Structural comparison of promoter and coding sequence of type I collagen alpha 1 chain gene duplicates between zebrafish and flounder/fugu lineages

Alpha 1 chain (Colα1(I)) and alpha 2 chain (Colα2(I)) are universal components of type I collagen in tetrapods, but rainbow trout (Oncorhynchus mykiss) and zebrafish (Danio rerio) have a third: alpha 3 chain (Colα3(I)). This study tests whether Colα3(I) is a duplicate of Colα1(I) by whole-genome duplication (WGD) that occurred early in the ray-fin fish lineage. We also examine how their promoter sequence was modified after WGD. We cloned Colα1(I), Colα2(I) and Colα3(I) cDNAs and their promoters from flounder (Paralichthys olivaceus) and obtained corresponding sequences from the genome databanks of two pufferfishes Takifugu rubripes and Tetraodon nigroviridis, by BLAST-Search using flounder sequences. Phylogenetic analysis of N-terminal sequences of ca. 100 amino acids, including signal peptide and N-propeptide sequences before short triple helical domain, indicates that Colα3(I), found only in teleosts, is a duplicate of Colα1(1) by WGD. Colα1(I) and Colα3(I) genes begin to be transcribed at different stages of Takifugu embryogenesis, suggesting that their structure of promoter is modified differently after WGD. In flounder, Takifugu and Tetraodon, the structure of proximal region of promoter is highly conserved within Colα1(I) and within Colα3(I); no homology is apparent except for the TATA element motif between Colα1(I) and Colα3(I) of each species. Unexpectedly, zebrafish Colα1(I) promoter is more homologous to Colα3(I) of flounder and fugu than Colα1(I) is. These results suggest that each duplicated Colα1(I) gene promoter inherited a unique structure after WGD, but the manner of modification differed between the phylogenetically separated zebrafish and flounder/pufferfish lineages.