The MerR-like protein BldC binds DNA direct repeats as cooperative multimers to regulate Streptomyces development

Abstract

Streptomycetes are notable for their complex life cycle and production of most clinically important antibiotics. A key factor that controls entry into development and the onset of antibiotic production is the 68-residue protein, BldC. BldC is a putative DNA-binding protein related to MerR regulators, but lacks coiled-coil dimerization and effector-binding domains characteristic of classical MerR proteins. Hence, the molecular function of the protein has been unclear. Here we show that BldC is indeed a DNA-binding protein and controls a regulon that includes other key developmental regulators. Intriguingly, BldC DNA-binding sites vary significantly in length. Our BldC-DNA structures explain this DNA-binding capability by revealing that BldC utilizes a DNA-binding mode distinct from MerR and other known regulators, involving asymmetric head-to-tail oligomerization on DNA direct repeats that results in dramatic DNA distortion. Notably, BldC-like proteins radiate throughout eubacteria, establishing BldC as the founding member of a new structural family of regulators.

Specialized and shared functions of diguanylate cyclases and phosphodiesterases inStreptomycesdevelopment

“…MtrA acts as both activator and repressor in other actinomycetes, but how it impacts bld and whi gene expression remains to be addressed in S. venezuelae . Another example is the MerR-like regulator, BldC, which binds to a number of promoters that are also direct targets of BldD; like MtrA, BldC can have both repressor and activator functions (25).…”

BldC delays entry into development to produce a sustained period of vegetative growth inStreptomyces venezuelae

“…5 and Table 1). Schumacher et al (11) characterized the interaction of S. coelicolor BldC with the promoters of two of its previously known targets, whiI and the smeA-ssfA operon. whiI encodes an orphan response regulator that is essential for the later stages of sporulation, when it forms a functional heterodimer with a second orphan response regulator, BldM, enabling WhiI to bind to DNA and regulate the expression of ~40 sporulation genes (14).…”

“…Schumacher et al (11) showed that BldC binds to DNA in a head-to-tail fashion at a variable number of direct repeats. So, for example, in the whiI- BldC structure, there are two direct repeats resulting in the head-to-tail oligomerisation of two BldC monomers, whereas in the smeA- BldC structure there are four direct repeats resulting in the head-to-tail oligomerisation of four BldC monomers.…”

“…To address this question, Schumacher et al (11) carried out biochemical and structural studies to characterize the binding of S. coelicolor BldC to the promoters of two known target genes, whiI and smeA . These studies showed that BldC binds DNA in a completely different way to classical MerR regulators, instead involving asymmetric, cooperative, head-to-tail oligomerization on DNA direct repeats with concomitant pronounced DNA distortion (11). The number of direct repeats present in BldC-binding sites is variable, thus allowing cooperative, head-to-tail binding of additional BldC monomers.…”

“…Although the work by Schumacher et al (11) has provided a clear mechanistic understanding of how BldC binds DNA, there has been less insight into its biological role and impact on Streptomyces development. In part, this is because previous studies have focussed on the classical model species, S. coelicolor , which sporulates only on solid medium.…”