Transcriptional regulation of two redundant 3-bromo-4-hydroxybenzoate catabolic operons via two different regulatory modes in strain H8.

UNLABELLED

Gene redundancy endows bacteria with enhanced adaptability to complex and fluctuating environments but results in genetic costs. Transcriptional regulation is considered an effective strategy for harmonizing adaptive benefits with physiological burdens. In our previous study, two redundant gene clusters (phbh1pcaApcaBorf404bhbR1 and phbh2pcaB2pcaA2bhbR2) involved in 3-bromo-4-hydroxybenzoate (3-Br-4-HB) catabolism were identified in strain H8. The LysR-type transcription regulator BhbR1, encoded by the bhbR1 gene, activated phbh1pcaApcaBorf404 transcription. Through DNase I footprinting assays, the presence of the inducer 3-Br-4-HB was found to shorten the BhbR1-bound region in the promoter, uncovering the protected -35 box, thereby activating transcription. The MarR-family transcription factor (MFTF) BhbR2, encoded by the bhbR2 gene, was different from typical inhibitive MFTFs and activated phbh2pcaB2pcaA2 transcription. BhbR2 was found to bind a 17-bp imperfect palindromic sequence (TTGATT-N5-AATCAA) in the target promoter. Intriguingly, the presence of 3-Br-4-HB neither dissociated BhbR2 from the promoter nor modified its binding site, indicating a novel regulatory mode. Despite a coincident trend in activating their respective operons in response to different concentrations of 3-Br-4-HB, BhbR1 and BhbR2 both showed a significant attenuation of the activation effect at high concentrations (>480 μM), highlighting the requisite co-existence of redundant 3-Br-4-HB catabolic operons and their regulatory genes. This study presents two distinct transcriptional regulation mechanisms of these two redundant 3-Br-4-HB catabolic operons in strain H8, expanding our understanding of the diversity of transcriptional regulation for enhancing adaptation.

IMPORTANCE

In bacteria, catabolic genes for pollutant degradation often possess functionally redundant duplicates, providing a genetic basis for rapid adaptation to complex polluted environments. Synergic regulation plays an important role in balancing the physiological burden of extra genetic material with the adaptive benefits conferred by genetic redundancy. Although the co-existence of two redundant 3-bromo-4-hydroxybenzoate (3-Br-4-HB)-catabolic operons has been proven to enhance the metabolic robustness and adaptability of the host strain H8, how these two inducible catabolic operons are regulated remains unclear. This study identified two regulators, the LysR-type transcription regulator BhbR1 and the MarR-family transcription factor BhbR2, which activated transcription of the two 3-Br-4-HB-catabolic operons using different modes, and also revealed interactions of these two regulators with their effectors and target promoters. These findings not only clarify two distinct transcriptional strategies employed by redundant catabolic operons but also enhance our understanding of the significance of regulatory diversity for bacterial adaptation to complex polluted environments.