Sequence characterization and in silico structure prediction of fatty acid desaturases in linseed varieties with differential fatty acid composition.
BACKGROUND
Linseed is the richest agricultural source of α-linolenic acid (ALA), an ω-3 fatty acid (FA) that offers several nutritional benefits. In the present study, sequence characterization of six desaturase genes (SAD1, SAD2, FAD2, FAD2-2, FAD3A and FAD3B) and 3D structure prediction of their proteins from ten Indian linseed varieties differing in ALA content were performed to determine whether the nucleotide and amino acid (AA) sequence variants have any functional implications in differential accumulation of ALA or other FAs in linseed.


RESULTS
The SAD and FAD2 genes exhibited few sequence variations among the ten varieties, forming only one or two protein isoforms. In contrast, the FAD3A and FAD3B genes showed more sequence variations and three or four protein isoforms. Interestingly, the two high-ALA varieties NL260 and Padmini had the same FAD3B nucleotide and protein isoforms, which differed from all other varieties. Surprisingly, no AA changes altered the 3D structures of the desaturase proteins.


CONCLUSIONS
Several nucleotide and AA sequence variations in desaturase genes were observed; however, they did not alter the 3D structure of any desaturase protein and were not correlated with FA levels among the ten linseed varieties, which had different ALA contents. This suggests a complex regulatory process of biosynthesis of FAs in linseed. © 2016 Society of Chemical Industry.
Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411 008, India.
Ashwini V
AV
Rajwade
Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411 008, India.
Rakesh S
RS
Joshi
Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411 008, India. ny.kadoo@ncl.res.in.
Narendra Y
http://orcid.org/0000-0002-9079-1226
NY
Kadoo
Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, 411 008, India. vs.gupta@ncl.res.in.
Vidya S
VS
Gupta
D000595:Amino Acid Sequence; D001483:Base Sequence; D003198:Computer Simulation; D044943:Fatty Acid Desaturases / Q000737:chemistry* / Q000235:genetics*; D005227:Fatty Acids / Q000032:analysis*; D019597:Flax / Q000737:chemistry* / Q000201:enzymology*; D018506:Gene Expression Regulation, Plant; D014644:Genetic Variation; D006239:Haplotypes; D008968:Molecular Conformation; D020033:Protein Isoforms / Q000737:chemistry / Q000235:genetics; D013045:Species Specificity; D017962:alpha-Linolenic Acid / Q000032:analysis
D005227:Fatty Acids; D020033:Protein Isoforms; D017962:alpha-Linolenic Acid; D044943:Fatty Acid Desaturases
ALA; fatty acid desaturases; fatty acids; flax; haplotypes; protein structure