Structural and functional basis of transcriptional regulation by TetR family protein CprB from S. coelicolor A3(2)

Abstract

Antibiotic production and resistance pathways in Streptomyces are dictated by the interplay of transcriptional regulatory proteins that trigger downstream responses via binding to small diffusible molecules. To decipher the mode of DNA binding and the associated allosteric mechanism in the sub-class of transcription factors that are induced by γ-butyrolactones, we present the crystal structure of CprB in complex with the consensus DNA element to a resolution of 3.25 Å. Binding of the DNA results in the restructuring of the dimeric interface of CprB, inducing a pendulum-like motion of the helix-turn-helix motif that inserts into the major groove. The crystal structure revealed that, CprB is bound to DNA as a dimer of dimers with the mode of binding being analogous to the broad spectrum multidrug transporter protein QacR from the antibiotic resistant strain Staphylococcus aureus. It was demonstrated that the CprB displays a cooperative mode of DNA binding, following a clamp and click model. Experiments performed on a subset of DNA sequences from Streptomyces coelicolor A3(2) suggest that CprB is most likely a pleiotropic regulator. Apart from serving as an autoregulator, it is potentially a part of a network of proteins that modulates the γ-butyrolactone synthesis and antibiotic regulation pathways in S. coelicolor A3(2).

Structural and Functional Characterization of a Ketosteroid Transcriptional Regulator of Mycobacterium tuberculosis

“…Intriguingly, KstR2 Mtb contains the Arg-X-Thr motif that is present in SlmA and induces a kink in the DNA (31). Similar models have been invoked to explain cooperative binding in each of two other TFRs, QacR and CprB (46,47), although QacR lacks the Arg residue and does not induce a kink in the DNA. Interestingly, single KstR2 boxes occur between divergently transcribed promoters (13) and gel shift assays indicate that KstR2 binds to each of the three boxes with the same stoichiometry (12).…”

“…Typically the TFR operators that bind two dimers are at least 22 bp in length (31,(45)(46)(47). By contrast, TFRs that bind operator sequences of less than 17 bp bind as a single dimer (46).…”

Quorum Sensing Gene Regulation by LuxR/HapR Master Regulators in Vibrios

“…Based on chromatin immunoprecipitation sequencing (ChIP-seq) data, there are 227 LuxR binding sites in the promoters of 115 genes, yielding an average of ϳ2 sites per promoter (74). Of note, some TetR-type proteins, such as QacR, bind cooperatively as dimers of dimers on opposite sides of the DNA helix (84)(85)(86). While the mechanism of DNA binding by LuxR proteins is unclear in the absence of a DNA-bound structure, it is possible that LuxR proteins bind DNA in this manner.…”

Butyrolactone signalling circuits for synthetic biology

“…Recognition of the signalling molecule occurs through the C-terminal region of the protein [24 ]. A recent publication [25] has shown that the GBL core directly interacts with the binding pocket of the receptor, implying that this structure is responsible for the recognition of the GBL, whereas the n-alkane C 2 residue may be responsible for the specificity of the binding, and therefore the threshold concentration necessary to perform the switch-like transition, as previously suggested by Hsiao et al [26].…”

“…The crystal structure of CprB, a GBL pseudo-receptor homologue bound to DNA has been elucidated recently [24 ]. Together with the earlier crystal structure of the apo form of the receptor [41] this creates an exciting opportunity to understand the molecular mechanisms of the receptor-GBL complex.…”