Systems-wide analysis of the ROK-family regulatory gene rokL6 and the control of aminosugar toxicity in Streptomyces coelicolor

Abstract

Streptomycetes are saprophytic bacteria that grow on complex polysaccharides, such as cellulose, starch, chitin and chitosan. For the monomeric building blocks glucose, maltose and N-acetylglucosamine (GlcNAc), the metabolic pathways are well documented, but that of glucosamine (GlcN) is largely unknown. Streptomyces nagB mutants, which lack glucosamine-6-phosphate deaminase activity, fail to grow in the presence of high concentrations of GlcN. Here we report that mutations in the gene for the ROK-family transcriptional regulator RokL6 relieve the toxicity of GlcN in nagB mutants, as a result of elevated expression of the Major Facilitator Superfamily (MFS) exporter SCO1448. Systems-wide analysis using RNA sequencing, ChIP-Seq, EMSAs, 5’RACE, bioinformatics and genetics revealed that RokL6 is an autoregulator that represses transcription of SCO1448 by binding to overlapping promoters in the rokL6-SCO1448 intergenic region. RokL6-independent expression of SCO1448 fully relieved toxicity of GlcN to nagB mutants. Taken together, our data show a novel system of RokL6 as a regulator that controls the expression of the MFS transporter SCO1448, which in turn protects cells against GlcN toxicity, most likely by exporting toxic metabolites out of the cell.