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The HTH DNA-binding grove and multidrug-binding pocket. (a) Side view of the electrostatic surface potential of StAcrR with the di(hydroxyethyl)ether molecule (PEG; carbon atoms (green); oxygen atoms (red)) bound at the ligand-binding pocket. (b) Left panel, side view of the superimposed structures of StAcrR (orange; PEG is in stick model (orange)), the Thermotoga maritima transcriptional regulator TM1030 (blue) with 24-bp DNA (yellow) oligonucleotide and the TM1030 protein (green; PDB ID: 2iek) with hexaethylene glycol (P6G; green sticks) bound. Right panel, side view of the superimposed structures of StAcrR (as in the left panel), the E. coli TetR (green; PDB ID: 1qpi) with 15-bp DNA (yellow) oligonucleotide and the E. coli TetR (gray; PDB ID: 2tct; (Kisker et al., 1995)) with 7-cholortetracycline (gray sticks) bound. Helices of StAcrR are labeled and corresponding Tyr (Phe41 in the 1qpi structure) residues that are used to measure the Tyr-Tyr distance in a TetR dimer are shown. Single protomer of a TetR dimer is shown only. Bottom panel, multiple sequence alignment (area of the N-terminal HTH DNA-binding domain) of the StAcrR (UniProtKB ID: Q7CR15), TM1030 (UniProtKB ID: Q9X0C0) and E. coli TetR (UniProtKB ID: P0ACT4) proteins. The C-terminal portion of the alignment has fewer conserved residues. Figure was generated with ESPript v2.2 (Gouet et al., 1999) using Similarity Global Score of 0.7, Similarity Diff Score of 0.5 and Similarity Type Risler. (c) Key residues (stick representation) that comprise the multidrug ligand-binding pocket. The 3r OMIT map (magenta mesh) of PEG.
Source publication
Multidrug transcription regulator AcrR from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 belongs to the tetracycline repressor family, one of the largest groups of bacterial transcription factors. The crystal structure of dimeric AcrR was determined and refined to 1.56 Å resolution. The tertiary and quaternary structures of AcrR...
Citations
... AcrR transcriptional regulators and their mutations have been seen to contribute towards drug resistance in Salmonella sp. [46]. Finally, the possible regulatory protein thioredoxin (Trx) protects against oxidative stress, a well-established response after treatment by antimicrobials such as disinfectants [47]. ...
Molecular insights into the mechanisms of resistance to disinfectants are severely limited, together with the roles of various mobile genetic elements. Genomic islands are a well-characterised molecular resistance element in antibiotic resistance, but it is unknown whether genomic islands play a role in disinfectant resistance. Through whole-genome sequencing and the bioinformatic analysis of Serratia sp. HRI, an isolate with high disinfectant resistance capabilities, nine resistance islands were predicted and annotated within the genome. Resistance genes active against several antimicrobials were annotated in these islands, most of which are multidrug efflux pumps belonging to the MFS, ABC and DMT efflux families. Antibiotic resistance islands containing genes encoding for multidrug resistance proteins ErmB (macrolide and erythromycin resistance) and biclomycin were also found. A metal fitness island harbouring 13 resistance and response genes to copper, silver, lead, cadmium, zinc, and mercury was identified. In the search for disinfectant resistance islands, two genomic islands were identified to harbour smr genes, notorious for conferring disinfectant resistance. This suggests that genomic islands are capable of conferring disinfectant resistance, a phenomenon that has not yet been observed in the study of biocide resistance and tolerance.
... As an example, AcrB gene mutations are believed to cause ciprofloxacin treatment failure [70]. The above EPs expression is also being regulated at the transcriptional level by regulatory proteins that belong to the TetR family, including AcrR [71], CmeR [72], NalC/NalD [73], TtgR [74] SmeT [75], and MtrR [76], as well as MexR of the MarR family [77]. The AA residues in EPs can serve as critical sites for the binding of substrates, and the switching of AA residues is likely to alter the substrate affinity [78]. ...
An effective response that combines prevention and treatment is still the most anticipated solution to the increasing incidence of antimicrobial resistance (AMR). As the phenomenon continues to evolve, AMR is driving an escalation of hard-to-treat infections and mortality rates. Over the years, bacteria have devised a variety of survival tactics to outwit the antibiotic's effects, yet given their great adaptability, unexpected mechanisms are still to be discovered. Over-expression of efflux pumps (EPs) constitutes the leading strategy of bacterial resistance, and it is also a primary driver in the establishment of multidrug resistance (MDR). Extensive efforts are being made to develop antibiotic resistance breakers (ARBs) with the ultimate goal of re-sensitizing bacteria to medications to which they have become unresponsive. EP inhibitors (EPIs) appear to be the principal group of ARBs used to impair the efflux system machinery. Due to the high toxicity of synthetic EPIs, there is a growing interest in natural, safe, and innocuous ones, whereby plant extracts emerge to be excellent candidates. Besides EPIs, further alternatives are being explored including the development of nanoparticle carriers, biologics, and phage therapy, among others. What roles do EPs play in the occurrence of MDR? What weapons do we have to thwart EP-mediated resistance? What are the obstacles to their development? These are some of the core questions addressed in the present review.
... Loop-to-helix transitions within helix a4, sometimes linked to the presence of helix-destabilising residues (Pro, Gly) and generally triggered by direct interactions of the helix with the inducer, have been reported for several TetR/AcrR-like repressors [33,34]. The allosteric mechanism of SCO3201, in contrast, relies on a composite hinge helix and the elongation of its 3 10 -segment in response to the expansion of the ligandbinding cavity. ...
TetR/AcrR‐like transcription regulators enable bacteria to sense a wide variety of chemical compounds and to dynamically adapt the expression levels of specific genes in response to changing growth conditions. Here, we describe the structural characterisation of SCO3201, an atypical TetR/AcrR family member from Streptomyces coelicolor that strongly represses antibiotic production and morphological development under conditions of overexpression. We present crystal structures of SCO3201 in its ligand‐free state as well as in complex with an unknown inducer, potentially a polyamine. In the ligand‐free state, the DNA‐binding domains of the SCO3201 dimer are held together in an unusually compact conformation and, as a result, the regulator cannot span the distance between the two half‐sites of its operator. Interaction with the ligand coincides with a major structural rearrangement and partial conversion of the so‐called hinge helix (α4) to a 310‐conformation, markedly increasing the distance between the DNA‐binding domains. In sharp contrast to what was observed for other TetR/AcrR‐like regulators, the increased interdomain distance might facilitate rather than abrogate interaction of the dimer with the operator. Such a ‘reverse’ induction mechanism could expand the regulatory repertoire of the TetR/AcrR family and may explain the dramatic impact of SCO3201 overexpression on the ability of S. coelicolor to generate antibiotics and sporulate.
... For instance, mutations of the acrB gene would cause the failure of ciprofloxacin therapy [52]. The expression of the above-mentioned efflux pumps is also regulated by transcriptional regulatory proteins belonging to the TetR family, including AcrR [53], CmeR [54], NalC/NalD [55,56], TtgR [57], SmeT [58], and MtrR [59], as well as MexR belonging to MarR family [60]. Table 1 shows the efflux pumps regulated by the TetR family and summarizes the residues that have been proved to be important for the binding of the activating molecule by mutational analysis. ...
Multidrug efflux pumps function at the frontline to protect bacteria against antimicrobials by decreasing the intracellular concentration of drugs. This protective barrier consists of a series of transporter proteins, which are located in the bacterial cell membrane and periplasm and remove diverse extraneous substrates, including antimicrobials, organic solvents, toxic heavy metals, etc., from bacterial cells. This review systematically and comprehensively summarizes the functions of multiple efflux pumps families and discusses their potential applications. The biological functions of efflux pumps including their promotion of multidrug resistance, biofilm formation, quorum sensing, and survival and pathogenicity of bacteria are elucidated. The potential applications of efflux pump-related genes/proteins for the detection of antibiotic residues and antimicrobial resistance are also analyzed. Last but not least, efflux pump inhibitors, especially those of plant origin, are discussed.
... AcrR is an important regulator of the AcrAB belonging to the TetR family [71,82,95]. Mutations of the acrR gene are associated with the increase in the AcrAB expression and acquisition of drug resistance by pathogenic strains of S. Typhimurium [68,96]. Nikaido et al. [95] reported that induction of acrAB and ramA expression in response to indole depends on RamR. ...
The widespread use of antibiotics, especially those with a broad spectrum of activity, has resulted in the development of multidrug resistance in many strains of bacteria, including Salmonella. Salmonella is among the most prevalent causes of intoxication due to the consumption of contaminated food and water. Salmonellosis caused by this pathogen is pharmacologically treated using
antibiotics such as fluoroquinolones, ceftriaxone, and azithromycin. This foodborne pathogen developed several molecular mechanisms of resistance both on the level of global and local transcription
modulators. The increasing rate of antibiotic resistance in Salmonella poses a significant global concern, and an improved understanding of the multidrug resistance mechanisms in Salmonella is essential for choosing the suitable antibiotic for the treatment of infections. In this review, we summarized the current knowledge of molecular mechanisms that control gene expression related to antibiotic resistance of Salmonella strains. We characterized regulators acting as transcription activators and repressors, as well as two-component signal transduction systems. We also discuss the background of the molecular mechanisms of the resistance to metals, regulators of multidrug resistance to antibiotics, global regulators of the LysR family, as well as regulators of histonelike proteins.
... Thermal shift assay. Thermal shift assays were performed as previously described (66). Purified FadR was used at a final concentration of 2 mM. ...
The mammalian gastrointestinal tract is a complex biochemical organ that generates a diverse milieu of host-and microbe-derived metabolites. In this environ-ment, bacterial pathogens sense and respond to specific stimuli, which are integrated into the regulation of their virulence programs. Previously, we identified the transcription factor FadR, a long-chain fatty acid (LCFA) acyl coenzyme A (acyl-CoA) sensor, as a novel virulence regulator in the human foodborne pathogen enterohemorrhagic Escherichia coli (EHEC). Here, we demonstrate that exogenous LCFAs directly inhibit the locus of enterocyte effacement (LEE) pathogenicity island in EHEC through sensing by FadR. Moreover, in addition to LCFAs that are 18 carbons in length or shorter, we intro-duce host-derived arachidonic acid (C20:4) as an additional LCFA that is recognized by the FadR system in EHEC. We show that arachidonic acid is processed by the acyl-CoA synthetase FadD, which permits binding to FadR and decreases FadR affinity for its target DNA sequences. This interaction enables the transcriptional regulation of FadR-re-sponsive operons by arachidonic acid in EHEC, including the LEE. Finally, we show that arachidonic acid inhibits hallmarks of EHEC disease in a FadR-dependent manner, including EHEC attachment to epithelial cells and the formation of attaching and effacing lesions. Together, our findings delineate a molecular mechanism demonstrating how LCFAs can directly inhibit the virulence of an enteric bacterial pathogen. More broadly, our findings expand the repertoire of ligands sensed by the canonical LFCA sensing machinery in EHEC to include arachidonic acid, an important bioactive lipid that is ubiqui-tous within host environments.
... 10 The transcriptional regulator of TtgR depresses not only the transcription of the TtgABC operon but also the expression of itself. As an important member of the TetR family of transcriptional repressors, [11][12][13][14] the TtgR operator has two functional domains: a highly conserved N-terminal helix-turn-helix DNA binding domain, and a less conserved C-terminal domain for dimerization and ligand binding. [15][16][17][18] There is an angle of about 801 between the two domains. ...
The transcriptional regulator TtgR belongs to the TetR family of transcriptional repressors. It depresses the transcription of the TtgABC operon and itself and thus regulates the extrusion of noxious chemicals with efflux pumps in bacterial cells. As the ligand-binding domain of TtgR is rather flexible, it can bind with a number of structurally diverse ligands, such as antibiotics, flavonoids and aromatic solvents. In the current work, we perform equilibrium and nonequilibrium alchemical free energy simulation to predict the binding affinities of a series of ligands targeting the TtgR protein and an agreement between the theoretical prediction and the experimental result is observed. End-point methods MM/PBSA and MM/GBSA are also employed for comparison. We further study the interaction maps and contacts between the protein and the ligand and identify important interactions in the protein–ligand binding cases. The dynamics fluctuation and secondary structures are also investigated. The current work sheds light on atomic and thermodynamic understanding of the TtgR–ligand interactions.
... Subsequently, the transcription of drug resistance-and pathogenesis-associated genes is initiated by DNA released from repressor proteins. Since tuberculosis is a serious disease, and numerous patients worldwide are infected with drug-resistant strains, understanding the on-off transcriptional regulatory mechanism of the TetR type will be helpful in increasing the efficiency of existing drugs [54][55][56]. ...
Transcriptional regulator proteins are closely involved in essential survival strategies in bacteria. AcrR is a one‐component allosteric repressor of the genes associated with lipid transport and antibiotic resistance. When fatty acid ligands bind to the C‐terminal ligand‐binding cavity of AcrR, a conformational change in the N‐terminal operator‐binding region of AcrR is triggered, which releases the repressed DNA and initiates transcription. This paper focuses on the structural transition mechanism of AcrR of Mycobacterium tuberculosis upon DNA and ligand binding. AcrR loses its structural integrity upon ligand‐mediated structural alteration and bends toward the promoter DNA in a more compact form, initiating a rotational motion. Our functional characterization of AcrR and description of the ligand‐ and DNA‐recognition mechanism may facilitate the discovery of new therapies for tuberculosis.
... Additionally, over-expression of acrR increased the tolerance for organic solvents in E. coli (Lee et al., 2014), and a mutation in AcrA led to drug resistance by influencing the permeability of bacterial outer membranes (Nikaido, 1994). Therefore, these studies further indicate that organic compounds in textile dyeing wastewater can increase the emergence and spread of antimicrobial resistance genes due to co-selection (Gullberg et al., 2011) or influence on efflux-pumps (Li et al., 2007;Manjasetty et al., 2016). ...
Domestic wastewater treatment plants as a reservoir of antibiotic resistance genes (ARGs) have received much attention, but the effect of dyes on the propagation of ARGs has rarely been investigated. In this study, we investigated the differences in distributions of ARGs and microbial communities using high-throughput qPCR and 16S rRNA gene sequencing, respectively, between mixed (dyeing and domestic) wastewater and domestic sewage. The relative abundance of ARGs in inflows of mixed wastewater (IW2 and IW3) was higher than that of domestic wastewater (IW1). The relative abundance of mobile genetic elements in the inflow of textile dyeing wastewater (IDW3) was 3- to 13-fold higher than that in other samples. Moreover, in IDW3, some distinct high abundance ARGs, particularly operons encoding efflux pumps (such as acrR-01, acrB-01 and acrF), were significantly correlated with Streptococcus of the Firmicutes. To explore why the abundance of ARGs was relatively high in mixed wastewater, six representative types of organic compounds in textile dyeing wastewater were used to test the effect on plasmid-based conjugative transfer from E. coli HB101 to E. coli NK5449. These six compounds all facilitated the transfer of resistance-carrying RP4 plasmid, and the highest transfer frequency (approximately 10⁻⁵-10⁻³) was over 4- to 200-fold higher than that in the control group (approximately 10⁻⁶-10⁻⁵). These results illustrated that the six common residual compounds, particularly low-dose substances in IDW3, could facilitate the dissemination of ARGs in aquatic environments. More importantly, this study revealed for the first time that dyeing contaminants influenced horizontal gene transfer (HGT) of ARGs.
... The structural changes in gating at the AChR ECD-TMD domain interface are not known, but it is conceivable that the upward displacement of the M2M3 linker apparent in GluCl and GLIC could be sufficient to influence the dynamics of both M2M3 and TBS loops, to link these separated regions energetically without perturbing the intervening ECD. For example, a loop↔helix transition is correlated with change in structure and function at a distant site in kinesin (Kikkawa et al., 2001), myosin (Skolnick, 1987;Harrington et al., 1988), GPCRs (Kjeldgaard et al., 1996;Sprang, 1997), and AcrR (Manjasetty et al., 2016). Certainly, M2M3-TBS coupling in pLGICs could be by both a rigid-body link and backbone dynamics, as these mechanisms are not mutually exclusive. ...
Nicotinic acetylcholine receptors are allosteric proteins that generate membrane currents by isomerizing (“gating”) between resting and active conformations under the influence of neurotransmitters. Here, to explore the mechanisms that link the transmitter-binding sites (TBSs) with the distant gate, we use mutant cycle analyses to measure coupling between residue pairs, phi value analyses to sequence domain rearrangements, and current simulations to reproduce a microsecond shut component (“flip”) apparent in single-channel recordings. Significant interactions between amino acids separated by >15 Å are rare; an exception is between the αM2–M3 linkers and the TBSs that are ∼30 Å apart. Linker residues also make significant, local interactions within and between subunits. Phi value analyses indicate that without agonists, the linker is the first region in the protein to reach the gating transition state. Together, the phi pattern and flip component suggest that a complete, resting↔active allosteric transition involves passage through four brief intermediate states, with brief shut events arising from sojourns in all or a subset. We derive energy landscapes for gating with and without agonists, and propose a structure-based model in which resting→active starts with spontaneous rearrangements of the M2–M3 linkers and TBSs. These conformational changes stabilize a twisted extracellular domain to promote transmembrane helix tilting, gate dilation, and the formation of a “bubble” that collapses to initiate ion conduction. The energy landscapes suggest that twisting is the most energetically unfavorable step in the resting→active conformational change and that the rate-limiting step in the reverse process is bubble formation.
