are poised to solve challenges in medicine, bioremediation, and biotechnology. One important goal is the possibility of upcycling polymers using enzymes. However, enzymes are often inactive in industrial, nonbiological conditions. It is particularly difficult to protect water-soluble enzymes at elevated temperatures by methods that preserve their functionality. Through atomistic and coarse-grained molecular dynamics simulations that capture protein conformational change, we show that an enzyme, PETase (polyethylene terephthalate [PET]), can be stabilized at elevated temperatures by complexation with random copolymers into nanoscale aggregates that do not precipitate into macroscopic phases. We demonstrated the efficiency of the method by simulating complexes of random copolymers and the enzyme PETase, which depolymerizes PET, a highly used polymer. These polymers are more industrially viable than peptides and can target specific domains on an enzyme. We design the mean composition of the random copolymers to control the polymer–enzyme surface contacts and the polymer conformation. When positioned on or near the active site, these polymer contacts can further stabilize the conformation of the active site at elevated temperatures. We explore the experimental implications of this active site stabilization method and show that PETase-random copolymer complexes have enhanced activity on both small molecule substrates and solid PET films. These results provide guidelines for engineering enzyme–polymer complexes with enhanced enzyme functionality in nonbiological environments.
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Chałupka J, Sikora A, Kozicka A, Marszałł MP. Overview: Enzyme-catalyzed Enantioselective Biotransformation of Chiral Active Compounds Used in Hypertension Treatment. CURR ORG CHEM 2020. [DOI: 10.2174/1385272824999201020204256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Enzymatic kinetic resolution is one of the methods which allows for the synthesis
of enantiomerically pure various active pharmaceutical ingredients. In contrast to chemical
routes, enzymatic reactions have characteristics, including mild reaction conditions, a few byproducts,
and relatively high activity of the used enzymes. β-adrenolytic drugs are widely
used in the treatment of hypertension and cardiovascular disorders. Due to the fact that β-
blockers possess an asymmetric carbon atom in their structure, they are presented in two
enantiomeric forms. It was reported by many studies that only the (S)-enantiomers of these
drugs possess the desired therapeutic effect, whereas the administration of the racemate may
cause dangerous side effects, such as bronchoconstriction or diabetes. Nevertheless, β-
blockers are still commercially available drugs mainly used in medicine as racemates, whereas there are several
methods that are widely used in order to obtain enantiomerically pure compounds.
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Affiliation(s)
- Joanna Chałupka
- Department of Medicinal Chemistry, Collegium Medicum in Bydgoszcz, Faculty of Pharmacy, Nicolaus Copernicus University in Toruń, Dr. A. Jurasza 2, 85-089 Bydgoszcz, Poland
| | - Adam Sikora
- Department of Medicinal Chemistry, Collegium Medicum in Bydgoszcz, Faculty of Pharmacy, Nicolaus Copernicus University in Toruń, Dr. A. Jurasza 2, 85-089 Bydgoszcz, Poland
| | - Aleksandra Kozicka
- Department of Medical Genetics, University in Cambridge, Lv 6 Addenbrooke’s Treatment Centre, Cambridge, United Kingdom
| | - Michał Piotr Marszałł
- Department of Medicinal Chemistry, Collegium Medicum in Bydgoszcz, Faculty of Pharmacy, Nicolaus Copernicus University in Toruń, Dr. A. Jurasza 2, 85-089 Bydgoszcz, Poland
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Gururaj P, Khushbu S, Monisha B, Selvakumar N, Chakravarthy M, Gautam P, Nandhini Devi G. Production, purification and application of Cutinase in enzymatic scouring of cotton fabric isolated from Acinetobacter baumannii AU10. Prep Biochem Biotechnol 2020; 51:550-561. [PMID: 33108946 DOI: 10.1080/10826068.2020.1836655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Conventional cotton scouring in the textile industry using alkali results in huge environmental impact which can be overcome by using enzymes. Pectinase along with cutinase gives enhanced bioscouring results. Cutin was extracted from tomato peels and was used as substrate in the microbial media. The strain isolated from tomato peel was identified as Acinetobacter baumannii AU10 by 16S rDNA sequencing. The cutinase production was optimized by Placket-Burman and Response Surface Methodology (RSM) and the maximum production of 82.75 U/mL obtained at sucrose 6.68% (w/v), gelatin 2.74 g/L at a temperature of 35.93 °C. Cutinase was purified by ammonium sulfate precipitation, hydrophobic interaction chromatography and ion exchange chromatography with a recovery of 25.6% and specific activity of 38030 U/mg. The confirmation test for the purity of cutinase was analyzed by RP-HPLC. The molecular mass of cutinase was determined as 28.9 kDa by SDS-PAGE technique. Scanning electron microscopic analysis showed a rough and open primary wall surface on the cutinase bioscoured fabric which confirmed its activity on cutin present in the cotton fabric. Additionally, the cutinase-bioscoured samples showed better absorbency than the untreated samples. Therefore, enzymatic scouring increases wetting capacity of scoured cotton and also helps to reduce environmental pollution.
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Affiliation(s)
- P Gururaj
- Centre for Food Technology, Department of Biotechnology, Anna University, Chennai, India
| | - S Khushbu
- Centre for Food Technology, Department of Biotechnology, Anna University, Chennai, India
| | - B Monisha
- Centre for Food Technology, Department of Biotechnology, Anna University, Chennai, India
| | - N Selvakumar
- Centre for Food Technology, Department of Biotechnology, Anna University, Chennai, India
| | - M Chakravarthy
- Centre for Food Technology, Department of Biotechnology, Anna University, Chennai, India
| | - P Gautam
- Centre for Food Technology, Department of Biotechnology, Anna University, Chennai, India
| | - G Nandhini Devi
- Centre for Food Technology, Department of Biotechnology, Anna University, Chennai, India
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