Cloning, mRNA expression and bioinformatic analysis of full length type collagen alpha 1 Ⅰ cDNA from grass carp (Ctenopharyngodon idellus)

Abstract

TypeⅠcollagen, as a number of collagen family, is the most abundant collagen and major components of the extracellular matrices of all metazoan life, and plays crucial roles in differentiation, formation of collagen fibers and tissue remodeling after injury, etc. Type Ⅰ collagen alpha 1(COL1A1) cDNA of grass carp (Ctenopharyngodon idella) was isolated through the RT-PCR and RACE approaches. The cDNA was 5 772-bp in length, including a 4 347-bp CDS (coding sequence) and encoded a polypeptide of 1 449 aa. The homology of COL1A1 amino acid with relative species (zebrafish, goldfish, etc.) was as high as 93% with zebra fish and goldfish. The protein peptide molecular weight was 137.2 ku and theoretical pI was 5.44 using ProtParam software on line. The protein peptides of COL1A1 possessed 6 α-helixes, 12 β-sheets, others of ruleless coil regions, and 18 regions of triple helical repeats, 22 low complexity regions, 17 function domains. There were two calcium-binding sites and one zinc-binding site in the COL1A1 protein peptide. COL1A1 mRNA was determined in all the tested 8 tissues (muscle, intestine, hepatopancreas, gill, skin, fin, kidney and spleen) of grass carp by semi- quantitative RT-PCR, and the mRNAs expression in gill, kidney, skin and fin significantly higher than other tissues (P0.05). The structure and bioinformatics characteristics of the COL1A1 from grass carp may help to further understand the function of COL1A1 gene in the repair process of damaged tissue in the grass carp.