Remarkable ability of Pandoraea pnomenusa B356 biphenyl dioxygenase to metabolize simple flavonoids

Abstract

Many investigations have provided evidence that plant secondary metabolites, especially flavonoids, may serve as signal molecules to trigger the abilities of bacteria to degrade chlorobiphenyls in soil. However, the bases for this interaction are largely unknown. In this work, we found that BphAEB356, the biphenyl/chlorobiphenyl dioxygenase from Pandoraea pnomenusa B356, is significantly better fitted to metabolize flavone, isoflavone, and flavanone than BphAELB400 from Burkholderia xenovorans LB400. Unlike those of BphAELB400, the kinetic parameters of BphAEB356 toward these flavonoids were in the same range as for biphenyl. In addition, remarkably, the biphenyl catabolic pathway of strain B356 was strongly induced by isoflavone, whereas none of the three flavonoids induced the catabolic pathway of strain LB400. Docking experiments that replaced biphenyl in the biphenyl-bound form of the enzymes with flavone, isoflavone, or flavanone showed that the superior ability of BphAEB356 over BphAELB400 is principally attributable to the replacement of Phe336 of BphAELB400 by Ile334 and of Thr335 of BphAELB400 by Gly333 of BphAEB356. However, biochemical and structural comparison of BphAEB356 with BphAEp4, a mutant of BphAELB400 which was obtained in a previous work by the double substitution Phe336Met Thr335Ala of BphAELB400, provided evidence that other residues or structural features of BphAEB356 whose precise identification the docking experiment did not allow are also responsible for the superior catalytic abilities of BphAEB356. Together, these data provide supporting evidence that the biphenyl catabolic pathways have evolved divergently among proteobacteria, where some of them may serve ecological functions related to the metabolism of plant secondary metabolites in soil. © 2012, American Society for Microbiology.