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Journal of Bacteriology, January 2009, p. 123-134, Vol. 191, No. 1
0021-9193/09/$08.00+0     doi:10.1128/JB.01112-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

The GAF-Like-Domain-Containing Transcriptional Regulator DfdR Is a Sensor Protein for Dibenzofuran and Several Hydrophobic Aromatic Compounds{triangledown} ,{dagger}

Toshiya Iida,1* Taro Waki,1,2 Kaoru Nakamura,1 Yuki Mukouzaka,1 and Toshiaki Kudo1,2

Environmental Molecular Biology Laboratory, RIKEN (The Institute of Physical and Chemical Research), Wako, Saitama 351-0198, Japan,1 Supramolecular Biology, International Graduate School of Arts and Science, Yokohama City University, Suehiro, Tsurumi-ku, Yokohama 230-0045, Japan2

Received 8 August 2008/ Accepted 15 October 2008

Dibenzofuran (DF) is one of the dioxin carbon skeletal compounds used as a model to study the microbial degradation of dioxins. This study analyzed the transcriptional regulation of the DF dioxygenase genes dfdA1 to dfdA4 in the DF-utilizing actinomycetes Rhodococcus sp. strain YK2 and Terrabacter sp. strain YK3. An open reading frame designated dfdR was detected downstream of the dfdC genes. The C-terminal part of the DfdR amino acid sequence has high levels of similarity to several LuxR-type DNA binding helix-turn-helix domains, and a GAF domain sequence in the central part was detected by a domain search analysis. A derivative of YK2 with dfdR disrupted was not able to utilize DF and did not exhibit DF-dependent dfdA1 transcriptional induction ability, and these dysfunctions were compensated for by introduction of dfdR. Promoter analysis of dfdA1 in Rhodococcus strains indicated that activation of the dfdA1 promoter (PdfdA1) was dependent on dfdR and DF and not on a metabolite of the DF pathway. The cell extract of a Rhodococcus strain that heterologously expressed DfdR showed electrophoretic mobility shift (EMS) activity for the PdfdA1 DNA fragment in a DF-dependent manner. In addition, PdfdA1 activation and EMS activity were observed with hydrophobic aromatic compounds comprising two or more aromatic rings, suggesting that DfdR has broad effector molecule specificity for several hydrophobic aromatic compounds.

* Corresponding author. Mailing address: Environmental Molecular Biology Laboratory, RIKEN, Wako, Saitama 351-0198, Japan. Phone: 81 (48) 462-1111, ext. 5674. Fax: 81 (48) 462-4672. E-mail: tiida{at}riken.jp

{triangledown} Published ahead of print on 24 October 2008.

{dagger} Supplemental material for this article may be found at http://jp.asm.org/.

Journal of Bacteriology, January 2009, p. 123-134, Vol. 191, No. 1
0021-9193/09/$08.00+0     doi:10.1128/JB.01112-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.





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