Crystal Structures of Two Transcriptional Regulators from Bacillus cereus Define the Conserved Structural Features of a PadR Subfamily

Abstract

PadR-like transcriptional regulators form a structurally-related family of proteins that control the expression of genes associated with detoxification, virulence and multi-drug resistance in bacteria. Only a few members of this family have been studied by genetic, biochemical and biophysical methods, and their structure/function relationships are still largely undefined. Here, we report the crystal structures of two PadR-like proteins from Bacillus cereus, which we named bcPadR1 and bcPadR2 (products of gene loci BC4206 and BCE3449 in strains ATCC 14579 and ATCC 10987, respectively). BC4206, together with its neighboring gene BC4207, was previously shown to become significantly upregulated in presence of the bacteriocin AS-48. DNA mobility shift assays reveal that bcPadR1 binds to a 250 bp intergenic region containing the putative BC4206–BC4207 promoter sequence, while in-situ expression of bcPadR1 decreases bacteriocin tolerance, together suggesting a role for bcPadR1 as repressor of BC4206–BC4207 transcription. The function of bcPadR2 (48% identical in sequence to bcPadR1) is unknown, but the location of its gene just upstream from genes encoding a putative antibiotic ABC efflux pump, suggests a role in regulating antibiotic resistance. The bcPadR proteins are structurally similar to LmrR, a PadR-like transcription regulator in Lactococcus lactis that controls expression of a multidrug ABC transporter via a mechanism of multidrug binding and induction. Together these proteins define a subfamily of conserved, relatively small PadR proteins characterized by a single C-terminal helix for dimerization. Unlike LmrR, bcPadR1 and bcPadR2 lack a central pore for ligand binding, making it unclear whether the transcriptional regulatory roles of bcPadR1 and bcPadR2 involve direct ligand recognition and induction.

Transcriptional Regulation of the Vanillate Utilization Genes ( vanABK Operon) of Corynebacterium glutamicum by VanR, a PadR-Like Repressor

“…In addition, protein crystallography, fusion of AphA to the DNA binding domain of LexA, and the use of crosslinking reagents showed that AphA protein forms a dimer (18,48). Obviously, members of the PadR-like proteins form dimers due to their C-terminal domain, which is a coiled-coil leucine zipper-like structure (23). Despite this structural resemblance, the already-known PadR-like regulators function in different regulatory pathways.…”

“…Subfamily 1 has a C-terminal domain of 80 to 90 residues, such as AphA from Vibrio cholerae (18), LadR from Listeria monocytogenes (19), and PadR from Pediococcus pentosaceus, Lactobacillus plantarum, or Bacillus subtilis (11,20,21). The proteins of subfamily 2 have a shorter C-terminal domain than subfamily 1 and contain 20 to 30 residues, such as LmrR from Lactococcus lactis (22) as well as Bacillus cereus PadR1 (bcPadR1) and bcPadR2 (23). Apart from their structures, physiological characteristics of the PadR, AphA, and LmrR regulators were intensively studied (21,(24)(25)(26).…”

Transcriptional Repressor PtvR Regulates Phenotypic Tolerance to Vancomycin in Streptococcus pneumoniae

“…Other members of this protein family are shown to regulate diverse processes, including multidrug resistance (53-55), virulence (56), and cellular metabolism (57,58). Many PadR family regulators repress the transcription of the target genes by binding to specific sequences of the promoter regions with a conserved N-terminal winged helix-turn-helix domain and thereby blocking the promoter-RNA polymerase interactions in the absence of inducers (e.g., phenolic acid and antibiotic) (46,59). Transcriptional derepression occurs when the regulator "falls off" the target DNA sequence after binding to the cognate inducers (e.g., phenolic acid and other toxic compounds) (46,59).…”

“…Many PadR family regulators repress the transcription of the target genes by binding to specific sequences of the promoter regions with a conserved N-terminal winged helix-turn-helix domain and thereby blocking the promoter-RNA polymerase interactions in the absence of inducers (e.g., phenolic acid and antibiotic) (46,59). Transcriptional derepression occurs when the regulator "falls off" the target DNA sequence after binding to the cognate inducers (e.g., phenolic acid and other toxic compounds) (46,59). The four copies of the B. subtilis PadR repressor are predicted to bind to four different sequence motifs in each promoter sequence of the phenolic acid response gene locus in the absence of phenolic acid (inducer) (48).…”

Communication between Binding Sites Is Required for YqjI Regulation of Target Promoters within the yqjH-yqjI Intergenic Region

“…1). YqjI is a member of the PadR family of transcriptional regulators but contains an additional N-terminal extension that is rich in potential metal-binding residues (such as Cys, His, and Glu) (7,8). Apo-YqjI is purified as both a monomer and in an oligomeric form.…”