title: New layers in understanding and predicting α-linolenic acid content in plants using amino acid characteristics of omega-3 fatty acid desaturase.
abstract: α-linolenic acid (ALA) is the most frequent omega-3 in plants. The content of ALA is highly variable, ranging from 0 to 1% in rice and corn to >50% in perilla and flax. ALA production is strongly correlated with the enzymatic activity of omega-3 fatty acid desaturase. To unravel the underlying mechanisms of omega-3 diversity, 895 protein features of omega-3 fatty acid desaturase were compared between plants with high and low omega-3. Attribute weighting showed that this enzyme in plants with high omega-3 content has higher amounts of Lys, Lys-Phe, and Pro-Asn but lower Aliphatic index, Gly-His, and Pro-Leu. The Random Forest model with Accuracy criterion when run on the dataset pre-filtered with Info Gain algorithm was the best model in distinguishing high omega-3 content based on the frequency of Lys-Lys in the structure of fatty acid desaturase. Interestingly, the discriminant function algorithm could predict the level of omega-3 only based on the six important selected attributes (out of 895 protein attributes) of fatty acid desaturase with 75% accuracy. We developed "Plant omega3 predictor" to predict the content of α-linolenic acid based on structural features of omega-3 fatty acid desaturase. The software calculates the 6 key structural protein features from imported Fasta sequence of omega-3 fatty acid desaturase or utilizes the imported features and predicts the ALA content using discriminant function formula. This work unravels an underpinning mechanism of omega-3 diversity via discovery of the key protein attributes in the structure of omega-3 desaturase offering a new approach to obtain higher omega-3 content.
authors.affiliation: Department of Crop Production and Plant Breeding, Faculty of Agriculture, Shiraz University, Shiraz, Iran. Electronic address: zahra.zinati@gmail.com.
authors.forename: Zahra
authors.initials: Z
authors.lastname: Zinati
authors.affiliation: Department of Crop Production and Plant Breeding, Faculty of Agriculture, Shiraz University, Shiraz, Iran. Electronic address: fatemeh.zamansani@gmail.com.
authors.forename: Fatemeh
authors.initials: F
authors.lastname: Zamansani
authors.affiliation: Bioinformatics Research Group and Department of Biology, School of Basic Sciences, University of Qom, Qom, Iran. Electronic address: a.h.kaivanjo@live.com.
authors.forename: Amir
authors.initials: A
authors.lastname: Hossein KayvanJoo
authors.affiliation: Saarland University, Department of Informatics, Saarbrucken, Germany. Electronic address: ebrahimi@mpi-inf.mpg.de.
authors.forename: Mahdi
authors.initials: M
authors.lastname: Ebrahimi
authors.affiliation: Bioinformatics Research Group and Department of Biology, School of Basic Sciences, University of Qom, Qom, Iran. Electronic address: mansour@future.org.
authors.forename: Mansour
authors.initials: M
authors.lastname: Ebrahimi
authors.affiliation: The University of Adelaide, School of Molecular and Biomedical Science, Adelaide, SA, Australia. Electronic address: esmaeil.ebrahimie@adelaide.edu.au.
authors.forename: Esmaeil
authors.initials: E
authors.lastname: Ebrahimie
authors.affiliation: The University of Adelaide, School of Agriculture, Food, and Wine, Adelaide, SA, Australia. Electronic address: manijeh.mohammadidehcheshmeh@adelaide.edu.au.
authors.forename: Manijeh
authors.initials: M
authors.lastname: Mohammadi Dehcheshmeh
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D044943:Fatty Acid Desaturases; D008969:Molecular Sequence Data; D010940:Plant Proteins / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D025941:Protein Interaction Mapping / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D017962:alpha-Linolenic Acid / Q000737:chemistry* / Q000378:metabolism
chemical_list: D000596:Amino Acids; D010940:Plant Proteins; D017962:alpha-Linolenic Acid; D044943:Fatty Acid Desaturases; C078565:omega-3 fatty acid desaturase
keywords: Amino acids; Bioinformatics; Discriminant function; Feature selection; Machine learning: modelling; Omega-3; Prediction; Random Forest model; α-Linolenic acid