Benzoate Decreases the Binding of
            <i>cis</i>
            ,
            <i>cis</i>
            -Muconate to the BenM Regulator despite the Synergistic Effect of Both Compounds on Transcriptional Activation

Clark, Todd J.; Phillips, Robert S.; Bundy, Becky M.; Momany, Cory; Neidle, Ellen L.

doi:10.1128/jb.186.4.1200-1204.2004

Cited by 22 publications

(28 citation statements)

References 21 publications

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“…In the presence of inducer, the hypersensitive band at Ϫ42 disappeared and occupation of the ABS shifted from Ϫ37 to Ϫ41 (141), suggesting that the bending angle is relaxed on interaction with the effector. Conformational changes on effector binding could be detected for benzoate and cis,cis-muconate binding to BenM (31). Measurements of the bending angle of the clcA promoter in the absence (71°) and in the presence (55°) of effector corroborate this idea of bending relaxation (140).…”

Section: Mechanisms Of Activationsupporting

confidence: 63%

“…For example, fumarate reversibly inhibits the formation of the clcA transcript in in vitro transcription assays in the presence of purified ClcR and 2-chloro-cis,cis-muconate (138). The presence of cis,cis-muconate decreases the affinity of the BenM protein for benzoate (31). All LTTRs repress their own expression, and both autorepression and activation of the catabolic operon promoter are exerted from the same binding site, which is called the regulator or repressor binding site (RBS) (20,216,227).…”

Section: Lysr Family Of Transcriptional Regulators Catabolic Operons mentioning

confidence: 99%

“…mRNA is drawn as a zigzagged arrow. (20,31,34). In addition, BenM represses benA transcription in the absence of inducer.…”

Section: Mechanisms Of Activationmentioning

confidence: 99%

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Bacterial Transcriptional Regulators for Degradation Pathways of Aromatic Compounds

Tropel

Meer

2004

Microbiol Mol Biol Rev

343

338

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Human activities have resulted in the release and introduction into the environment of a plethora of aromatic chemicals. The interest in discovering how bacteria are dealing with hazardous environmental pollutants has driven a large research community and has resulted in important biochemical, genetic, and physiological knowledge about the degradation capacities of microorganisms and their application in bioremediation, green chemistry, or production of pharmacy synthons. In addition, regulation of catabolic pathway expression has attracted the interest of numerous different groups, and several catabolic pathway regulators have been exemplary for understanding transcription control mechanisms. More recently, information about regulatory systems has been used to construct whole-cell living bioreporters that are used to measure the quality of the aqueous, soil, and air environment. The topic of biodegradation is relatively coherent, and this review presents a coherent overview of the regulatory systems involved in the transcriptional control of catabolic pathways. This review summarizes the different regulatory systems involved in biodegradation pathways of aromatic compounds linking them to other known protein families. Specific attention has been paid to describing the genetic organization of the regulatory genes, promoters, and target operon(s) and to discussing present knowledge about signaling molecules, DNA binding properties, and operator characteristics, and evidence from regulatory mutants. For each regulator family, this information is combined with recently obtained protein structural information to arrive at a possible mechanism of transcription activation. This demonstrates the diversity of control mechanisms existing in catabolic pathways

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Section: Mechanisms Of Activationsupporting

confidence: 63%

Section: Lysr Family Of Transcriptional Regulators Catabolic Operons mentioning

confidence: 99%

See 1 more Smart Citation

Bacterial Transcriptional Regulators for Degradation Pathways of Aromatic Compounds

Tropel

Meer

2004

Microbiol Mol Biol Rev

343

338

View full text Add to dashboard Cite

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“…6B), allowing us to carry out a fluorescence titration assay. Titration of the protein with increasing amounts of benzoyl-CoA yields a binding isotherm with a dissociation constant (K d ) of 157 Ϯ 58 M, a value that is within the range of that obtained with other transcriptional regulators that control aromatic degradation pathways (54). This analysis assumes a single binding site for benzoyl-CoA that should be located at the C-terminal domain of BzdR, as deduced from the structural model of the protein (7).…”

Section: Conformational Changes In Bzdr Upon Benzoyl-coa Binding-mentioning

confidence: 99%

Biochemical Characterization of the Transcriptional Regulator BzdR from Azoarcus sp. CIB

Durante‐Rodríguez

Valderrama

Mancheño

et al. 2010

Journal of Biological Chemistry

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The BzdR transcriptional regulator that controls the P N promoter responsible for the anaerobic catabolism of benzoate in Azoarcus sp. CIB constitutes the prototype of a new subfamily of transcriptional regulators. Here, we provide some insights about the functional-structural relationships of the BzdR protein. Analytical ultracentrifugation studies revealed that BzdR is homodimeric in solution. An electron microscopy three-dimensional reconstruction of the BzdR dimer has been obtained, and the predicted structures of the respective N-and C-terminal domains of each BzdR monomer could be fitted into such a reconstruction. Gel retardation and ultracentrifugation experiments have shown that the binding of BzdR to its cognate promoter is cooperative. Different biochemical approaches revealed that the effector molecule benzoyl-CoA induces conformational changes in BzdR without affecting its oligomeric state. The BzdRdependent inhibition of the P N promoter and its activation in the presence of benzoyl-CoA have been established by in vitro transcription assays. The monomeric BzdR4 and BzdR5 mutant regulators revealed that dimerization of BzdR is essential for DNA binding. Remarkably, a BzdR⌬L protein lacking the linker region connecting the N-and C-terminal domains of BzdR is also dimeric and behaves as a super-repressor of the P N promoter. These data suggest that the linker region of BzdR is not essential for protein dimerization, but rather it is required to transfer the conformational changes induced by the benzoyl-CoA to the DNA binding domain leading to the release of the repressor. A model of action of the BzdR regulator has been proposed.

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“…This finding expands our current view of the PaaX regulon to include the catabolism of toxic aromatic compounds, such as styrene, and places the PaaX protein at the center of an interesting case of an integrated regulatory strategy for the catabolism of aromatic compounds (reviewed by Shingler [34]), namely, a mechanism in which transcriptional control of the expression of the catabolic genes integrates responses to both a substrate (styrene through StyR/StyS) and a pathway intermediate (PA-CoA through PaaX). Conceptually, this regulatory scheme is reminiscent of that reported for the sub-strate benzoate and intermediate cis-muconate in control of benzoate catabolism through the ␤-ketoadipate pathway (7,8).…”

mentioning

confidence: 99%

Coregulation by Phenylacetyl-Coenzyme A-Responsive PaaX Integrates Control of the Upper and Lower Pathways for Catabolism of Styrene by Pseudomonas sp. Strain Y2

et al. 2006

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The P styA promoter of Pseudomonas sp. strain Y2 controls expression of the styABCD genes, which are required for the conversion of styrene to phenylacetate, which is further catabolized by the products of two paa gene clusters. Two PaaX repressor proteins (PaaX1 and PaaX2) regulate transcription of the paa gene clusters of this strain. In silico analysis of the P styA promoter region revealed a sequence located just within styA that is similar to the reported PaaX binding sites of Escherichia coli and the proposed PaaX binding sites of the paa genes of Pseudomonas species. Here we show that protein extracts from some Pseudomonas strains that have paaX genes, but not from a paaX mutant strain, can bind and retard the migration of a P styA specific probe. Purified maltose-binding protein (MBP)-PaaX1 fusion protein specifically binds the P styA promoter proximal PaaX site, and this binding is eliminated by the addition of phenylacetyl-coenzyme A. The sequence protected by MBP-PaaX1 binding was defined by DNase I footprinting. Moreover, MBP-PaaX1 represses transcription from the P styA promoter in a phenylacetyl-coenzyme A-dependent manner in vitro. Finally, the inactivation of both paaX gene copies of Pseudomonas sp. strain Y2 leads to a higher level of transcription from the P styA promoter, while heterologous expression of the PaaX1 in E. coli greatly decreases transcription from the P styA promoter. These findings reveal a control mechanism that integrates regulation of styrene catabolism by coordinating the expression of the styrene upper catabolic operon to that of the paa-encoded central pathway and support a role for PaaX as a major regulatory protein in the phenylacetyl-coenzyme A catabolon through its response to the levels of this central metabolite.

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Benzoate Decreases the Binding of cis , cis -Muconate to the BenM Regulator despite the Synergistic Effect of Both Compounds on Transcriptional Activation

Cited by 22 publications

References 21 publications

Bacterial Transcriptional Regulators for Degradation Pathways of Aromatic Compounds

Bacterial Transcriptional Regulators for Degradation Pathways of Aromatic Compounds

Biochemical Characterization of the Transcriptional Regulator BzdR from Azoarcus sp. CIB

Coregulation by Phenylacetyl-Coenzyme A-Responsive PaaX Integrates Control of the Upper and Lower Pathways for Catabolism of Styrene by Pseudomonas sp. Strain Y2

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