Insight into the induction mechanism of the GntR/HutC bacterial transcription regulator YvoA

Abstract

YvoA is a GntR/HutC transcription regulator from Bacillus subtilis implicated in the regulation of genes from the N-acetylglucosamine-degrading pathway. Its 2.4-Å crystal structure reveals a homodimeric assembly with each monomer displaying a two-domain fold. The C-terminal domain, which binds the effector N-acetylglucosamine-6-phosphate, adopts a chorismate lyase fold, whereas the N-terminal domain contains a winged helix–turn–helix DNA-binding domain. Isothermal titration calorimetry and site-directed mutagenesis revealed that the effector-binding site in YvoA coincides with the active site of related chorismate lyase from Escherichia coli. The characterization of the DNA- and effector-binding properties of two disulfide-bridged mutants that lock YvoA in two distinct conformational states provides for the first time detailed insight into the allosteric mechanism through which effector binding modulates DNA binding and, thereby regulates transcription in a representative GntR/HutC family member. Central to this allosteric coupling mechanism is a loop-to-helix transition with the dipole of the newly formed helix pointing toward the phosphate of the effector. This transition goes in hand with the emergence of internal symmetry in the effector-binding domain and, in addition, leads to a 122° rotation of the DNA-binding domains that is best described as a jumping-jack-like motion.

Regulon of the N -Acetylglucosamine Utilization Regulator NagR in Bacillus subtilis

“…However, Resch and collaborators demonstrated that once bound to GlcNAc-6-P, NagR is still able to bind half-side dre in vitro. This is compatible with a model in which the regulator acts as both an activator and a repressor beyond the canonical mutually exclusive effector-bound or DNA-bound regulator logic (49). If GlcNAc-6-P should prove capable of inducing a jumping-jacklike motion of NagR (as proposed by Resch et al) in vivo or if the NagR/GlcNAc-6-P complex is still able to recognize and bind half-side dre, this automatically raises the question of how widespread the distribution of half-NagR-binding sites in the B. subtilis chromosome is.…”

“…3A). GlcN-6-P was also reported to inhibit the DNA-binding capability of DasR in S. coelicolor (51), whereas isothermal calorimetry titration measurements for binding of GlcN-6-P to YvoA conducted by Resch and colleagues had been inconclusive (49). Interestingly, the crystal structure in this study had been solved for YvoA in complex with GlcNAc-6-P, which had not appeared to interfere with dre binding in EMSA.…”

“…A recent study revealed the crystal structure of YvoA (49), which belongs to the HutC subfamily of GntR-type transcriptional regulators (50). The ortholog of YvoA in streptomycetes, DasR (deficient in aerial hyphae and spore formation), has been analyzed in depth: next to its involvement in the control of GlcNAc utilization (52), DasR plays a pivotal role in the regulation of antibiotic synthesis and differentiation (51,53).…”

Multiple allosteric effectors control the affinity of DasR for its target sites

“…EMSAs performed with DasR of Saccharopolyspora erythraea (DasR sery ) also revealed that GlcN-6P was able to modulate its DNA-binding capability though in a different way than the simple dissociation of the regulatory protein from its target dre observed for DasR of S. coelicolor (DasR sco ) as, instead, multiple retarded bands were observed upon incubation of DasR sery with GlcN-6P [6]. In Bacilli, the GntR/HutC family NagR (formerly named YvoA [16]) is the DasR orthologue which appears to only control genes for GlcNAc transport and phosphorylation by the PTS (nagP), and the genes for its subsequent deacetylation into GlcN-6P (nagA), and GlcN-6P deamination and isomerization into fructose-6-phosphate (nagB) [17]. The first attempt to identify the allosteric effector of NagR revealed a similar inhibitory effect of GlcN-6P on the DNA-binding ability of NagR as described for DasR sco [17].…”

NagR Differentially Regulates the Expression of the glmS and nagAB Genes Required for Amino Sugar Metabolism by Streptococcus mutans

“…When GlcNAc is present in the environment, intracellular GlcNAc-6-P accumulates and activates the expression of genes for GlcNAc and GlcN catabolism by disrupting the interaction between NagC and dre sites (5,(11)(12)(13). In the Gram-positive bacterium Bacillus subtilis, a GntR/HutC-type regulator, designated NagR (formerly YvoA), binds to nonhomologous operator sites, also called dre (14,15), to control the transcription of nagA, nagB, and nagP, which codes for a GlcNAc-specific PTS permease. Unlike in E. coli, though, the allosteric effector(s) that alleviates repression of these target genes by NagR remains undetermined (14,16,17).…”