Research Article: Structure-based molecular characterization and regulatory mechanism of the LftR transcription factor from Listeria monocytogenes: Conformational flexibilities and a ligand-induced regulatory mechanism

Date Published: April 10, 2019

Publisher: Public Library of Science

Author(s): Choongdeok Lee, Meong Il Kim, Jaewan Park, Minsun Hong, Finbarr Hayes.


Listeria monocytogenes is a foodborne pathogen that causes listeriosis and can lead to serious clinical problems, such as sepsis and meningitis, in immunocompromised patients and neonates. Due to a growing number of antibiotic-resistant L. monocytogenes strains, listeriosis can steadily become refractory to antibiotic treatment. To develop novel therapeutics against listeriosis, the drug resistance mechanism of L. monocytogenes needs to be determined. The transcription factor LftR from L. monocytogenes regulates the expression of a putative multidrug resistance transporter, LieAB, and belongs to the PadR-2 subfamily of the PadR family. Despite the functional significance of LftR, our molecular understanding of the transcriptional regulatory mechanism for LftR and even for the PadR-2 subfamily is highly limited. Here, we report the crystal structure of LftR, which forms a dimer and protrudes two winged helix-turn-helix motifs for DNA recognition. Structure-based mutational and comparative analyses showed that LftR interacts with operator DNA through a LftR-specific mode as well as a common mechanism used by the PadR family. Moreover, the LftR dimer harbors one intersubunit cavity in the center of the dimeric structure as a putative ligand-binding site. Finally, conformational flexibilities in the LftR dimer and in the cavity suggest that a ligand-induced regulatory mechanism would be used by the LftR transcription factor.

Partial Text

Listeria monocytogenes is a gram-positive bacillus that is responsible for listeriosis in humans. Listeriosis occurs by gastrointestinal ingestion of food contaminated by L. monocytogenes [1]. L. monocytogenes is able to penetrate the mucosal membranes of the intestine, brain barrier, and placenta. Therefore, L. monocytogenes can cause serious problems, such as sepsis, meningitis, and even death, in elderly and immunocompromised individuals, and may induce miscarriage or stillbirth in pregnant women [2–6]. In particular, because L. monocytogenes can grow at low temperature, extra caution is required for food storage even during refrigeration [7]. Moreover, since the number of antibiotic-resistant L. monocytogenes strains is increasing [8], listeriosis has steadily become refractory to antibiotic treatment. Therefore, it is necessary to obtain in-depth knowledge about the drug resistance mechanism of L. monocytogenes and to develop novel antibiotics against listeriosis.

The lftR gene encodes a Listeria protein facilitating invasion that was identified as a transcriptional regulator of a putative multidrug resistance transporter in an opportunistic pathogen, L. monocytogenes. In this study, we identified two LftR structures and presented the conformational flexibility of LftR, which is essential for ligand-induced transcriptional regulation. A putative operator site of LftR was proposed and its interaction with LftR was experimentally verified by biophysical and biochemical analyses. Our mutational and modeling studies, combined with comparative analyses of the structures and sequences of PadR family members, suggest that LftR recognizes operator DNA in a PadR family-conserved manner as well as through an LftR-specific mode. Moreover, we confirmed that ethidium bromide is an artificial ligand of LftR. Therefore, our study provides in-depth insight into ligand and DNA recognition by the LftR transcriptional regulator. To elucidate the regulatory mechanism of LftR in atomic resolution, formation of a complex of LftR structures with ligand or operator DNA will be required.