Structural basis of effector and operator recognition by the phenolic acid-responsive transcriptional regulator PadR

Park, Sun Cheol; Kwak, Yun Mi; Song, Wan Seok; Hong, Minsun; Yoon, Sung‐il

doi:10.1093/nar/gkx1055

Cited by 50 publications

(53 citation statements)

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“…We suggest that AphA preferentially binds to the inverted repeat sequence 5’-ATGCAA-N 4 -TTGCAT-3’ (Figure 1d). Consistent with this, structures of PadR family regulators demonstrate DNA binding as a dimer with two-fold symmetry [33]. Confusion likely arose previously because the sequence 5’-TGCA-3’ is embedded as a direct repeat within the larger motif identified here (Figure 1d).…”

Section: Discussionsupporting

confidence: 75%

“…Importantly, the degree to which migration altered was different for each protein (compare lanes 1-3 in Figure 3d). This is most likely because CRP bends the DNA by 90° whilst AphA has little effect [21,32,33]. Addition of AphA reduced the abundance of complexes due to CRP and increased the abundance of the complexes due to AphA (Figure 3d, lane 4).…”

Section: Resultsmentioning

confidence: 99%

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The quorum sensing transcription factor AphA directly regulates natural competence inVibrio cholerae

Haycocks

Warren

Walker

et al. 2019

Preprint

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1Many bacteria use population density to control gene expression via quorum sensing. In Vibrio 2 cholerae, quorum sensing coordinates virulence, biofilm formation, and DNA uptake by natural 3 competence. The transcription factors AphA and HapR, expressed at low-and high-cell density 4 respectively, play a key role. In particular, AphA triggers the entire virulence cascade upon host 5 colonisation. In this work we have mapped genome-wide DNA binding by AphA. We show that 6AphA is versatile, exhibiting distinct modes of DNA binding and promoter regulation. 7Unexpectedly, whilst HapR is known to induce natural competence, we demonstrate that AphA 8 also intervenes. Most notably, AphA is a direct repressor of tfoX, the master activator of 9 competence. Hence, production of AphA markedly suppressed DNA uptake; an effect largely 10 circumvented by ectopic expression of tfoX. Our observations suggest dual regulation of 11 competence. At low cell density AphA is a master repressor whilst HapR activates the process at 12 high cell density. Thus, we provide deep mechanistic insight into the role of AphA and highlight 13 how V. cholerae utilises this regulator for diverse purposes. 14 AUTHOR SUMMARY 15Cholera remains a devastating diarrhoeal disease responsible for millions of cases, thousands of deaths, 16 and a $3 billion financial burden every year. Although notorious for causing human disease, the 17 microorganism responsible for cholera is predominantly a resident of aquatic environments. Here, the 18 organism survives in densely packed communities on the surfaces of crustaceans. Remarkably, in this 19 situation, the microbe can feast on neighbouring cells and acquire their DNA. This provides a useful 20 food source and an opportunity to obtain new genetic information. In this paper, we have investigated 21 how acquisition of DNA from the local environment is regulated. We show that a "switch" within the 22 microbial cell, known to activate disease processes in the human host, also controls DNA uptake. Our 23 results explain why DNA scavenging only occurs in suitable environments and illustrates how 24 interactions between common regulatory switches affords precise control of microbial behaviours. 25Quorum sensing detects changes in bacterial population density reported by auto-inducer molecules 36[17]. This information is used to modify patterns of gene expression [18]. For example, CqsS is a 37 membrane bound sensor kinase that detects cholera auto-inducer 1 (CAI-1) [19]. When kin are scarce, 38and CAI-1 levels low, CqsS triggers a regulatory cascade, which cumulates in expression of five quorum 39 regulatory RNAs [20]. These RNA molecules activate translation of AphA, a PadR family transcription 40 factor with an N-terminal winged helix-turn-helix DNA binding motif [20][21][22]. In turn, AphA activates 41 expression of tcpPH [23]. This event ignites the entire virulence gene expression programme [16]. 42 Surprisingly, given the central role of AphA, the regulator is poorly understood. For instance, 43 transcriptome ...

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Section: Discussionsupporting

confidence: 75%

Section: Resultsmentioning

confidence: 99%

The quorum sensing transcription factor AphA directly regulates natural competence inVibrio cholerae

Haycocks

Warren

Walker

et al. 2019

Preprint

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“…VanR binds its effector using the interdomain cavity that is generated between the NTD and the CTD, as observed for PadR (Fig. A) . Moreover, VanR and PadR dimers each simultaneously bind two effector molecules.…”

Section: Resultsmentioning

confidence: 71%

“…However, our comparative analysis of the VanR and PadR structures combined with a mutational study allows us to propose a transcriptional derepression mechanism used by VanR. In PadR, effector binding to the interdomain pocket induces NTD‐CTD interdomain reorganization through the allosteric center of Q32 and F33 located at the α2‐α3 loop . Vanillate binding to VanR may analogously cause conformational changes in the VanR structure to disfavor DNA binding.…”

Section: Resultsmentioning

confidence: 99%

“…PadR and LmrR, which represent subfamily‐1 and subfamily‐2, respectively, thus differ in effector‐recognition modes and presumably in effector‐mediated transcriptional regulation mechanisms. The effector‐binding site of PadR is located in the interdomain pocket, whereas those of other two‐domain transcription factors are generally confined to the C‐terminal domain . It should therefore be determined whether the effector‐binding mode of PadR is conserved in the PadR subfamily‐1 or limited only to PadR.…”

Section: Introductionmentioning

confidence: 99%

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Crystal structure of the VanR transcription factor and the role of its unique α‐helix in effector recognition

et al. 2018

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VanR is a negative transcriptional regulator of bacteria that belongs to the PadR family and modulates the expression of vanillate transport and degradation proteins in response to vanillate. Although VanR plays a key role in the utilization of vanillate as a carbon source, it is barely understood how VanR recognizes its effector. Thus, our knowledge concerning the gene regulatory mechanism of VanR is limited. Here, we reveal the vanillate-binding mode of VanR through structural, biophysical, and mutational studies. Similar to other PadR family members, VanR forms a functional dimer, and each VanR subunit consists of an N-terminal DNA-binding domain (NTD) and a C-terminal dimerization domain (CTD). One VanR dimer simultaneously binds two vanillate molecules using two interdomain cavities, as observed in PadR. In contrast to these common features, VanR contains an additional α-helix, αi, that has not been found in other PadR family members. The αi helix functions as an interdomain crosslinker that mediates interactions between the NTD and the CTD. In addition, the VanR-specific αi helix plays a key role in the formation of a unique effector-binding site. As a result, the effector-binding mode of VanR is distinguishable from that of PadR in the location and accessibility of the effector-binding site as well as the orientation of its bound effector. Furthermore, we propose the DNA-binding mode and vanillate-mediated transcriptional regulation mechanism of VanR based on comparative structural and mutational analyses. DATABASES: The atomic coordinates and the structure factors for VanR (PDB ID 5Z7B) have been deposited in the Protein Data Bank, www.pdb.org.

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Effects of Phenolic Compounds on Biofilm Formation by Table Olive‐Related Microorganisms

López‐García,

Benítez‐Cabello,

Arroyo‐López

2024

Food Science & Nutrition

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The process of biofilm formation during table olive fermentation is crucial to turning this fermented vegetable into a probiotic food. Some phenolic compounds have been described as important quorum‐sensing molecules during biofilm development. The present in vitro study examined the effects of three phenolic compounds widely found in table olive fermentations (Oleuropein 0–3000 ppm, Hydroxytyrosol 0–3000 ppm, and Tyrosol 0–300 ppm) on the development of single biofilm by diverse microorganisms isolated from table olives (Lactiplantibacillus pentosus 13B4, Lp119, and LPG1; Lactiplantibacillus plantarum Lp15 and LAB23; and yeasts Wickerhamomyces anomalus Y12, Candida boidinii Y13, and Saccharomyces cerevisiae Y18). Biofilm formation was quantified in vitro by crystal violet staining in microtiter plates after incubation at 30°C for 96 h. A clear tendency to decrease the biofilm production was observed for the L. plantarum strains when any of the three phenolic compounds were added to the medium, which was statistically significant (p ≤ 0.05) for certain concentrations and phenols. In the case of yeasts, no statistical influence on biofilm formation was noticed when the phenolic compounds were dosed to the culture medium. Finally, the effects of the phenolic compounds on the L. pentosus strains were dependent on the strain assayed. Thereby, addition of phenolic compounds on 13B4 or Lp119 strains did not have statistical influence on biofilm production. On the contrary, the probiotic LPG1 strain noticed a statistical increase in biofilm production when a low concentration of tyrosol (50 ppm) was added to the medium. Results obtained in this work could be useful to control the biofilm formation process on olive epidermis during table olive fermentation to include beneficial microorganisms.

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Structural basis of effector and operator recognition by the phenolic acid-responsive transcriptional regulator PadR

Cited by 50 publications

References 50 publications

The quorum sensing transcription factor AphA directly regulates natural competence inVibrio cholerae

The quorum sensing transcription factor AphA directly regulates natural competence inVibrio cholerae

Crystal structure of the VanR transcription factor and the role of its unique α‐helix in effector recognition

Effects of Phenolic Compounds on Biofilm Formation by Table Olive‐Related Microorganisms

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