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

Mohammad Fazel Soltani Gishini; Alireza Zebarjadi; Maryam Abdoli-nasab; Mokhtar Jalali Javaran; Danial Kahrizi; David Hildebrand

doi:10.1007/s10142-019-00718-8

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

Mohammad Fazel Soltani Gishini, Alireza Zebarjadi, Maryam Abdoli-nasab, Mokhtar Jalali Javaran, Danial Kahrizi, David Hildebrand

Plant and Soil Sciences

Research output: Contribution to journal › Article › peer-review

5 Scopus citations

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.

Original language	English
Pages (from-to)	433-458
Number of pages	26
Journal	Functional and Integrative Genomics
Volume	20
Issue number	3
DOIs	https://doi.org/10.1007/s10142-019-00718-8
State	Published - May 1 2020

Bibliographical note

Funding Information:
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.

Publisher Copyright:
© 2019, Springer-Verlag GmbH Germany, part of Springer Nature.

Keywords

Codon usage
Conserved histidine
Delta 15 desaturase
Ion channel
Retention signal

ASJC Scopus subject areas

Genetics

Access to Document

10.1007/s10142-019-00718-8

Cite this

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

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 = "Codon usage, Conserved histidine, Delta 15 desaturase, Ion channel, Retention signal",

author = "{Soltani Gishini}, {Mohammad Fazel} and Alireza Zebarjadi and Maryam Abdoli-nasab and {Jalali Javaran}, Mokhtar and Danial Kahrizi and David Hildebrand",

note = "Funding Information: 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. Publisher Copyright: {\textcopyright} 2019, Springer-Verlag GmbH Germany, part of Springer Nature.",

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doi = "10.1007/s10142-019-00718-8",

language = "English",

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Endoplasmic reticulum retention signaling and transmembrane channel proteins predicted for oilseed ω3 fatty acid desaturase 3 (FAD3) genes. / Soltani Gishini, Mohammad Fazel; Zebarjadi, Alireza; Abdoli-nasab, Maryam et al.
In: Functional and Integrative Genomics, Vol. 20, No. 3, 01.05.2020, p. 433-458.

Research output: Contribution to journal › Article › peer-review

TY - JOUR

T1 - Endoplasmic reticulum retention signaling and transmembrane channel proteins predicted for oilseed ω3 fatty acid desaturase 3 (FAD3) genes

AU - Soltani Gishini, Mohammad Fazel

AU - Zebarjadi, Alireza

AU - Abdoli-nasab, Maryam

AU - Jalali Javaran, Mokhtar

AU - Kahrizi, Danial

AU - Hildebrand, David

N1 - Funding Information: 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. Publisher Copyright: © 2019, Springer-Verlag GmbH Germany, part of Springer Nature.

PY - 2020/5/1

Y1 - 2020/5/1

N2 - 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.

AB - 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.

KW - Codon usage

KW - Conserved histidine

KW - Delta 15 desaturase

KW - Ion channel

KW - Retention signal

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JO - Functional and Integrative Genomics

JF - Functional and Integrative Genomics

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ER -

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

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

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