Nanoplasmonic SERS reveals previously uncharacterised indole derivative in E. coli metabolism

Tryptophanase (TnaA) is a promiscuous enzyme that regulates the production of amino acid-derived metabolites essential for bacterial communication. TnaA is known to convert tryptophan into indole, a known signalling molecule, but other routes remain obscure. Here, we show that nanoplasmonic surface-enhanced Raman spectroscopy (SERS) enables label-free detection of indole in Escherichia coli with a limit of detection of 100 nM - over 500-fold more sensitive than previously reported and significantly outperforming existing colorimetric assays. Using this ultrasensitive approach, we perform SERS on wild-type and tnaA knockout E. coli strains and discover a distinct TnaA-dependent metabolic signature in both standard and uropathogenic strains when cultures are supplemented with amino acids other than tryptophan. Quantitative spectral analysis reveals an indole-like metabolite whose Raman signature does not correspond to free indole or any known indole derivative characterised by mass spectrometry. This observation implies previously unidentified bacterial metabolic pathways involving amino acid reallocation which can depend on environmental conditions. Given the central role of TnaA in bacterial signalling and virulence, these findings raise new hypotheses regarding the biological role of indole derivatives and TnaA-mediated byproducts. More broadly, our results establish nanoplasmonic SERS as a powerful technique for probing enzyme activity and bioactive metabolite production in vivo at concentrations well below the detection limits of existing methods.