Biogenesis of the pipecolate moiety of neuroprotective agent meridamycin in Streptomyces sp. NRRL30748 was investigated in feeding studies using lysine specifically labeled with 15 N at the a-amino or the e-amino nitrogen position. Fourier transform mass spectrometry analysis with ultra-high mass resolving power and accurate mass measurement capability was employed to resolve the 15 N peak of labeled meridamycin from the 13 C peak of unlabeled meridamycin, allowing the precise calculation of labeling contents under each condition. The relative enrichment of 15 N-labeled meridamycin was B43% with L-[a-15 N]-lysine feeding and B14% with L-[e-15 N]-lysine feeding, suggesting two distinguishable pathways, with concomitant loss of either the e-amino group or the a-amino group of lysine, were involved in the generation of the pipecolate moiety of meridamycin in this bacterium. PCR cloning using degenerate primers identified a proC gene encoding a putative pyrroline-5-carboxylate reductase, which was expected to catalyze the conversion of piperideine-6-carboxylate to pipecolate. However, inactivation of this locus did not significantly affect the incorporation of a-15 N-or e-15 N-labeled lysine into meridamycin, indicating the existence of an alternative route for the last step of the lysine e-transamination pathway. This work revealed the diversity and complexity of the biosynthetic pathways for pipecolate synthesis in the meridamycin producing bacterium Streptomyces sp. NRRL30748.