Biotransformation of indole by Cupriavidus sp. strain KK10 proceeds through N-heterocyclic- and carbocyclic-aromatic ring cleavage and production of indigoids

• Cupriavidus sp. strain KK10 biotransformed the N-heteroaromatic pollutant, indole.
• Both N-heterocyclic and carbocyclic ring fission products were identified.
• A comprehensive pathway for aerobic indole biotransformation was constructed.
• Indigoids, including indigo and indirubin were confirmed from this strain.
• Pyrrole-2,3-dicarboxylic acid was confirmed from indole for the first time.

Comprehensive analyses of the biotransformation of the N-heteroaromatic environmental pollutant, indole, by a newly isolated soil bacterium designated strain KK10, were conducted by liquid chromatography negative electrospray ionization tandem mass spectrometry (LC/ESI(−)–MS/MS). Numerous indole bioproducts were revealed and provided evidence for multiple pathways of indole biotransformation by this strain including unreported pathways. Oxidation of the N-heterocyclic ring of indole and ring cleavage through N-formylanthranilic acid and gentisic acid was characterized in addition to a carbocyclic ring-cleavage pathway which was documented for the first time. Three carbocyclic aromatic ring cleavage products of indole were proposed and the structure of 2,3-pyrrole-dicarboxylic acid was confirmed following synthesis and analyses of an authentic standard of this compound. Eight downstream ring-fission products were identified overall and these results confirmed the lower pathways of indole biotransformation. Indigo, indirubin and other indigoid compounds were produced by strain KK10 and confirmed N-heterocyclic-ring oxidations in the upper pathways. Nearly complete sequencing of the 16S rRNA gene of strain KK10 and phylogenetic analysis revealed that it was a new member of the genus Cupriavidus. Cupriavidus strains that biotransform N-heteroaromatic pollutants have not been described. These results expand both our understanding of the versatile catabolic capabilities of members of the genus Cupriavidus and provide evidence for alternative biotransformation mechanisms for indole in the environment by bacteria.