In silico analysis of regulatory elements of the bldD gene of antibiotic-producing Streptomyces species

Abstract

Background: Streptomyces are known for their ability to produce a great variety of antibiotics and other bioactive compounds. The production of these molecules is temporally and genetically coordinated with the bacterial morphological changes. These changes are regulated by transcriptional regulators which coincide with antibiotics production.  The bldD transcriptional regulator BldD protein is identified as one of the key players in the complex morphogenesis and activator of antibiotic production in Streptomyces species.  However, much has remained to be explored about the regulatory mechanisms and level of gene expression of bldD gene in different antibiotics producing Streptomyces species.

Results: we have identified the TSS and the promoters in the upstream coding regions of the bldD gene of the 13 antibiotic-producing Streptomyces species. All, 13/13 (100%) of bldD genes have a single transcription start site (TSS) flanking the coding regions. Using the MEME algorithm five motifs (MtS1- MtS5) are identified, of which Motif 1 (MtS1) has the lowest E-value and the most regulatory motifs for bldD genes among the five discovered motifs. In additions; using the TOMTOM web program, we identified 13 transcription factors associated with MtS1. The analysis of the CpG Island of the gene indicated the presence of lower CpG islands. In additions, Phylogenetic tree were constructed and the results showed the bldD genes containing of streptomyces species are very closely related to other groups of Streptomyces. 

Conclusions: Insilco analysis of gene and gene product is very crucial to get important insight on the gene and mechanisms that trigger them to produce bioactive compounds. In additions, understanding of regulatory elements of the gene that encodes the key activator of antibiotic biosynthesis in Streptomyces species paves the way to enhance the laboratory-based experiments for the production antibiotics.