Phenylacetyl Coenzyme A Is an Effector Molecule of the TetR Family Transcriptional Repressor PaaR from Thermus thermophilusHB8

Sakamoto, Keiko; Agari, Yoshihiro; Kuramitsu, Seiki; Shinkai, Akeo

doi:10.1128/jb.05203-11

Cited by 21 publications

(45 citation statements)

References 29 publications

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“…MdoR regulates expression of the mdo gene, which is required for oxidation of methanol. The TFRs NicS, PaaR, and RolR are involved in the regulation of metabolism pathways for nicotinic acid, phenyl acetic acid, and resorcinol, respectively (148)(149)(150). In each case, the TFR has been shown to interact with the molecule being degraded or a catabolic intermediate.…”

Section: Tfrs and Carbon Metabolismmentioning

confidence: 99%

The TetR Family of Regulators

Cuthbertson

Nodwell

2013

Microbiol Mol Biol Rev

480

512

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SUMMARY The most common prokaryotic signal transduction mechanisms are the one-component systems in which a single polypeptide contains both a sensory domain and a DNA-binding domain. Among the >20 classes of one-component systems, the TetR family of regulators (TFRs) are widely associated with antibiotic resistance and the regulation of genes encoding small-molecule exporters. However, TFRs play a much broader role, controlling genes involved in metabolism, antibiotic production, quorum sensing, and many other aspects of prokaryotic physiology. There are several well-established model systems for understanding these important proteins, and structural studies have begun to unveil the mechanisms by which they bind DNA and recognize small-molecule ligands. The sequences for more than 200,000 TFRs are available in the public databases, and genomics studies are identifying their target genes. Three-dimensional structures have been solved for close to 200 TFRs. Comparison of these structures reveals a common overall architecture of nine conserved α helices. The most important open question concerning TFR biology is the nature and diversity of their ligands and how these relate to the biochemical processes under their control.

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Section: Tfrs and Carbon Metabolismmentioning

confidence: 99%

The TetR Family of Regulators

Cuthbertson

Nodwell

2013

Microbiol Mol Biol Rev

480

512

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“…PaaR negatively regulates the expression of two operons encoding several putative paa genes for phenylacetic acid (PAA) degradation (33). Phenylacetyl (PA)-CoA is a ligand of PaaR and was effective for transcriptional derepression (33). In this study, we performed functional and structural analyses of the TTHB023 protein and discussed its similarities with several other TetR family proteins.…”

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confidence: 99%

“…FadR binds a medium-to-long straight chain (C 10 to C 18 ) fatty acyl-coenzyme A (CoA) molecule as a ligand to derepress the target genes (1). PaaR negatively regulates the expression of two operons encoding several putative paa genes for phenylacetic acid (PAA) degradation (33). Phenylacetyl (PA)-CoA is a ligand of PaaR and was effective for transcriptional derepression (33).…”

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confidence: 99%

“…A DNA fragment (0.1 mM), biotinylated at the 5= end of one strand, was diluted to 50 nM in 10 mM HEPES-NaOH (pH 7.4) buffer containing 0.5 M NaCl, 3 mM EDTA, and 0.005% surfactant P20, and then applied to a streptavidin-coated (SA) biosensor chip (GE Healthcare), as described previously (33). All experiments for measuring the DNA and protein interactions were performed at 25°C using buffer A (10 mM HEPES-NaOH, pH 7.4, 0.3 M NaCl, 3 mM EDTA, 0.005% surfactant P20).…”

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confidence: 99%

“…Total RNA, isolated from wild-type T. thermophilus HB8 cells cultured at 70°C for 6 h in rich medium, was treated with DNase I, followed by ethanol precipitation, as described previously (36). Rapid amplification of cDNA ends (5= RACE) was performed with a 5= Full RACE Core Set (TaKaRa Bio), as described previously (33). The first-strand cDNA was synthesized with the 5= phos-phorylated primers P23, P24, and P25 for the TTHA0750, TTHA0987, and TTHB023 genes, respectively (see Table S1 in the supplemental material).…”

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confidence: 99%

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Transcriptional Repression Mediated by a TetR Family Protein, PfmR, from Thermus thermophilus HB8

Agari

Sakamoto

Kuramitsu

et al. 2012

Journal of Bacteriology

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PfmR is one of four TetR family transcriptional regulators found in the extremely thermophilic bacterium, Thermus thermophilus HB8. We identified three promoters with strong negative regulation by PfmR, both in vivo and in vitro. PfmR binds pseudopalindromic sequences, with the consensus sequence of 5=-TACCGACCGNTNGGTN-3= surrounding the promoters. According to the amino acid sequence and three-dimensional structure analyses of the PfmR-regulated gene products, they are predicted to be involved in phenylacetic acid and fatty acid metabolism. In vitro analyses revealed that PfmR weakly cross-regulated with the TetR family repressor T. thermophilus PaaR, which controls the expression of the paa gene cluster putatively involved in phenylacetic acid degradation but not with another functionally identified TetR family repressor, T. thermophilus

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Structure and function of a TetR family transcriptional regulator, SbtR, from thermus thermophilus HB8

et al. 2013

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SbtR is one of the four TetR family transcriptional regulators present in the extremely thermophilic bacterium, Thermus thermophilus HB8. We identified 10 genes controlled by four promoters with negative regulation by SbtR in vitro. The SbtR-regulated gene products include probable transporters, probable enzymes for sugar or amino acid metabolism, and nucleic acid-related enzymes. SbtR binds pseudopalindromic sequences, with the consensus sequence of 5'-TGACCCNNKGGTCA-3' surrounding the promoters, and has a proposed 1:1 dimer binding stoichiometry. The X-ray crystal structure analysis revealed that SbtR comprises either nine or 10 α-helices and forms a dimer, as in the typical TetR family proteins. Similar to many characterized TetR family regulators, SbtR has a predicted ligand-binding pocket at the center of each monomer. Interestingly, the SbtR dimer contains an intermolecular disulfide bridge, formed between the Cys164 residues at the entrance of the pocket. The Cys164Ser and Cys164Ala mutant SbtR proteins formed homodimers similar to that of the wild type, but their thermal stabilities were lower by about 8°C, indicating that the disulfide bridge contributes to the thermal stability of the protein. However, altered repression activity of the mutants was not observed in vitro. From these results, we propose that ligand-binding is essential for SbtR to disengage from DNA, in a similar manner to the other characterized TetR family regulators. The formation and reduction of the disulfide bond might function in controlling the ligand-binding affinity of this transcriptional regulator.

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Phenylacetyl Coenzyme A Is an Effector Molecule of the TetR Family Transcriptional Repressor PaaR from Thermus thermophilusHB8

Cited by 21 publications

References 29 publications

The TetR Family of Regulators

The TetR Family of Regulators

Transcriptional Repression Mediated by a TetR Family Protein, PfmR, from Thermus thermophilus HB8

Structure and function of a TetR family transcriptional regulator, SbtR, from thermus thermophilus HB8

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