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Godase VP, Kumar VR, Kumar AR. Potential of Y. lipolytica epoxide hydrolase for efficient production of enantiopure (R)-1,2-octanediol. AMB Express 2023; 13:77. [PMID: 37495892 PMCID: PMC10371975 DOI: 10.1186/s13568-023-01584-1] [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: 03/28/2023] [Accepted: 07/11/2023] [Indexed: 07/28/2023] Open
Abstract
The recombinant Yleh from a tropical marine yeast Yarrowia lipolytica NCIM 3589 exhibited a high epoxide hydrolase activity of 9.34 ± 1.80 µmol min-1 mg-1 protein towards 1,2-epoxyoctane (EO), at pH 8.0 and 30 °C. The reaction product was identified as 1,2-Octanediol (OD) by GC-MS using EO and H2O18 as substrate, affirming the functionality of Yleh as an epoxide hydrolase. For EO, the Km, Vmax, and kcat/Km values were 0.43 ± 0.017 mM, 0.042 ± 0.003 mM min-1, and 467.17 ± 39.43 mM-1 min-1, respectively. To optimize the reaction conditions for conversion of racemic EO by Yleh catalyst to enantiopure (R)-1,2-octanediol, initially, Response Surface Methodology was employed. Under optimized reaction conditions of 15 mM EO, 150 µg purified Yleh at 30 °C a maximal diol production of 7.11 mM was attained in a short span of 65 min with a yield of 47.4%. Green technology using deep eutectic solvents for the hydrophobic substrate (EO) were tested as co-solvents in Yleh catalyzed EO hydrolysis. Choline chloride-Glycerol, produced 9.08 mM OD with an increased OD yield of 60.5%. Thus, results showed that deep eutectic solvents could be a promising solvent for Yleh-catalyzed reactions making Yleh a potential biocatalyst for the biosynthesis of enantiopure synthons.
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Affiliation(s)
- Vijaya P Godase
- Biochemistry Research Laboratory, Department of Biotechnology (Formerly Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, 411007, Pune, India
- Department of Biochemistry, Shivaji University, 416004, Kolhapur, India
| | - V Ravi Kumar
- Chemical Engineering and Process Development Division, National Chemical Laboratory, 411008, Pune, India
| | - Ameeta Ravi Kumar
- Biochemistry Research Laboratory, Department of Biotechnology (Formerly Institute of Bioinformatics and Biotechnology), Savitribai Phule Pune University, 411007, Pune, India.
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Virués-Segovia JR, Muñoz-Mira S, Durán-Patrón R, Aleu J. Marine-derived fungi as biocatalysts. Front Microbiol 2023; 14:1125639. [PMID: 36922968 PMCID: PMC10008910 DOI: 10.3389/fmicb.2023.1125639] [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: 12/16/2022] [Accepted: 02/08/2023] [Indexed: 03/03/2023] Open
Abstract
Marine microorganisms account for over 90% of ocean biomass and their diversity is believed to be the result of their ability to adapt to extreme conditions of the marine environment. Biotransformations are used to produce a wide range of high-added value materials, and marine-derived fungi have proven to be a source of new enzymes, even for activities not previously discovered. This review focuses on biotransformations by fungi from marine environments, including bioremediation, from the standpoint of the chemical structure of the substrate, and covers up to September 2022.
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Affiliation(s)
- Jorge R Virués-Segovia
- Departamento de Química Orgánica, Facultad de Ciencias, Campus Universitario Río San Pedro s/n, Torre sur, 4ª Planta, Universidad de Cádiz, Cádiz, Spain
| | - Salvador Muñoz-Mira
- Departamento de Química Orgánica, Facultad de Ciencias, Campus Universitario Río San Pedro s/n, Torre sur, 4ª Planta, Universidad de Cádiz, Cádiz, Spain
| | - Rosa Durán-Patrón
- Departamento de Química Orgánica, Facultad de Ciencias, Campus Universitario Río San Pedro s/n, Torre sur, 4ª Planta, Universidad de Cádiz, Cádiz, Spain
| | - Josefina Aleu
- Departamento de Química Orgánica, Facultad de Ciencias, Campus Universitario Río San Pedro s/n, Torre sur, 4ª Planta, Universidad de Cádiz, Cádiz, Spain
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Mamaev D, Zvyagilskaya R. Yarrowia lipolytica: a multitalented yeast species of ecological significance. FEMS Yeast Res 2021; 21:6141120. [PMID: 33595651 DOI: 10.1093/femsyr/foab008] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 02/13/2021] [Indexed: 02/07/2023] Open
Abstract
Yarrowia lipolytica is characterized by GRAS (Generally regarded as safe) status, the versatile substrate utilization profile, rapid utilization rates, metabolic diversity and flexibility, the unique abilities to tolerate to extreme environments (acidic, alkaline, hypersaline, heavy metal-pollutions and others) and elevated biosynthesis and secreting capacities. These advantages of Y. lipolytica allow us to consider it as having great ecological significance. Unfortunately, there is still a paucity of relevant review data. This mini-review highlights ecological ubiquity of Y. lipolytica species, their ability to diversify and colonize specialized niches. Different Y. lipolytica strains, native and engineered, are beneficial in degrading many environmental pollutants causing serious ecological problems worldwide. In agriculture has a potential to be a bio-control agent by stimulating plant defense response, and an eco-friendly bio-fertilizer. Engineered strains of Y. lipolytica have become a very promising platform for eco-friendly production of biofuel, commodities, chemicals and secondary metabolites of plant origin, obtaining which by other method were limited or economically infeasible, or were accompanied by stringent environmental problems. Perspectives to use potential of Y. lipolytica's capacities for industrial scale production of valuable compounds in an eco-friendly manner are proposed.
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Affiliation(s)
- Dmitry Mamaev
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow 119071, Russian Federation
| | - Renata Zvyagilskaya
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 33, bld. 2 Leninsky Ave., Moscow 119071, Russian Federation
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Bendigiri C, Harini K, Yenkar S, Zinjarde S, Sowdhamini R, RaviKumar A. Evaluating Ylehd, a recombinant epoxide hydrolase from Yarrowia lipolytica as a potential biocatalyst for the resolution of benzyl glycidyl ether. RSC Adv 2018; 8:12918-12926. [PMID: 35541265 PMCID: PMC9079618 DOI: 10.1039/c8ra00628h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 03/26/2018] [Indexed: 11/22/2022] Open
Abstract
Glycidyl ethers and their vicinal diols are important building blocks in the organic synthesis of anti-cancer and anti-obesity drugs. Ylehd, an epoxide hydrolase from tropical marine yeast Yarrowia lipolytica, was explored for its enantioselective properties by kinetic, thermodynamic and in silico studies. Kinetic resolution of racemic phenyl glycidyl ether (PGE) yielded (S)-epoxide while for benzyl glycidyl ether (BGE) (R)-epoxide was obtained, with vicinal diols of the opposite configuration. Amongst the enantiomers of PGE and BGE, the (S)-selective conversion of benzyl glycidyl ether to its corresponding diol, (S)-3-benzyloxy-1,2-propanediol while retaining (R)-BGE was most favourable with 95% ee in 20 min. Enantioselective conversion of specific enantiomer of BGE to its corresponding diols was attributed to the favourable kinetic and thermodynamic parameters as well as to the number and proximity of water molecules near the base H325 in the active site pocket. The easily available and highly active Ylehd could be a potential biocatalyst for large scale preparation of pharmaceutically relevant chiral (R)-benzyl glycidyl ether and (S)-3-benzyloxy-1,2-propanediol. Ylehd, an enantioselective epoxide hydrolase with potential application in resolution of racemic benzyl glycidyl ether.![]()
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Affiliation(s)
- Chandrika Bendigiri
- Institute of Bioinformatics and Biotechnology
- Savitribai Phule Pune University
- Pune 411 007
- India
| | - K. Harini
- National Centre for Biological Sciences
- Bengaluru
- India
| | - Sajal Yenkar
- Institute of Bioinformatics and Biotechnology
- Savitribai Phule Pune University
- Pune 411 007
- India
| | - Smita Zinjarde
- Institute of Bioinformatics and Biotechnology
- Savitribai Phule Pune University
- Pune 411 007
- India
| | - R. Sowdhamini
- National Centre for Biological Sciences
- Bengaluru
- India
| | - Ameeta RaviKumar
- Institute of Bioinformatics and Biotechnology
- Savitribai Phule Pune University
- Pune 411 007
- India
- Department of Biotechnology
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Bendigiri C, Zinjarde S, RaviKumar A. Ylehd, an epoxide hydrolase with promiscuous haloalkane dehalogenase activity from tropical marine yeast Yarrowia lipolytica is induced upon xenobiotic stress. Sci Rep 2017; 7:11887. [PMID: 28928379 PMCID: PMC5605520 DOI: 10.1038/s41598-017-12284-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 09/01/2017] [Indexed: 01/08/2023] Open
Abstract
Recalcitrant environmental pollutants, like bromoorganics and epoxides are hydrolysed with limited substrate specificities by microbial oxygenases, reductases, hydrolases and dehalogenases. Here, we report the identification and characterisation of a protein (XP_504164) from the tropical marine yeast Yarrowia lipolytica NCIM 3589, known to degrade bromoorganics and epoxides. Multiple sequence alignment suggests it belongs to α/β superfamily with conservation of catalytic triad and oxyanion hole motifs. The corresponding gene cloned and protein (Ylehd) expressed in E. coli BL21AI exhibited epoxide hydrolase activity (24 ± 0.7 nmol s−1 mg−1 protein) at pH 8.0 and promiscuous haloalkane dehalogenase (1.5 ± 0.2 nmol s−1 mg−1 protein) at pH 4.5. Recombinant Ylehd catalyses structurally diverse epoxides and bromoorganics with maximum catalytic efficiency (kcat/Km) of 96.56 and 10.1 mM−1 s−1 towards 1,2-Epoxyoctane (EO) and 1-Bromodecane (BD). The expression of Ylehd was highly induced in presence of BD and EO but not in glucose grown cells as studied by immunoblot analyses, q-PCR and activity levels. Immunoelectron microscopy confirmed higher expression in presence of xenobiotics and located it to cytosol. Such inducible nature of Ylehd suggests its physiological role in xenobiotic stress mitigation. This study represents the first functional characterisation of a bifunctional EH/HLD in eukaryotic microbes with broad substrate specificity making it a potential biocatalyst for bioremediation/biosensing of mixed pollutants.
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Affiliation(s)
- Chandrika Bendigiri
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune, 411007, India
| | - Smita Zinjarde
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune, 411007, India
| | - Ameeta RaviKumar
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Pune, 411007, India. .,Department of Biotechnology, Savitribai Phule Pune University, Pune, 411007, India.
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Vatsal AA, Zinjarde SS, RaviKumar A. Phenol Is the Initial Product Formed during Growth and Degradation of Bromobenzene by Tropical Marine Yeast, Yarrowia lipolytica NCIM 3589 via an Early Dehalogenation Step. Front Microbiol 2017; 8:1165. [PMID: 28690604 PMCID: PMC5481318 DOI: 10.3389/fmicb.2017.01165] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 06/07/2017] [Indexed: 11/13/2022] Open
Abstract
Bromobenzene (BrB), a hydrophobic, recalcitrant organic compound, is listed by the environmental protection agencies as an environmental and marine pollutant having hepatotoxic, mutagenic, teratogenic, and carcinogenic effects. The tropical marine yeast Yarrowia lipolytica 3589 was seen to grow aerobically on BrB and displayed a maximum growth rate (μmax) of 0.04 h-1. Furthermore, we also observed an increase in cell size and sedimentation velocity for the cells grown on BrB as compared to the glucose grown cells. The cells attached to the hydrophobic bromobenzene droplets through its hydrophobic and acid-base interactions. The BrB (0.5%, 47.6 mM) was utilized by the cells with the release of a corresponding amount of bromide (12.87 mM) and yielded a cell mass of 1.86 g/L after showing 34% degradation in 96 h. Maximum dehalogenase activity of 16.16 U/mL was seen in the cell free supernatant after 24 h of growth. Identification of metabolites formed as a result of BrB degradation, namely, phenol, catechol, cis, cis muconic acid, and carbon dioxide were determined by LC-MS and GC-MS. The initial attack on bromobenzene by Y. lipolytica cells lead to the transient accumulation of phenol as an early intermediate which is being reported for the first time. Degradation of phenol led to catechol which was degraded by the ortho- cleavage pathway forming cis, cis muconic acid and then to Krebs cycle intermediates eventually leading to CO2 production. The study shows that dehalogenation via an extracellular dehalogenase occurs prior to ring cleavage with phenol as the preliminary degradative compound being produced. The yeast was also able to grow on the degradative products, i.e., phenol and catechol, to varying degrees which would be of potential relevance in the degradation and remediation of xenobiotic environmental bromoaromatic pollutants such as bromobenzene.
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Affiliation(s)
| | | | - Ameeta RaviKumar
- Biochemistry Research Laboratory, Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune UniversityPune, India
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Vatsal A, Potdar C, Zinjarde SS, Ravi Kumar V, Kulkarni BD, RaviKumar A. Role of aliasing and interacting factors in the enhanced production of dehalogenase from Yarrowia lipolytica for degradation of brominated compounds. J IND ENG CHEM 2016. [DOI: 10.1016/j.jiec.2016.07.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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