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The protocatechuate (PCA) 4,5-cleavage (PCA45) pathway is the essential catabolic route for the degradation of various aromatic acids in the genusComamonas . All of the PCA45 pathway genes,orf1-pmdKEFDABC , as well as another PCA 4,5-dioxygenase gene,pmdA II B II , were isolated from a phthalate-degrading bacterium,Comamonas sp. strain E6. Disruption ofpmdB andpmdD in E6, which code for the β subunit of PCA 4,5-dioxygenase and 2-pyrone-4,6-dicarboxylate (PDC) hydrolase, respectively, resulted in a growth defect on PCA, indicating that these genes are essential for the growth of E6 on PCA. On the other hand, inactivation ofpmdB II did not affect the growth of E6 on PCA. Disruption ofpmdK , which is related to a 4-hydroxybenzoate/PCA transporter ofPseudomonas putida , resulted in growth retardation on PCA. The insertional inactivation oforf1 in E6, whose deduced amino acid sequence has no similarity with proteins of known function, led to the complete loss of growth on PCA and the accumulation of PDC and 4-oxalomesaconate (OMA) from PCA. These results indicated the involvement oforf1 in the PCA45 pathway, and this gene, designatedpmdU , was suggested to code for OMA tautomerase. Reverse transcription-PCR analysis suggested that thepmdUKEFDABC genes constitute an operon. The transcription start site of thepmd operon was mapped at 167 nucleotides upstream of the initiation codon ofpmdU . Thepmd promoter activity was enhanced 20-fold when the cells were grown in the presence of PCA. Inducers of thepmd operon were found to be PCA and PDC, but PDC was the more effective inducer.

Characterization of the Protocatechuate 4,5-Cleavage Pathway Operon in Comamonas sp. Strain E6 and Discovery of a Novel Pathway Gene