The XRE family protein DbuR is a transcriptional repressor of the dbu operon in Pseudomonas putida.

Pseudomonas putida is a ubiquitous, metabolically versatile microbe that has gained visibility as a chassis for bioengineering. The dbu operon in P. putida, comprised of a D-branched-chain amino acid (D-BCAA) oxidase (DbuA), a Rid2 protein (DbuB), and a transporter (DbuC), was previously characterized for its role in the catabolism of D-branched-chain amino acids. In the present study, we show that the addition of any of three D-BCAAs catabolized by these gene products increases expression of the dbu genes. The presence of D-tyrosine does not increase transcription of the dbu genes, nor is it used as a sole nitrogen source by P. putida. Derepression of the dbu operon allows catabolism of D-tyrosine, thus uncovering an additional capacity of the dbu gene products. Results herein show that the dbuR gene, which is divergently transcribed from the operon, encodes a xenobiotic response element (XRE) family transcription factor that is a transcriptional repressor of the dbu genes. The effect of D-BCAA on dbu expression appears to be at least partially independent of DbuR, suggesting transcriptional regulation of this operon involves multiple components. In total, this work contributes to understanding the complex regulatory and metabolic networks of the environmentally and economically important microbe P. putida.IMPORTANCEPseudomonas putida is a broadly utilized bioengineering chassis, primarily due to the versatile and robust metabolic network of the organism. P. putida, like many microorganisms, employs a complex regulatory network to coordinate its metabolism, allowing it to adapt to changing environments and dynamic nutrient availability. The physiological role of the D-branched-chain amino acid (D-BCAA) utilization pathway (dbu) operon in D-BCAA metabolism by P. putida has been defined, and herein we provide insights into the regulation of the genes in this operon. DbuR is encoded by a gene near the dbu operon, and this protein represses the expression of the dbu genes. A new metabolic capability (catabolism of D-tyrosine) of P. putida was revealed, a capability that increases the potential of this organism as a chassis for bioengineering. This work expands current knowledge of P. putida and contributes insights into the metabolic and regulatory capabilities of this environmentally, industrially, and economically relevant microbe.