Identification of a vitamin D3-specific hydroxylase genes through actinomycetes genome mining

We previously completed whole-genome sequencing of a rare actinomycete named Sebekia benihana, and identified the complete S. benihana cytochrome P450 complement (CYPome), including 21 cytochrome P450 hydroxylase (CYP), seven ferredoxin (FD), and four ferredoxin reductase (FDR) genes. Through targeted CYPome disruption, a total of 32 S. benihana CYPome mutants were obtained. Subsequently, a novel cyclosporine A region-specific hydroxylase was successfully determined to be encoded by a CYP-sb21 gene by screening the S. benihana CYPome mutants. Here, we report that S. benihana is also able to mediate vitamin D₃ (VD₃) hydroxylation. Among the 32 S. benihana CYPome mutants tested, only a single S. benihana CYP mutant, ΔCYP-sb3a, failed to show regio-specific hydroxylation of VD₃ to 25-hydroxyvitamin D₃ and 1α,25-dihydroxyvitamin D₃. Moreover, the VD₃ hydroxylation activity in the ΔCYP-sb3a mutant was restored by CYP-sb3a gene complementation. Since all S. benihana FD and FDR disruption mutants maintained VD₃ hydroxylation activity, we conclude that CYP-sb3a, a member of the bacterial CYP107 family, is the only essential component of the in vivo regio-specific VD₃ hydroxylation process in S. benihana. Expression of the CYP-sb3a gene exhibited VD₃ hydroxylation in the VD₃ non-hydroxylating Streptomyces coelicolor, implying that the regio-specific hydroxylation of VD₃ is carried out by a specific P450 hydroxylase in S. benihana.