Transcriptional regulator DhyR positively modulates biosynthesis of daptomycin in Streptomyces rosesporus

The production of daptomycin (DAP) is precisely regulated by a complex regulatory network in Streptomyces roseosporus (S. roseosporus). Although the most biosynthetic pathway of DAP has been elucidated, the regulatory mechanism of its biosynthesis at transcriptional level is not fully understood. In the present study, a transcriptional regulator DhyR has been identified based on our previous quantification proteomics identification in S. roseosporus, and further the dhyR gene deletion mutant has been carried out to reveal DhyR function through transcriptome sequencing and loss-of function validation, which demonstrates DhyR positively regulates DAP biosynthesis in S. rosesporus. In-frame gene deletion of dhyR results in the significant downregulation of the transcription levels of all structural genes in DAP biosynthetic gene cluster and significantly decreases production of DAP. In contrast, overexpression of dhyR enhances transcription levels of DAP biosynthetic gene cluster and leads to a 23% increase of DAP yield. Moreover, the deletion of dhyR resultes in the significant down-regulation of transcription levels of another three regulatory genes, including atrA, depR1 and ssig-05090, which have been demonstrated to be closely associated with the DAP biosynthesis. Transcriptome analyses also support that DhyR modulates carbohydrate metabolism, amino acid metabolism and synthesis and transport pathways of siderophore in S. roseosporus. In summary, our findings indicate that DhyR functions as a pleiotropic regulator of primary and secondary metabolism to involve in DAP biosynthetic regulation of S. roseosporus. To investigate the function of transcriptional regulator DhyR in Streptomyces rosesporus MT19, we established the deletion of dhyR gene strain by CRISPR-Cas9 system. Comparative gene expression profiling anaysis of RNA-seq data for wide-type Streptomyces rosesporus and its deletion of dhyR gene strain.