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Endoplasmic reticulum retention signaling and transmembrane channel proteins predicted for oilseed ω3 fatty acid desaturase 3 (FAD3) genes

  • Mohammad Fazel Soltani Gishini
  • Alireza ZebarjadiEmail author
  • Maryam Abdoli-nasab
  • Mokhtar Jalali Javaran
  • Danial Kahrizi
  • David HildebrandEmail author
Original Article
  • 40 Downloads

Abstract

Oilseed crop oils contain a variety of unsaturated fatty acids that are synthesized and regulated by fatty acid desaturases (FADs). In this study, 14 FAD3 (ω3 desaturase) protein sequences from oilseeds are analyzed and presented through the application of several computational tools. The results indicated a close relationship between Brassica napus and Camelina sativa, as well as between Salvia hispanica and Perilla frutescens FAD3s, due to a high similarity in codon preferences in codon usage clusters and the phylogenetic tree. The cis-acting element results reveal that the seed-specific promoter region of BnFAD3 contains the critical conserved boxes such as HSE and ABRE, which are involved in responsiveness to heat stress and abscisic acid. The presence of the aforementioned conserved boxes may increase cold acclimation as well as tolerance to drought and high salinity. Omega(ω)3 desaturases contain a Skn-1 motif which is a cis-acting regulatory element required involved in endosperm development. In oilseed FAD3s, leucine is the most repeated amino acid in FAD3 proteins. The study conveyed that B. napus, Camelina sativa, Linum usitatissimum, Vernicia fordii, Gossypium hirsutum, S. hispanica, Cannabis sativa, and P. frutescens have retention signal KXKXX/XKXX at their c-terminus sites, which is one of the most important characteristics of FADs. Additionally, it was found that BnFAD3 is a transmembrane protein that can convert ω6 to ω3 fatty acids and may simultaneously act as a potassium ion channel in the ER.

Keywords

Delta 15 desaturase Conserved histidine Retention signal Codon usage Ion channel 

Notes

Acknowledgments

Molecular graphics and analyses were performed with the UCSF Chimera package. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIGMS P41-GM103311). Special thanks to Rebecca Caldbeck, Haleigh Whitlock, and Connor Coatney at the University of Kentucky for editing and reviewing of this manuscript.

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© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Production Engineering and Plant Genetics, Faculty of Sciences and Agricultural Engineering, Campus of Agriculture and Natural ResourcesRazi UniversityKermanshahIran
  2. 2.Department of Biotechnology, Institute of Science, High Technology and Environmental ScienceGraduate University of Advanced TechnologyKermanIran
  3. 3.Department of Plant Breeding & Biotechnology, Faculty of AgricultureTarbiat Modarres UniversityTehranIran
  4. 4.Department of Plant & Soil SciencesUniversity of KentuckyLexingtonUSA

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