Title: Identification of SoxR dependent genes in S. coelicolor using RNA-Seq
Authors: Nawar Naseer and Monica Chander
Affiliation: Biology Department, Bryn Mawr College, Bryn Mawr, Pennsylvania
Our goal is to understand the function of the transcription factor, SoxR, in the antibiotic-producing soil bacterium Streptomyces coelicolor. Previous research from our lab has established that in S. coelicolor, SoxR is activated by the endogenously produced redox-active antibiotic actinorhodin (Act), and five SoxR regulated genes were identified (bioinformatically) and subsequently verified as SoxR targets (Dela Cruz et al., 2010). These genes encode proteins which bear resemblance to enzymes in the Act biosynthetic pathway. Thus, SoxR may regulate mechanisms that allow S. coelicolor to adapt to toxic endogenous metabolites. In an attempt to identify additional SoxR targets in S. coelicolor we conducted RNA-Seq analysis to compare the transcriptomes of wild type and soxR mutant strains. This revealed four previously unidentified genes that were significantly under-expressed in the soxR mutant compared to WT. Three of these genes encode redox-associated enzymes that belong in same functional category as known SoxR targets. The fourth (SCO1177) encodes a putative transcriptional regulator, and it is possible that SoxR indirectly regulates some genes via SCO1177. In order to determine if SoxR directly regulates any of the newly identified genes, band shift assays will be conducted with purified SoxR and the appropriate promoter fragments. To establish if SCO1177 acts as an intermediate regulator, this gene will be deleted, and the expression of SoxR dependent genes will be analyzed in the resulting background.
Dela Cruz, R., Y. Gao, S. Penumetcha, R. Sheplock, K. Weng, and M. Chander, 2010, Expression of the Streptomyces coelicolor SoxR regulon is intimately linked with actinorhodin production: Journal of bacteriology, v. 192, p. 6428-6438.