The regulatory mechanism of 2,4,6-trichlorophenol catabolic operon expression by HadR in Ralstonia pickettii DTP0602

Abstract

Ralstonia pickettii DTP0602 utilizes 2,4,6-trichlorophenol (2,4,6-TCP) as its sole source of carbon. The expression of catabolic pathway genes (hadA, hadB and hadC) for 2,4,6-TCP has been reported to be regulated by the LysR-type transcriptional regulator (LTTR) HadR. Generally, coinducers are recognized as being important for the function of LTTRs, and alteration of the LTTR-protection sequence and the degree of DNA bending are characteristic of LTTRs with or without a recognized coinducer. In this study, we describe the mechanism by which HadR regulates the expression of 2,4,6-TCP catabolic genes. The 2,4,6-TCP catabolic pathway genes in DTP0602 consist of two transcriptional units: hadX-hadA-hadB-hadC and monocistronic hadR. Purified HadR binds to the hadX promoter and HadR-DNA complex formation was induced in the presence of 16 types of substituted phenols, including chloro-and nitro-phenols and tribromo-phenol. In contrast with observations of other well-characterized LTTRs, the tested phenols showed no diversity of the bending angle of the HadR binding fragment. The expression of 2,4,6-TCP catabolic pathway genes, which are regulated by HadR, was not influenced by the DNA bending angle of HadR. Moreover, the transcription of hadX, hadA and hadB was induced in the presence of seven types of substituted phenols, whereas the other substituted phenols, which induced formation of the HadR-DNA complex, did not induce the transcription of hadX, hadA or hadB in vivo.

Catabolism of Phenol and Its Derivatives in Bacteria

“…The HadR protein was proved to bind to the promoter of the hadX gene, and the formation of the HadR-deoxyribonucleic acid (DNA) complex was found to be induced by 16 different phenol derivatives. However, only seven of these substituted phenols induced transcription of the hadXABC operon in vivo (Torii, Machida, Hara, Hatta, & Takizawa, 2013). The expression of the second had gene cluster containing the gene encoding MR ( Figure 10) seems to be negatively controlled by another LysR-type regulator HadS (Hatta et al, 2012).…”

Bacterial degradation of chlorophenols and their derivatives

“…Torii et al . [111] investigated how HadR regulates 2,4,6-TCP catabolic pathway gene expression in Ralstonia pickettii DTP0602. They found that purified HadR binds to the hadX promoter and HadR–DNA complex formation is induced in the presence of 16 types of substituted phenols, including CPs, nitrophenols and tribromophenols.…”

PnpM, a LysR-Type Transcriptional Regulator Activates the Hydroquinone Pathway in para-Nitrophenol Degradation in Pseudomonas sp. Strain WBC-3

“…These LTTRs cause the inducer-dependent shortening of the protected region from positions −80 to −20 to positions −80 to −30 and then a relaxation of the DNA bending. This was thought to be important in the release of the recognition site of RNA polymerase and the conformational change of regulator-DNA complex suitable for transcriptional activation (Toledano et al, 1994 ; Wang and Winans, 1995a , b ; van Keulen et al, 2003 ; Porrua et al, 2007 ; Torii et al, 2013 ; Kubota et al, 2014 ). Nevertheless, in this study, the behavior of PnpM toward the pnpCDEFG promoter is somewhat different from the sliding dimer model for most LTTRs.…”