Characterization of the initial degradation mechanism involved in C -glycosylated isoflavone puerarin in soil microorganism

Puerarin is C8-glycosylated daidzein and an active ingredient in the Chinese herbal medicine “Kakkonto.” It is used in the early stage of cold treatment. A previous study reported that intestinal bacteria can remove the sugar moiety from puerarin. Despite their potential roles, C -glycosylated flavonoid-metabolizing microorganisms, including those acting on puerarin, have only been found in the gut but not been identified in natural environments. In this study, we identified a puerarin-catabolizing microorganism by screening from soil and clarified two-step deglycosylation reaction. The first step in the metabolism of puerarin was the oxidation of a sugar moiety, catalyzed by a FAD-dependent oxidase named PurA. PurA is the first example of a C -glycoside oxidase that showed activity toward isoflavone- C -glycosides. Notably, PurA exhibited a broader substrate specificity, acting on both C6- and C8-glycosylated flavonoids. This feature was not found in previously reported C -glycoside oxidases and could be useful to synthesize aglycone compounds from C -glycosides in the future. The second step involved the cleavage of the C-C bond between the sugar moiety and daidzein, which was catalyzed by a C -glycoside deglycosylation enzyme named PurBC. Surprisingly, the initial enzyme in puerarin catabolic pathway in this strain differs from that found in the intestinal bacteria. These findings indicate that, in natural environments, bacteria distinct from intestinal microbiota are responsible for puerarin degradation. Our findings provide a novel insight into microbial C -glycoside metabolism in soil environments. IMPORTANCE Plants, fungi, bacteria, and insects synthesize various kinds of unique compounds. Those synthesized compounds are generally degraded by microorganisms; otherwise, they would accumulate on the surface of the Earth. However, in many cases, their fate in the natural environment remains poorly understood. In this study, we isolated a bacterium from soil by the enrichment culture method and identified it as Paenarthrobacter sp. No. 37. This strain was able to grow in the medium containing puerarin as the sole carbon source. It revealed that strain No. 37 can utilize puerarin as a source of carbon and energy. Furthermore, a puerarin degradation activity was induced upon the addition of puerarin to the culture medium. Thus, we successfully identified a bacterium that physiologically catabolizes puerarin and potentially other C -glycosylated compounds. By uncovering C -glycoside metabolism in natural environments, our findings shed light on the part of microbial contribution to the degradation and regeneration of plant-derived natural compounds in biogeochemical cycles.