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Wang J, Singer SD, Chen G. Biotechnological advances in the production of unusual fatty acids in transgenic plants and recombinant microorganisms. Biotechnol Adv 2024; 76:108435. [PMID: 39214484 DOI: 10.1016/j.biotechadv.2024.108435] [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: 04/14/2024] [Revised: 07/28/2024] [Accepted: 08/25/2024] [Indexed: 09/04/2024]
Abstract
Certain plants and microorganisms can produce high amounts of unusual fatty acids (UFAs) such as hydroxy, conjugated, cyclic, and very long-chain polyunsaturated fatty acids, which have distinct physicochemical properties and significant applications in the food, feed, and oleochemical industries. Since many natural sources of UFAs are not ideal for large-scale agricultural production or fermentation, it is attractive to produce them through synthetic biology. Although several UFAs have been commercially or pre-commercially produced in transgenic plants and microorganisms, their contents in transgenic hosts are generally much lower than in natural sources. Moreover, reproducing this success for a wider spectrum of UFAs has remained challenging. This review discusses recent advancements in our understanding of the biosynthesis, accumulation, and heterologous production of UFAs, and addresses the challenges and potential strategies for achieving high UFA content in engineered plants and microorganisms.
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Affiliation(s)
- Juli Wang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 116 St and 85 Ave, Edmonton, Alberta T6G 2P5, Canada
| | - Stacy D Singer
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, Alberta T1J 4B1, Canada
| | - Guanqun Chen
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 116 St and 85 Ave, Edmonton, Alberta T6G 2P5, Canada.
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2
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Kim J, Lee EJ, Lee KE, Nho YH, Ryu J, Kim SY, Yoo JK, Kang S, Seo SW. Docsubty: FLALipid extract derived from newly isolated Rhodotorula toruloides LAB-07 for cosmetic applications. Comput Struct Biotechnol J 2023; 21:2009-2017. [PMID: 36968014 PMCID: PMC10036517 DOI: 10.1016/j.csbj.2023.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 03/10/2023] [Accepted: 03/11/2023] [Indexed: 03/15/2023] Open
Abstract
Rhodotorula toruloides is a non-conventional yeast with a natural carotenoid pathway. In particular, R. toruloides is an oleaginous yeast that can accumulate lipids in high content, thereby gaining interest as a promising industrial host. In this study, we isolated and taxonomically identified a new R. toruloides LAB-07 strain. De novo genome assembly using PacBio and Illumina hybrid platforms yielded 27 contigs with a 20.78 Mb genome size. Subsequent genome annotation analysis based on RNA-seq predicted 5296 protein-coding genes, including the fatty acid production pathway. We compared lipid production under different media; it was highest in the yeast extract salt medium with glycerol as a carbon source. Polyunsaturated α-linolenic acid was detected among the fatty acids, and docking phosphatidylcholine as a substrate to modeled Fad2, which annotated as Δ12-fatty acid desaturase showed bifunctional Δ12, 15-desaturation is structurally possible in that the distances between the diiron center and the carbon-carbon bond in which desaturation occurs were similar to those of structurally identified mouse stearoyl-CoA desaturase. Finally, the applicability of the extracted total lipid fraction of R. toruloides was investigated, demonstrating an increase in filaggrin expression and suppression of heat-induced MMP-1 expression when applied to keratinocytes, along with the additional antioxidant activity. This work presents a new R. toruloides LAB-07 strain with genomic and lipidomic data, which would help understand the physiology of R. toruloides. Also, the various skin-related effect of R. toruloides lipid extract indicates its potential usage as a promising cosmetic ingredient.
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Hu H, Swift A, Mauro-Herrera M, Borrone J, Borja G, Doust AN. Transcriptomic analysis of seed development in Paysonia auriculata (Brassicaceae) identifies genes involved in hydroxy fatty acid biosynthesis. FRONTIERS IN PLANT SCIENCE 2023; 13:1079146. [PMID: 36714715 PMCID: PMC9880434 DOI: 10.3389/fpls.2022.1079146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/21/2022] [Indexed: 06/18/2023]
Abstract
Paysonia auriculata (Brassicaceae) produces multiple hydroxy fatty acids as major components of the seed oil. We tracked the changes in seed oil composition and gene expression during development, starting 14 days after flowers had been pollinated. Seed oil changes showed initially higher levels of saturated and unsaturated fatty acids (FAs) but little accumulation of hydroxy fatty acids (HFAs). Starting 21 days after pollination (DAP) HFA content sharply increased, and reached almost 30% at 28 DAP. Total seed oil also increased from a low of approximately 2% at 14 DAP to a high of approximately 20% by 42 DAP. We identified almost all of the fatty acid synthesis and modification genes that are known from Arabidopsis, and, in addition, a strong candidate for the hydroxylase gene that mediates the hydroxylation of fatty acids to produce valuable hydroxy fatty acids (HFAs) in this species. The gene expression network revealed is very similar to that of the emerging oil crop, Physaria fendleri, in the sister genus to Paysonia. Phylogenetic analyses indicate the hydroxylase enzyme, FAH12, evolved only once in Paysonia and Physaria, and that the enzyme is closely related to FAD2 enzymes. Phylogenetic analyses of FAD2 and FAH12 in the Brassicaceae and outgroup genera suggest that the branch leading to the hydroxylase clade of Paysonia and Physaria is under relaxed selection, compared with the strong purifying selection found across the FAD2 lineages.
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Ben Ayed R, Chirmade T, Hanana M, Khamassi K, Ercisli S, Choudhary R, Kadoo N, Karunakaran R. Comparative Analysis and Structural Modeling of Elaeis oleifera FAD2, a Fatty Acid Desaturase Involved in Unsaturated Fatty Acid Composition of American Oil Palm. BIOLOGY 2022; 11:529. [PMID: 35453727 PMCID: PMC9032008 DOI: 10.3390/biology11040529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 03/13/2022] [Accepted: 03/23/2022] [Indexed: 11/17/2022]
Abstract
American oil palm (Elaeis oleifera) is an important source of dietary oil that could fulfill the increasing worldwide demand for cooking oil. Therefore, improving its production is crucial and could be realized through breeding and genetic engineering approaches aiming to obtain high-yielding varieties with improved oil content and quality. The fatty acid composition and particularly the oleic/linoleic acid ratio are major factors influencing oil quality. Our work focused on a fatty acid desaturase (FAD) enzyme involved in the desaturation and conversion of oleic acid to linoleic acid. Following the in silico identification and annotation of Elaeis oleifera FAD2, its molecular and structural features characterization was performed to better understand the mechanistic bases of its enzymatic activity. EoFAD2 is 1173 nucleotides long and encodes a protein of 390 amino acids that shares similarities with other FADs. Interestingly, the phylogenetic study showed three distinguished groups where EoFAD2 clustered among monocotyledonous taxa. EoFAD2 is a membrane-bound protein with five transmembrane domains presumably located in the endoplasmic reticulum. The homodimer organization model of EoFAD2 enzyme and substrates and respective substrate-binding residues were predicted and described. Moreover, the comparison between 24 FAD2 sequences from different species generated two interesting single-nucleotide polymorphisms (SNPs) associated with the oleic/linoleic acid contents.
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Affiliation(s)
- Rayda Ben Ayed
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Sidi Mansour Road, P.O. Box 1177, Sfax 3018, Tunisia
| | - Tejas Chirmade
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pashan, Pune 411008, India; (T.C.); (N.K.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mohsen Hanana
- Laboratory of Extremophile Plants, Centre of Biotechnology of Borj-Cédria, B.P. 901, Hammam Lif 2050, Tunisia;
| | - Khalil Khamassi
- Field Crop Laboratory (LR16INRAT02), Institut National de la Recherche Agronomique de Tunisie (INRAT), University of Carthage, Tunis 1004, Tunisia;
| | - Sezai Ercisli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum 25240, Turkey;
| | - Ravish Choudhary
- Division of Seed Science and Technology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India;
| | - Narendra Kadoo
- CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pashan, Pune 411008, India; (T.C.); (N.K.)
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Rohini Karunakaran
- Unit of Biochemistry, Centre of Excellence for Biomaterials Engineering, Faculty of Medicine, AIMST University, Semeling, Bedong 08100, Malaysia
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Tupec M, Culka M, Machara A, Macháček S, Bím D, Svatoš A, Rulíšek L, Pichová I. Understanding desaturation/hydroxylation activity of castor stearoyl Δ9-Desaturase through rational mutagenesis. Comput Struct Biotechnol J 2022; 20:1378-1388. [PMID: 35386101 PMCID: PMC8940945 DOI: 10.1016/j.csbj.2022.03.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/11/2022] [Accepted: 03/11/2022] [Indexed: 01/17/2023] Open
Abstract
Rationally designed mutations in the Δ9 desaturase promoted hydroxylation activity. Proton and electron transfer to the active site is crucial for the Δ9D to desaturate Detailed analysis of all enzymatic products of the Δ9D was carried out Insight into the chemo-, and stereoselectivity of non-heme diiron enzymes was obtained
A recently proposed reaction mechanism of soluble Δ9 desaturase (Δ9D) allowed us to identify auxiliary residues His203, Asp101, Thr206 and Cys222 localized near the di-iron active site that are supposedly involved in the proton transfer (PT) to and from the active site. The PT, along with the electron transfer (ET), seems to be crucial for efficient desaturation. Thus, perturbing the major PT chains is expected to impair the native reaction and (potentially) amplify minor reaction channels, such as the substrate hydroxylation. To verify this hypothesis, we mutated the four residues mentioned above into their counterparts present in a soluble methane monooxygenase (sMMO), and determined the reaction products of mutants. We found that the mutations significantly promote residual monohydroxylation activities on stearoyl-CoA, often at the expense of native desaturation activity. The favored hydroxylation positions are C9, followed by C10 and C11. Reactions with unsaturated substrate, oleoyl-CoA, yield erythro-9,10-diol, cis-9,10-epoxide and a mixture of allylic alcohols. Additionally, using 9- and 11-hydroxystearoyl-CoA, we showed that the desaturation reaction can proceed only with the hydroxyl group at position C11, whereas the hydroxylation reaction is possible in both cases, i.e. with hydroxyl at position C9 or C11. Despite the fact that the overall outcome of hydroxylation is rather modest and that it is mostly the desaturation/hydroxylation ratio that is affected, our results broaden understanding of the origin of chemo- and stereoselectivity of the Δ9D and provide further insight into the catalytic action of the NHFe2 enzymes.
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Affiliation(s)
- Michal Tupec
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Martin Culka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Aleš Machara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Stanislav Macháček
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Daniel Bím
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
| | - Aleš Svatoš
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
- Max-Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, Jena 07745, Germany
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
- Corresponding authors.
| | - Iva Pichová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, Prague 16610, Czech Republic
- Corresponding authors.
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Brachmann AO, Probst SI, Rüthi J, Dudko D, Bode HB, Piel J. A Desaturase‐Like Enzyme Catalyzes Oxazole Formation in
Pseudomonas
Indolyloxazole Alkaloids. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Alexander O. Brachmann
- Eidgenössische Technische Hochschule (ETH) Zürich Institute of Microbiology Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
| | - Silke I. Probst
- Eidgenössische Technische Hochschule (ETH) Zürich Institute of Microbiology Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
| | - Joel Rüthi
- Eidgenössische Technische Hochschule (ETH) Zürich Institute of Microbiology Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
| | - Darya Dudko
- Eidgenössische Technische Hochschule (ETH) Zürich Institute of Microbiology Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
| | - Helge B. Bode
- Goethe Universität Frankfurt Institute of Molecular Biological Science Max-von-Laue Str. 9 60438 Frankfurt am Main Germany
- Senckenberg Gesellschaft für Naturforschung Senckenberganlage 25 60325 Frankfurt am Main Germany
- Buchmann Institute for Molecular Life Sciences (BMLS) Johann Wolfgang Goethe Universität Max-von-Laue-Straße 15 60438 Frankfurt am Main Germany
- Max-Planck-Institute for Terrestrial Microbiology Department of Natural Products in Organismic Interactions 35043 Marburg Germany
| | - Jörn Piel
- Eidgenössische Technische Hochschule (ETH) Zürich Institute of Microbiology Vladimir-Prelog-Weg 4 8093 Zürich Switzerland
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Brachmann AO, Probst SI, Rüthi J, Dudko D, Bode HB, Piel J. A Desaturase-Like Enzyme Catalyzes Oxazole Formation in Pseudomonas Indolyloxazole Alkaloids. Angew Chem Int Ed Engl 2021; 60:8781-8785. [PMID: 33460275 DOI: 10.1002/anie.202014491] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/08/2020] [Indexed: 11/10/2022]
Abstract
Indolyloxazole alkaloids occur in diverse micro- and macroorganisms and exhibit a wide range of pharmacological activities. Despite their ubiquitous occurrence and simple structures, the biosynthetic pathway remained unknown. Here, we used transposon mutagenesis in the labradorin producer Pseudomonas entomophila to identify a cryptic biosynthetic locus encoding an N-acyltransferase and a non-heme diiron desaturase-like enzyme. Heterologous expression in E. coli demonstrates that both enzymes are sufficient to produce indolyloxazoles. Probing their function in stable-isotope feeding experiments, we provide evidence for an unusual desaturase mechanism that generates the oxazole by decarboxylative cyclization.
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Affiliation(s)
- Alexander O Brachmann
- Eidgenössische Technische Hochschule (ETH) Zürich, Institute of Microbiology, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Silke I Probst
- Eidgenössische Technische Hochschule (ETH) Zürich, Institute of Microbiology, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Joel Rüthi
- Eidgenössische Technische Hochschule (ETH) Zürich, Institute of Microbiology, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Darya Dudko
- Eidgenössische Technische Hochschule (ETH) Zürich, Institute of Microbiology, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Helge B Bode
- Goethe Universität Frankfurt, Institute of Molecular Biological Science, Max-von-Laue Str. 9, 60438, Frankfurt am Main, Germany.,Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, 60325, Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences (BMLS), Johann Wolfgang Goethe Universität, Max-von-Laue-Straße 15, 60438, Frankfurt am Main, Germany.,Max-Planck-Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043, Marburg, Germany
| | - Jörn Piel
- Eidgenössische Technische Hochschule (ETH) Zürich, Institute of Microbiology, Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
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Park YK, Nicaud JM. Metabolic Engineering for Unusual Lipid Production in Yarrowia lipolytica. Microorganisms 2020; 8:E1937. [PMID: 33291339 PMCID: PMC7762315 DOI: 10.3390/microorganisms8121937] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 12/15/2022] Open
Abstract
Using microorganisms as lipid-production factories holds promise as an alternative method for generating petroleum-based chemicals. The non-conventional yeast Yarrowia lipolytica is an excellent microbial chassis; for example, it can accumulate high levels of lipids and use a broad range of substrates. Furthermore, it is a species for which an array of efficient genetic engineering tools is available. To date, extensive work has been done to metabolically engineer Y. lipolytica to produce usual and unusual lipids. Unusual lipids are scarce in nature but have several useful applications. As a result, they are increasingly becoming the targets of metabolic engineering. Unusual lipids have distinct structures; they can be generated by engineering endogenous lipid synthesis or by introducing heterologous enzymes to alter the functional groups of fatty acids. In this review, we describe current metabolic engineering strategies for improving lipid production and highlight recent researches on unusual lipid production in Y. lipolytica.
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Affiliation(s)
- Young-Kyoung Park
- Micalis Institute, AgroParisTech, INRAE, Université Paris-Saclay, 78352 Jouy-en-Josas, France;
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Zaremska V, Tan J, Lim S, Knoll W, Pelosi P. Isoleucine Residues Determine Chiral Discrimination of Odorant‐Binding Protein. Chemistry 2020; 26:8720-8724. [DOI: 10.1002/chem.202000872] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/11/2020] [Indexed: 01/26/2023]
Affiliation(s)
- Valeriia Zaremska
- Biosensor TechnologiesAustrian Institute of Technology GmbH Konrad-Lorenz Straße, 24 3430 Tulln Austria
| | - Jiajun Tan
- Biosensor TechnologiesAustrian Institute of Technology GmbH Konrad-Lorenz Straße, 24 3430 Tulln Austria
- School of Chemical and Biomedical EngineeringNanyang Technological University 70 Nanyang Drive Singapore 637457 Singapore
| | - Sierin Lim
- Biosensor TechnologiesAustrian Institute of Technology GmbH Konrad-Lorenz Straße, 24 3430 Tulln Austria
- School of Chemical and Biomedical EngineeringNanyang Technological University 70 Nanyang Drive Singapore 637457 Singapore
| | - Wolfgang Knoll
- Biosensor TechnologiesAustrian Institute of Technology GmbH Konrad-Lorenz Straße, 24 3430 Tulln Austria
| | - Paolo Pelosi
- Biosensor TechnologiesAustrian Institute of Technology GmbH Konrad-Lorenz Straße, 24 3430 Tulln Austria
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Robin J, Gueroult M, Cheikhrouhou R, Guicherd M, Borsenberger V, Marty A, Bordes F. Identification of a crucial amino acid implicated in the hydroxylation/desaturation ratio of CpFAH12 bifunctional hydroxylase. Biotechnol Bioeng 2019; 116:2451-2462. [PMID: 31282998 PMCID: PMC6771796 DOI: 10.1002/bit.27102] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/20/2019] [Accepted: 06/22/2019] [Indexed: 12/12/2022]
Abstract
Claviceps purpurea bifunctional Δ12-hydroxylase/desaturase, CpFAH12, and monofunctional desaturase CpFAD2, share 86% of sequence identity. To identify the underlying determinants of the hydroxylation/desaturation specificity, chimeras of these two enzymes were tested for their fatty acid production in an engineered Yarrowia lipolytica strain. It reveals that transmembrane helices are not involved in the hydroxylation/desaturation specificity whereas all cytosolic domains have an impact on it. Especially, replacing the CpFAH12 cytosolic part near the second histidine-box by the corresponding CpFAD2 part annihilates all hydroxylation activity. Further mutagenesis experiments within this domain identified isoleucine 198 as the crucial element for the hydroxylation activity of CpFAH12. Monofunctional variants performing the only desaturation were obtained when this position was exchanged by the threonine of CpFAD2. Saturation mutagenesis at this position showed modulation in the hydroxylation/desaturation specificity in the different variants. The WT enzyme was demonstrated as the most efficient for ricinoleic acid production and some variants showed a better desaturation activity. A model based on the recently discovered membrane desaturase structures indicate that these changes in specificity are more likely due to modifications in the di-iron center geometry rather than changes in the substrate binding mode.
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Affiliation(s)
- Julien Robin
- LISBP, CNRS, INRA, INSAUniversité de ToulouseToulouseFrance
| | - Marc Gueroult
- UMR URCA/CNRS 7369 Matrice Extracellulaire et Dynamique Cellulaire (MEDyC)Université de Reims Champagne‐ArdenneFrance
| | | | - Marie Guicherd
- LISBP, CNRS, INRA, INSAUniversité de ToulouseToulouseFrance
| | | | - Alain Marty
- LISBP, CNRS, INRA, INSAUniversité de ToulouseToulouseFrance
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