Antibiotic binding releases autoinhibition of the TipA multidrug-resistance transcriptional regulator

Abstract

Investigations of bacterial resistance strategies can aid in the development of new antimicrobial drugs as a countermeasure to the increasing worldwide prevalence of bacterial antibiotic resistance. One such strategy involves the TipA class of transcription factors, which constitute minimal autoregulated multidrug resistance (MDR) systems against diverse antibiotics. However, we have insufficient information regarding how antibiotic binding induces transcriptional activation to design molecules that could interfere with this process. To learn more, we determined the crystal structure of SkgA from Caulobacter crescentus as a representative TipA protein. We identified an unexpected spatial orientation and location of the antibiotic binding TipAS effector domain in the apo state. We observed that the α6-α7 region of the TipAS domain, which is canonically responsible for forming the lid of antibiotic binding cleft to tightly enclose the bound antibiotic, is involved in the dimeric interface and stabilized via interaction with the DNA-binding domain in the apo state. Further structural and biochemical analyses demonstrated that the unliganded TipAS domain sterically hinders promoter DNA binding, but undergoes a remarkable conformational shift upon antibiotic binding to release this autoinhibition via a switch of its α6-α7 region. Hence, the promoters for MDR genes including tipA and RNA polymerases become available for transcription, enabling efficient antibiotic resistance. These insights into the molecular mechanism of activation of TipA proteins advance our understanding of TipA proteins as well as bacterial MDR systems, and may provide important clues to block bacterial resistance.

CvkR, a novel MerR-type transcriptional regulator, is a repressor of class 2 type V-K CRISPR-associated transposase systems

“…Effector binding, however, can trigger a conformational change, which brings both HTH domains closer together and distorts the DNA to increase the σ-factor affinity for the promoter 29, 35 . The effector for this regulator is usually a metal ion, but there are also MerR interactions with antibiotics, oxidative stress, or lipophilic compounds 29, 36–38 . MerR-like proteins without effector interactions are also known 39 .…”

Bacterial Transcriptional Regulators: A Road Map for Functional, Structural, and Biophysical Characterization

“…For this to occur, bacteria must correctly sense and transduce various environmental signals by using complex signaling pathways that ultimately lead to the transcription of specific genes required for survival in each situation. This response is orchestrated by transcriptional regulators (TRs) that can function as singlecomponent systems, as DNA-binding proteins with the ability to modulate function as a response to the presence of some specific chemical species [1], or as part of a more complex signaling pathway [2,3]. Recently, structural details of small molecule and metal ion sensing riboswitches have also appeared [4,5], making it clear that both protein and RNA have the level of specificity necessary to regulate transcription outcomes in response to small molecules.…”