Nanoplasmonic SERS-Enabled Structural Identification of an Uncharacterized Metabolite Directly in E. coli Cultures

Bacteria produce a rich array of metabolites that mediate communication and host interactions. However, identifying bioactive small molecules directly within living bacterial cultures remains a central challenge in microbiology, as conventional approaches typically require isolation, purification, or chemical labeling that can disturb the metabolic processes under study. Here, we study the metabolic activity of tryptophanase (TnaA)-a promiscuous enzyme which regulates the production of amino acid-derived bioactive metabolites essential for bacterial communication-directly from the supernatant of living Escherichia coli cultures, without extraction. TnaA is known to convert tryptophan into indole, an important signaling molecule influencing a range of behaviors-from bacterial quorum sensing to urinary tract infections-but other conversion routes remain obscure. We show that nanoplasmonic surface-enhanced Raman spectroscopy (SERS) combined with targeted genetic subtraction enables the label-free, cellular characterization and structural identification of TnaA-derived metabolites directly from E. coli culture solutions, without isolation or purification. We systematically profile the SERS spectra of wild-type and tnaA gene knockout strains (E. coli BW25113 and the uropathogenic 536) supplemented with each of the twenty amino acids, uncovering a previously unreported TnaA-dependent metabolic signature, I*, whose Raman fingerprint does not match free indole or any common indole derivative characterized by mass spectrometry. Using isotopomer-labelled substrates together with structural reference compounds, we perform label-free structural deduction of I* directly from SERS spectra. We find I*'s structure is consistent with an intact indole ring carrying a C3 substituent, likely produced indirectly from intracellular tryptophan. These findings introduce a novel indole metabolite, raise new hypotheses regarding the biological role of TnaA-mediated byproducts in bacterial signalling and virulence, and demonstrate that nanoplasmonic SERS provides a powerful framework for probing enzyme activity and bioactive metabolite production directly from living bacterial cultures with nanomolar sensitivity and structural specificity.