Molecular Mechanisms of Ligand-Mediated Attenuation of DNA Binding by MarR Family Transcriptional Regulators

Abstract

Bacteria and archaea encode members of the large multiple antibiotic resistance regulator (MarR) family of transcriptional regulators. Generally, MarR homologs regulate activity of genes involved in antibiotic resistance, stress responses, virulence or catabolism of aromatic compounds. They constitute a diverse group of transcriptional regulators that includes both repressors and activators, and the conventional mode of regulation entails a genetic locus in which the MarR homolog and a gene under its regulation are encoded divergently; binding of the MarR homolog to the intergenic region typically represses transcription of both genes, while binding of a specific ligand to the transcription factor results in attenuated DNA binding and hence activated gene expression. For many homologs, the natural ligand is unknown. Crystal structures reveal a common architecture with a characteristic winged helix domain for DNA binding, and recent structural information of homologs solved both in the absence and presence of their respective ligands, as well as biochemical data, is finally converging to illuminate the mechanisms by which ligand-binding causes attenuated DNA binding. As MarR homologs regulate pathways that are critical to bacterial physiology, including virulence, a molecular understanding of mechanisms by which ligands affect a regulation of gene activity is essential. Specifying the position of ligand-binding pockets further has the potential to aid in identifying the ligands for MarR homologs for which the ligand remains unknown.

Structural insights into protein-protein interactions governing regulation in transcription initiation and ubiquitination

“…Importantly, the MarR-DNA bound structures consistently shows that the H4 and H4', DNArecognition helices from wHTH motif binds to the major groove and that the Wings from each monomer subunit places specific MarR-contacts with the minor groove of the DNA (Fig. 4c) (ref 48 ). Comparing all the DNA bound MarR structures (Table 2), the relative position of DNA-recognition H4 and H4' helices are placed in similar positions and the distance measure of the mid-points of these two helices (see inset in Fig.…”

“…The dimerization domain and the wHTH domain are connected by the helix2, H2, which maintains the relative orientations of the subdomains in the intersubunit dimer 48 . While mutational analyses on the dimerization helices have been shown to impact DNA interaction 54 , the key pattern recognizing the DNA promoter region is deployed in the wHTH motif 47 .…”

“…Few MarR members are shown to bind small molecule ligands inhibiting its repression activity of DNA binding both in vitro and in vivo, and thereby functionally linking environmental signals with gene expression responses 48 . The crystal structure of E.coli MarR only crystallized in presence of salicylate 49 , although the physiological role of this ligand bound is not identified, but the MarR-ligand bound shows the structure incompatible with DNA binding.…”

“…With the continued structural studies on MarR homologues, it is now evident that many MarR members are also regulated by ligand-binding, includes MarR, MTH313, ST1710, all bound to sodium salicylate 49,52 , and the structures of MarR homologues bound to natural ligand, such as HucR-urate 60 and TcaR-antibiotics 61 ( Table 2). The salicylate binding site is located in a deep pocket at the dimerization and DNA binding lobe, inducing a conformational change that appears to be incompatible with DNA binding 48 . While the antibiotic bound complexes have recently pointed out the essential cavities for drug binding, as evidenced by the TcaR-drug bound structures 61 , further arguments underpin that the interfaces are located at the helical dimerization domain and the winged HTH DNArecognition region.…”

“…Escherichia coli and the proteins belonging to this family are distributed throughout the bacterial and the archaeal species, counting to almost 12,000 MarR-like proteins identified, but the physiological role is only known for around 100 members so far 48 (Refer to Table 2 for the list of MarR homologues, and that are encoded in respective bacterial organisms). In general, MarR homologues function as molecular systems that are critical to bacterial physiology such as responding to specific ligands and metabolites, oxidative stress agents, virulence or pathogenic factors and multi-drug resistance.…”