Optimization of the Palindromic Order of the TtgR Operator Enhances Binding Cooperativity

Krell, Tino; Terán, Wilson; Mayorga, Obdulio López; Rivas, Germán; Jiménez, Mercedes; Daniels, Craig; Molina-Henares, Antonio-Jesús; Martínez-Bueno, Manuel; Gallegos, Marı́a-Trinidad; Ramos, Juan L.

doi:10.1016/j.jmb.2007.04.025

Cited by 41 publications

(39 citation statements)

References 26 publications

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“…4). This suggests MfsR-His6 to form homodimers in solution, which is in agreement with several observations that TetR family members occur as homodimers (31,32). Even larger protein bands were seen in cross-linked preparations (e.g., 95 kDa) ( Fig.…”

Section: Resultssupporting

confidence: 92%

The TetR-Type MfsR Protein of the Integrative and Conjugative Element (ICE) ICE clc Controls both a Putative Efflux System and Initiation of ICE Transfer

et al. 2014

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Integrative and conjugating elements (ICE) are self-transferable DNAs widely present in bacterial genomes, which often carry a variety of auxiliary genes of potential adaptive benefit. One of the model ICE is ICEclc, an element originally found in Pseudomonas knackmussii B13 and known for its propensity to provide its host with the capacity to metabolize chlorocatechols and 2-aminophenol. In this work, we studied the mechanism and target of regulation of MfsR, a TetR-type repressor previously found to exert global control on ICEclc horizontal transfer. By using a combination of ICEclc mutant and transcriptome analysis, gene reporter fusions, and DNA binding assays, we found that MfsR is a repressor of both its own expression and that of a gene cluster putatively coding for a major facilitator superfamily efflux system on ICEclc (named mfsABC). Phylogenetic analysis suggests that mfsR was originally located immediately adjacent to the efflux pump genes but became displaced from its original cis target DNA by a gene insertion. This resulted in divergence of the original bidirectional promoters into two separated individual regulatory units. Deletion of mfsABC did not result in a strong phenotype, and despite screening a large number of compounds and conditions, we were unable to define the precise current function or target of the putative efflux pump. Our data reconstruct how the separation of an ancestor mfsR-mfsABC system led to global control of ICEclc transfer by MfsR.

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Section: Resultssupporting

confidence: 92%

The TetR-Type MfsR Protein of the Integrative and Conjugative Element (ICE) ICE clc Controls both a Putative Efflux System and Initiation of ICE Transfer

et al. 2014

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“…The DtxR, Fur, QacR, TrpR, TtgR, and XylR proteins have been shown to interact with DNA at overlapping binding sites (2,11,24,26,27,41,47). The in vitro behavior of several of these proteins mimics that of CodY.…”

Section: Discussionmentioning

confidence: 99%

Bacillus subtilis CodY Operators Contain Overlapping CodY Binding Sites

Wray

Fisher

2011

J Bacteriol

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CodY is a global transcriptional regulator that is activated by branched-chain amino acids. A palindromic 15-bp sequence motif, AATTTTCNGAAAATT, is associated with CodY DNA binding. A gel mobility shift assay was used to examine the effect of pH on the binding of Bacillus subtilis CodY to the hutPp and ureAp 3 promoters. CodY at pH 6.0 has higher affinity for DNA, more enhanced activation by isoleucine, and a lower propensity for nonspecific DNA binding than CodY at pH 8.0. DNase I footprinting was used to identify the CodYprotected regions in the hutPp and ureAp 3 promoters. The CodY-protected sequences for both promoters were found to contain multiple copies of the 15-bp motif with 6-bp overlaps. Mutational analysis of the hutPp regulatory region revealed that two overlapping sequence motifs were required for CodY-mediated regulation. The presence of overlapping sequence motifs in the regulatory regions of many B. subtilis CodY-regulated genes suggests that CodY binds to native operators that contain overlapping binding sites.

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“…Positive cooperativity also can be seen in terms of transcription factors binding to promoters with multiple binding sites. One example of positive cooperativity of transcription factors is seen with the TtgR operator of Pseudomonas putida strain DOT-T1E (40). TtgR, which can form dimers in solution, exhibits biphasic cooperative binding at this promoter (40).…”

Section: Discussionmentioning

confidence: 99%

“…One example of positive cooperativity of transcription factors is seen with the TtgR operator of Pseudomonas putida strain DOT-T1E (40). TtgR, which can form dimers in solution, exhibits biphasic cooperative binding at this promoter (40). ToxT is thought to have optimal activity when acting as a dimer (27)(28)(29)(30)(31).…”

Section: Discussionmentioning

confidence: 99%

Bicarbonate Increases Binding Affinity of Vibrio cholerae ToxT to Virulence Gene Promoters

Thomson

Withey

2014

J Bacteriol

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The major Vibrio cholerae virulence gene transcription activator, ToxT, is responsible for the production of the diarrhea-inducing cholera toxin (CT) and the major colonization factor, toxin coregulated pilus (TCP). In addition to the two primary virulence factors mentioned, ToxT is responsible for the activation of accessory virulence genes, such as aldA, tagA, acfA, acfD, tcpI, and tarAB. ToxT activity is negatively modulated by bile and unsaturated fatty acids found in the upper small intestine. Conversely, previous work identified another intestinal signal, bicarbonate, which enhances the ability of ToxT to activate production of CT and TCP. The work presented here further elucidates the mechanism for the enhancement of ToxT activity by bicarbonate. Bicarbonate was found to increase the activation of ToxT-dependent accessory virulence promoters in addition to those that produce CT and TCP. Bicarbonate is taken up into the V. cholerae cell, where it positively affects ToxT activity by increasing DNA binding affinity for the virulence gene promoters that ToxT activates regardless of toxbox configuration. The increase in ToxT binding affinity in the presence of bicarbonate explains the elevated level of virulence gene transcription.

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Optimization of the Palindromic Order of the TtgR Operator Enhances Binding Cooperativity

Cited by 41 publications

References 26 publications

The TetR-Type MfsR Protein of the Integrative and Conjugative Element (ICE) ICE clc Controls both a Putative Efflux System and Initiation of ICE Transfer

The TetR-Type MfsR Protein of the Integrative and Conjugative Element (ICE) ICE clc Controls both a Putative Efflux System and Initiation of ICE Transfer

Bacillus subtilis CodY Operators Contain Overlapping CodY Binding Sites

Bicarbonate Increases Binding Affinity of Vibrio cholerae ToxT to Virulence Gene Promoters

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