Elucidating the molecular mechanism of tryptophan‐derived indole metabolite biosynthesis in Lactiplantibacillus plantarum DPUL ‐ S164

BACKGROUND: Our previous research has revealed that the Lactiplantibacillus plantarum DPUL-S164 metabolizes tryptophan (Trp) to produce indole-3-lactic acid (ILA), indole-3-acetic acid (IAA) and indole-3-carboxaldehyde (I3C). This study systematically elucidated the molecular regulatory mechanism of this strain for the metabolism of Trp to produce ILA, I3C and IAA through genome-wide functional annotation, bioinformatics analysis, high-performance liquid chromatography, and real-time fluorescence quantitative polymerase chain reaction. RESULTS: Under Trp-enriched conditions, the three indole derivatives showed significant time-dependent cumulative effects, with ILA biosynthesis exhibiting the most significant up-regulation. Molecular mechanistic studies have shown that the metabolic pathway involves synergistic regulation of multiple gene modules. The genes involved in Trp metabolism of DPUL-S164 was found to include genes encoding aromatic amino acid transaminases (AraT), genes encoding lactate dehydrogenase (ldh or ldhA) and genes encoding aldehyde dehydrogenase (ALD). During the process of DPUL-S164 metabolizing Trp to produce ILA, I3C, or IAA, the key candidate genes for AraT, ldh, ldhA, and ALD were significantly up-regulated over 3-24 h. In addition, this study identified gene0696 and gene0697 as a functional metabolic gene cluster in DPUL-S164 and involved in the regulation of its metabolic Trp-producing ILA pathway, which may be involved in the regulation of Trp metabolism as a key candidate gene cluster. CONCLUSION: This discovery not only provides a new theoretical basis for elucidating the molecular mechanism of Trp metabolism in Lactobacillus, but also lays an important foundation for the subsequent metabolic engineering and synthetic biology research by identifying the core functional genes. © 2026 Society of Chemical Industry.