SNP discovery and structural insights into OeFAD2 unravelling high oleic/linoleic ratio in olive oil

Rayda Ben Ayed; Fabienne Moreau; Hajer Ben Hlima; Ahmed Rebai; Sezai Ercisli; Narendra Kadoo; Mohsen Hanana; Amine Assouguem; Riaz Ullah; Essam A Ali

doi:10.1016/j.csbj.2022.02.028

SNP discovery and structural insights into OeFAD2 unravelling high oleic/linoleic ratio in olive oil

Comput Struct Biotechnol J. 2022 Mar 4:20:1229-1243. doi: 10.1016/j.csbj.2022.02.028. eCollection 2022.

Authors

Rayda Ben Ayed¹, Fabienne Moreau², Hajer Ben Hlima³, Ahmed Rebai¹, Sezai Ercisli⁴, Narendra Kadoo^{5

6}, Mohsen Hanana⁷, Amine Assouguem⁸, Riaz Ullah⁹, Essam A Ali¹⁰

Affiliations

¹ Laboratory of Molecular and Cellular Screening Processes, Genomics and Bioinformatics Group, Centre of Biotechnology of Sfax, PB 1177, 3018 Sfax, Tunisia.
² Institut National de la Recherche Agronomique (INRA), 2 Place Pierre Viala, 34000 Montpellier, France.
³ Laboratoire de Génie Enzymatique et de Microbiologie, Equipe de Biotechnologie des Algues, Ecole Nationale d'Ingénieurs de Sfax, Université de Sfax, 3038 Sfax, Tunisia.
⁴ Ataturk University, Faculty of Agriculture, Department of Horticulture, 25240 Erzurum, Turkey.
⁵ CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India.
⁶ Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
⁷ Laboratory of Extrêmophile Plants, Biotechnology Center of Borj-Cédria, B.P. 901, 2050 Hammam Lif, Tunisia.
⁸ Laboratory of Functional Ecology and Environment, Faculty of Sciences and Technology, Sidi Mohamed Ben Abdellah University, Imouzzer Street, Fez P.O. Box 2202, Morocco.
⁹ Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia.
¹⁰ Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia.

Abstract

Fatty Acid Desaturase 2 (FAD2), a key enzyme in the fatty acid biosynthesis pathway, is involved in the desaturation and conversion of oleic acid to linoleic acid. Therefore, it plays a crucial role in oleic/linoleic acid ratio and the quality of olive oil. DNA sequencing of 19 FAD2 genes from a set of olive oil varieties revealed several single-nucleotide polymorphisms (SNPs) and highlighted associations between some of the SNPs and saturated fatty acids contents. This was further confirmed by SNP-interaction and machine learning approach. Haplotype diversity analysis led to the discovery of three highly polymorphic SNPs and four haplotypes harboring differential oleic/linoleic acid ratios. Moreover, a combination of molecular modeling and docking experiments allowed a deeper and better understanding of the structure-function relationship of the FAD2 enzyme. Sequence patterns and variations involved in the regulation of the FAD2 activity were also identified. Furthermore, S82C and H213N substitutions in OeFAD2 make the Oueslati variety more interesting in terms of fatty acid profile and oleic acid level.

Keywords: Docking; Fatty acid desaturase; Haplotype; Machine learning; Oleic/linoleic acid ratio; Protein structure.